Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-29 23:55 -0400 (Sat, 29 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/32HostnameOS / ArchCHECK
biodbExpasy 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-29 09:55 -0400 (Sat, 29 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_20
git_last_commit: 4403c2f
git_last_commit_date: 2024-10-29 11:09:35 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on palomino8

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

raw results


Summary

Package: biodbExpasy
Version: 1.10.0
Command: F:\biocbuild\bbs-3.20-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_1.10.0.tar.gz
StartedAt: 2025-03-29 16:03:05 -0400 (Sat, 29 Mar 2025)
EndedAt: 2025-03-29 16:03:59 -0400 (Sat, 29 Mar 2025)
EllapsedTime: 54.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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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)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2025-03-29 16:03:50.032][biodb::testContext]
biodb.INFO [2025-03-29 16:03:50.035][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:50.037][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-29 16:03:50.038][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:50.039][biodb::testContext]
biodb.INFO [2025-03-29 16:03:50.047][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:50.050][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:50.073][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:50.074][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:03:50.076][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:03:50.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.080][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:03:50.096][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:03:50.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.101][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:03:50.102][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:03:50.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.107][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:03:50.108][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:03:50.109][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:03:50.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.114][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:03:50.115][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:03:50.116][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:03:50.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.120][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:03:50.122][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:03:50.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.126][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:03:50.127][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:03:50.128][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:03:50.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.133][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:03:50.134][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:03:50.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.138][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:03:50.139][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:03:50.141][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:03:50.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.145][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:50.146][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:03:50.147][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:03:50.149][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:03:50.150][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:03:50.151][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:03:50.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.155][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:03:50.156][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:03:50.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.161][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:03:50.162][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:03:50.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.166][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:03:50.168][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:03:50.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.172][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:03:50.173][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:03:50.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.177][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:03:50.179][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:03:50.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.183][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:50.184][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:03:50.188][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:03:50.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.192][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:03:50.193][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:03:50.194][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:03:50.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.201][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:03:50.228][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.242][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:03:50.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:50.252][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.254][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.257][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:50.258][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:50.259][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.260][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:03:50.262][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:50.263][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.264][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.265][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:50.265][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:50.265][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:50.265][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:50.265][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:50.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:50.268][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.269][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.270][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:50.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.273][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.274][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.276][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:50.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:50.278][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.279][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.280][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:03:50.282][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.284][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:50.285][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.286][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:50.287][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.289][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.290][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.292][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:50.294][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:50.295][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.296][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:03:50.297][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:50.298][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.300][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.301][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:50.301][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:50.301][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:50.301][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:50.301][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:50.302][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:50.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.306][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:50.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.309][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.310][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.311][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:50.312][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:50.314][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.315][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.316][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:03:50.318][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.319][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:03:50.321][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.322][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:50.323][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.324][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.325][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.326][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.328][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:50.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:50.330][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.331][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:03:50.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:50.334][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.336][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.338][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.340][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:50.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.346][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:50.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.352][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.354][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.356][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:50.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:50.360][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.362][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.364][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:03:50.367][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.370][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:50.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:50.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.377][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.383][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:50.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:50.387][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.389][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:03:50.391][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:50.393][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.395][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.397][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:50.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.404][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:50.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.410][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.412][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:50.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:50.415][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.417][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.420][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:50.421][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.523][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:03:50.527][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:03:50.529][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:03:50.531][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:03:50.532][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:03:50.534][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:03:50.536][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:50.537][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:50.539][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:03:50.540][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:03:50.542][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:03:50.543][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:03:50.545][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:50.547][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:50.548][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:03:50.550][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:03:50.551][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:03:50.553][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:03:50.554][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:03:50.556][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:03:50.558][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:03:50.559][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:03:50.561][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:03:50.562][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:03:50.564][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:03:50.565][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:03:50.567][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:03:50.569][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:03:50.570][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:03:50.572][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:03:50.573][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:03:50.575][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:03:50.576][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:03:50.578][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:03:50.580][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:03:50.581][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:03:50.583][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:03:50.584][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:03:50.586][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:03:50.588][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:03:50.589][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:03:50.591][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:03:50.592][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:03:50.594][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:03:50.595][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:03:50.597][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:03:50.599][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:03:50.600][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:03:50.602][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:03:50.603][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:03:50.605][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:03:50.607][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:03:50.608][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:03:50.610][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:03:50.611][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:03:50.613][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:03:50.614][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:03:50.616][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:03:50.618][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:03:50.619][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:03:50.621][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:03:50.622][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:03:50.624][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:03:50.625][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:03:50.627][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:03:50.629][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:03:50.630][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:03:50.632][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:03:50.633][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:03:50.635][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:03:50.636][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:03:50.638][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:03:50.639][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:03:50.641][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:03:50.643][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:03:50.644][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:03:50.646][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:03:50.647][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:03:50.649][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:03:50.650][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:03:50.652][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:03:50.653][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:03:50.655][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:03:50.688][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:03:50.691][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:50.694][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:50.695][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.697][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:50.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:50.837][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:50.845][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:03:50.847][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.849][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-29 16:03:50.850][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.851][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:50.852][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.853][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.854][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.856][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.857][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-29 16:03:50.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:50.859][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.860][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-29 16:03:50.861][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:50.863][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-29 16:03:50.863][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:03:50.863][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:03:50.863][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:03:50.864][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:50.865][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:50.866][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:03:50.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.870][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:50.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:50.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:50.873][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:50.874][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-29 16:03:50.875][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:50.876][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:50.877][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:50.878][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:50.884][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:03:50.910][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:03:50.912][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-29 16:03:50.915][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:03:50.919][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-29 16:03:50.923][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:50.924][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:50.925][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-29 16:03:50.935][biodb::testThat]
biodb.INFO [2025-03-29 16:03:50.936][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-29 16:03:50.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:50.939][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:50.943][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2025-03-29 16:03:50.945][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:03:50.949][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-29 16:03:50.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:50.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:50.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:50.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:50.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:50.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:50.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:03:50.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:50.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:50.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:50.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.014][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.030][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.040][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:03:51.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.044][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.049][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.054][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.059][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:03:51.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.167][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.172][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.177][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.186][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:51.220][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-03-29 16:03:51.223][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.228][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:51.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:51.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.238][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:51.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.285][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.327][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.331][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.336][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.369][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.370][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.373][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.403][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.404][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.422][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.432][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.437][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.442][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.444][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.447][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.462][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.467][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.472][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.477][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.478][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.480][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.481][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.496][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.497][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.500][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.506][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.508][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.516][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.518][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.526][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.528][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.548][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2025-03-29 16:03:51.583][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:03:51.585][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-29 16:03:51.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:51.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:51.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:51.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:51.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:51.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:51.599][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.TRACE[2025-03-29 16:03:51.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.607][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.617][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:03:51.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:51.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.622][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.627][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.637][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:51.671][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-03-29 16:03:51.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.694][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:51.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.699][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:51.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:51.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.703][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:51.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:51.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.725][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.767][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.772][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.776][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:51.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.813][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.814][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.816][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.837][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.846][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.848][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.850][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.865][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.873][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.878][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.889][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.890][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.894][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.908][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:51.910][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:51.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.919][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.920][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:51.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:51.929][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:51.930][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:51.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:51.932][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:51.944][biodb::testThat]
biodb.INFO [2025-03-29 16:03:51.945][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-29 16:03:51.946][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:51.948][biodb::testThat]
biodb.DEBUG[2025-03-29 16:03:51.950][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-03-29 16:03:51.957][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-29 16:03:51.980][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2025-03-29 16:03:51.983][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2025-03-29 16:03:51.985][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-03-29 16:03:51.986][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-29 16:03:51.987][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-03-29 16:03:51.989][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-29 16:03:51.990][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-29 16:03:51.991][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-29 16:03:51.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:51.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:51.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:52.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:52.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:52.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:52.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:52.010][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2025-03-29 16:03:52.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-29 16:03:52.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-29 16:03:52.031][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2025-03-29 16:03:52.889][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2025-03-29 16:03:53.356][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-29 16:03:53.360][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2025-03-29 16:03:53.380][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2025-03-29 16:03:53.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:53.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:53.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:53.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:53.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:53.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:53.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:53.427][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-03-29 16:03:53.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-29 16:03:53.443][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-29 16:03:53.457][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-03-29 16:03:53.950][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-03-29 16:03:54.413][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-29 16:03:54.416][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-03-29 16:03:54.421][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-03-29 16:03:54.424][private$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[2025-03-29 16:03:54.427][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-29 16:03:54.429][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-03-29 16:03:54.431][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-29 16:03:54.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:54.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:54.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:54.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:54.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:54.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:54.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:03:54.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.461][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:54.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:54.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.471][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:03:54.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:54.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.481][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.500][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.505][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.514][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:54.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:54.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:54.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:54.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:54.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:54.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:54.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:03:54.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.553][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:54.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:03:54.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.564][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:03:54.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:03:54.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.573][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.578][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.588][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:03:54.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:54.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:54.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:54.635][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-03-29 16:03:54.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:54.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:54.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:54.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:54.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:54.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:54.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:54.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:54.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:54.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:54.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:54.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:54.682][biodb::testThat]
biodb.INFO [2025-03-29 16:03:54.683][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-29 16:03:54.684][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:54.685][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:54.689][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.695][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.698][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:54.699][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-03-29 16:03:54.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:54.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:54.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:54.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:54.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:54.746][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-03-29 16:03:54.749][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-29 16:03:54.752][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-29 16:03:54.753][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-29 16:03:54.755][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-03-29 16:03:55.255][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-03-29 16:03:55.765][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-29 16:03:55.767][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-03-29 16:03:55.772][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-03-29 16:03:55.779][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-03-29 16:03:55.801][biodb::testThat]
biodb.INFO [2025-03-29 16:03:55.802][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-29 16:03:55.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:55.805][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:55.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:55.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:55.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:55.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:55.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:55.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:55.879][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-29 16:03:55.883][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-29 16:03:55.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-03-29 16:03:55.898][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-29 16:03:55.901][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-03-29 16:03:55.930][biodb::testThat]
biodb.INFO [2025-03-29 16:03:55.931][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-29 16:03:55.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:55.934][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:55.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:55.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:55.952][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:55.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:55.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:55.956][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:55.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:55.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:55.961][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:55.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:55.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:55.994][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:55.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:55.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:55.999][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:56.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:56.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:56.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:56.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:56.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:56.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:56.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:56.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:56.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:56.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:56.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:56.026][biodb::testThat]
biodb.INFO [2025-03-29 16:03:56.028][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-29 16:03:56.029][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:56.030][biodb::testThat]
biodb.INFO [2025-03-29 16:03:56.043][biodb::testThat]
biodb.INFO [2025-03-29 16:03:56.044][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-29 16:03:56.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:56.046][biodb::testThat]
biodb.INFO [2025-03-29 16:03:56.058][biodb::testThat]
biodb.INFO [2025-03-29 16:03:56.059][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-29 16:03:56.060][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:56.061][biodb::testThat]
biodb.DEBUG[2025-03-29 16:03:56.075][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2025-03-29 16:03:56.562][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2025-03-29 16:03:57.069][biodb::testThat]
biodb.INFO [2025-03-29 16:03:57.071][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-29 16:03:57.072][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:57.073][biodb::testThat]
biodb.DEBUG[2025-03-29 16:03:57.538][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2025-03-29 16:03:58.013][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:58.014][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:58.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:58.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:58.018][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:58.019][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:58.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:58.021][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:58.023][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:03:58.024][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-29 16:03:58.025][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-29 16:03:58.026][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:03:58.027][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.030][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.040][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-29 16:03:58.052][biodb::testContext]
biodb.INFO [2025-03-29 16:03:58.053][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:58.055][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-29 16:03:58.056][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:58.057][biodb::testContext]
biodb.INFO [2025-03-29 16:03:58.060][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:58.062][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:58.067][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:58.068][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:03:58.070][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:03:58.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.074][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:03:58.075][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:03:58.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.080][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:03:58.081][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:03:58.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.085][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:03:58.086][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:03:58.088][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:03:58.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.092][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:03:58.093][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:03:58.094][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:03:58.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.099][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:03:58.100][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:03:58.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.104][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:03:58.105][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:03:58.107][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:03:58.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.111][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:03:58.112][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:03:58.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.117][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:03:58.118][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:03:58.119][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:03:58.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.123][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:58.125][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:03:58.126][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:03:58.127][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:03:58.128][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:03:58.130][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:03:58.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.134][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:03:58.135][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:03:58.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.140][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:03:58.141][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:03:58.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.145][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:03:58.152][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:03:58.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.156][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:03:58.157][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:03:58.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.162][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:03:58.163][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:03:58.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.168][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:58.169][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:03:58.172][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:03:58.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.177][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:03:58.178][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:03:58.179][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:03:58.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.184][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:03:58.186][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.200][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:03:58.201][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.202][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:58.204][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.205][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.206][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.207][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.208][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:58.210][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:58.211][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.212][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:03:58.213][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:58.214][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.216][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.217][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:58.217][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:58.217][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:58.217][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:58.217][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:58.218][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:58.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.220][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.221][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:58.223][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.224][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.225][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.226][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.227][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:58.228][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:58.229][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.231][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.232][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:03:58.234][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.235][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:58.236][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.238][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:58.239][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.241][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.242][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.244][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:58.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:58.246][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.247][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:03:58.248][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:58.255][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.257][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:58.257][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:58.257][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:58.257][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:58.257][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:58.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:58.260][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.262][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:58.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.267][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.268][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:58.269][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:58.270][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.271][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.273][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:03:58.275][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.276][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:03:58.277][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.278][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:58.279][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.281][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.282][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.283][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.284][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:58.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:58.287][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.288][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:03:58.289][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:58.290][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.291][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.293][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.294][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:58.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.297][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:58.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.302][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:58.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:58.305][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.306][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.308][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:03:58.310][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.311][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:58.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:58.315][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.316][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.317][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.318][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.319][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:58.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:58.322][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.323][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:03:58.324][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:58.325][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.326][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.328][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.329][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:58.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:58.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.336][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.337][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.338][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:58.339][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:58.340][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.341][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.343][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:58.344][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.448][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:03:58.449][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:03:58.451][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:03:58.453][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:03:58.454][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:03:58.456][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:03:58.457][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:58.459][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:58.461][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:03:58.462][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:03:58.464][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:03:58.465][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:03:58.467][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:58.469][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:58.470][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:03:58.477][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:03:58.478][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:03:58.480][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:03:58.481][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:03:58.483][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:03:58.485][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:03:58.486][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:03:58.488][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:03:58.489][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:03:58.491][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:03:58.493][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:03:58.494][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:03:58.496][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:03:58.497][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:03:58.499][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:03:58.501][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:03:58.502][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:03:58.504][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:03:58.505][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:03:58.507][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:03:58.508][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:03:58.510][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:03:58.512][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:03:58.513][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:03:58.515][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:03:58.516][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:03:58.518][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:03:58.520][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:03:58.521][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:03:58.523][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:03:58.524][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:03:58.526][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:03:58.527][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:03:58.529][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:03:58.531][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:03:58.532][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:03:58.534][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:03:58.535][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:03:58.537][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:03:58.538][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:03:58.540][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:03:58.542][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:03:58.543][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:03:58.545][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:03:58.546][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:03:58.548][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:03:58.549][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:03:58.551][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:03:58.552][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:03:58.554][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:03:58.556][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:03:58.557][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:03:58.559][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:03:58.560][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:03:58.562][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:03:58.563][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:03:58.565][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:03:58.567][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:03:58.568][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:03:58.570][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:03:58.576][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:03:58.578][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:03:58.580][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:03:58.581][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:03:58.583][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:03:58.584][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:03:58.586][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:03:58.588][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:03:58.589][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:03:58.592][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:58.593][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:58.594][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.596][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.657][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[2025-03-29 16:03:58.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.693][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[2025-03-29 16:03:58.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:58.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:58.734][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:58.736][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:03:58.738][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.739][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-29 16:03:58.740][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.741][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:58.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.744][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.745][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.746][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.747][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-29 16:03:58.748][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:58.749][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.751][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-29 16:03:58.752][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:58.753][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-29 16:03:58.753][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:03:58.753][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:03:58.753][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:03:58.754][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:58.755][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:58.757][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:03:58.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:58.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:58.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:58.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:58.765][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-29 16:03:58.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:58.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:58.768][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:58.769][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:58.771][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:03:58.774][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:03:58.776][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-29 16:03:58.777][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:03:58.779][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-29 16:03:58.780][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:58.781][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:58.783][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-29 16:03:58.784][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:03:58.785][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-29 16:03:58.786][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-29 16:03:58.812][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:03:58.814][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:58.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:58.816][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:58.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:58.818][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:58.820][FUN] Functions in observer 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-3.20-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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.10.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log'
for details.

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package 'biodbExpasy' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)