Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-08 23:55 -0400 (Sat, 08 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
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 12/33HostnameOS / ArchCHECK
biodbNci 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-08 09:55 -0400 (Sat, 08 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on lconway

To the developers/maintainers of the biodbNci 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: biodbNci
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
StartedAt: 2024-06-08 16:04:14 -0400 (Sat, 08 Jun 2024)
EndedAt: 2024-06-08 16:05:04 -0400 (Sat, 08 Jun 2024)
EllapsedTime: 49.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-06-08 16:05:01.433][biodb::testContext]
biodb.INFO [2024-06-08 16:05:01.436][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:05:01.437][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-08 16:05:01.437][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:05:01.438][biodb::testContext]
biodb.INFO [2024-06-08 16:05:01.443][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:05:01.444][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:05:01.450][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:01.450][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:05:01.451][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:05:01.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.454][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:05:01.467][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:05:01.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.470][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:05:01.471][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:05:01.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.473][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:05:01.474][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:05:01.475][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:05:01.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.477][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:05:01.478][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:05:01.479][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:05:01.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.482][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:05:01.482][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:05:01.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.485][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:05:01.486][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:05:01.486][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:05:01.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.489][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:05:01.490][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:05:01.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.492][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:05:01.493][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:05:01.494][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:05:01.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.497][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:05:01.497][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:05:01.498][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:05:01.499][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:05:01.499][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:05:01.500][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:05:01.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.503][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:05:01.504][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:05:01.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.506][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:05:01.507][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:05:01.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.510][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:05:01.510][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:05:01.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.513][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:05:01.514][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:05:01.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.516][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:05:01.517][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:05:01.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.519][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:05:01.520][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:05:01.536][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:05:01.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.539][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:05:01.540][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:05:01.541][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:05:01.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.545][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:05:01.568][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.584][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:05:01.585][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:01.586][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.587][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.588][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.588][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.589][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:05:01.590][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:01.591][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.591][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:05:01.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:01.593][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.594][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.594][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:05:01.594][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:05:01.594][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:05:01.594][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:05:01.594][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:05:01.595][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:01.596][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.597][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:01.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.599][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.600][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.601][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:01.602][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:01.602][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.603][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.604][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:05:01.605][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.606][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:05:01.607][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.607][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:01.608][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.609][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.609][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.610][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.611][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:05:01.612][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:01.612][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.613][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:05:01.614][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:01.615][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.615][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.616][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:05:01.616][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:05:01.616][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:05:01.616][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:05:01.616][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:05:01.617][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:01.618][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.618][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.619][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:01.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.620][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.621][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.622][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.622][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:01.623][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:01.624][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.625][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.625][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:05:01.627][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.627][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:05:01.628][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.629][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:01.630][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.630][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.631][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.632][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.632][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:05:01.633][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:01.634][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.635][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:05:01.635][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:01.636][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.637][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.638][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.638][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:01.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.640][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:01.641][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.643][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.643][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.644][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:01.645][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:01.645][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.646][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.647][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:05:01.648][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.649][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:05:01.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.650][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:01.651][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.652][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.653][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.653][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.654][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:05:01.655][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:01.656][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.656][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:05:01.657][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:01.658][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.659][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.659][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.660][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:01.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:01.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.665][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:01.666][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:01.667][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.668][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.670][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:01.671][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.722][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[2024-06-08 16:05:01.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.729][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:05:01.733][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:05:01.734][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:05:01.735][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:05:01.736][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:05:01.737][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:05:01.738][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:05:01.739][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:05:01.740][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:05:01.741][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:05:01.741][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:05:01.742][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:05:01.743][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:05:01.744][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:05:01.745][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:05:01.746][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:05:01.747][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:05:01.748][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:05:01.749][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:05:01.750][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:05:01.751][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:05:01.752][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:05:01.753][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:05:01.754][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:05:01.755][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:05:01.756][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:05:01.757][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:05:01.758][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:05:01.759][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:05:01.760][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:05:01.761][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:05:01.762][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:05:01.763][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:05:01.764][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:05:01.765][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:05:01.766][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:05:01.767][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:05:01.768][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:05:01.769][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:05:01.770][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:05:01.771][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:05:01.772][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:05:01.773][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:05:01.774][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:05:01.775][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:05:01.776][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:05:01.776][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:05:01.778][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:05:01.779][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:05:01.780][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:05:01.781][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:05:01.782][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:05:01.782][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:05:01.783][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:05:01.784][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:05:01.786][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:05:01.787][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:05:01.788][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:05:01.789][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:05:01.790][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:05:01.791][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:05:01.792][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:05:01.793][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:05:01.794][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:05:01.795][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:05:01.796][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:05:01.797][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:05:01.798][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:05:01.799][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:05:01.800][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:05:01.801][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:05:01.802][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:05:01.803][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:05:01.803][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:05:01.804][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:05:01.805][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:05:01.806][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:05:01.807][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:05:01.808][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:05:01.809][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:05:01.810][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:05:01.811][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:05:01.812][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:05:01.817][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:05:01.818][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:05:01.820][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:01.821][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.822][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:01.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:01.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:01.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:01.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:01.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:01.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:01.907][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-08 16:05:01.914][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-08 16:05:01.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.916][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-08 16:05:01.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.917][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:01.918][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.919][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-08 16:05:01.919][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.921][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-08 16:05:01.922][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:01.922][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.923][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-08 16:05:01.924][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-08 16:05:01.925][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:01.926][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.927][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:05:01.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.929][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:01.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:01.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:01.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:01.931][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:05:01.931][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:05:01.931][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-08 16:05:01.931][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-08 16:05:01.932][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:01.933][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:01.933][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:01.934][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:01.938][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-08 16:05:01.956][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-08 16:05:01.957][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-08 16:05:01.960][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-08 16:05:01.963][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-08 16:05:01.966][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:05:01.966][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:05:01.967][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:05:01.968][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:05:01.969][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:05:01.970][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-08 16:05:02.001][biodb::testThat]
biodb.INFO [2024-06-08 16:05:02.002][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-08 16:05:02.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:02.003][biodb::testThat]
biodb.TRACE[2024-06-08 16:05:02.006][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-06-08 16:05:02.007][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:05:02.009][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:05:02.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:05:02.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:02.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:02.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:02.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:02.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:02.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:05:02.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.095][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.107][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:05:02.155][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-06-08 16:05:02.157][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.160][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:02.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:02.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.165][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:02.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:02.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.192][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.239][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.242][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.245][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.266][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.267][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.268][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.282][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.287][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.288][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.289][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.290][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.308][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.309][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.310][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.328][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.329][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.331][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.349][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.350][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.351][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.361][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.361][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.363][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.370][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.371][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.373][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.376][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.377][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.382][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.383][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.384][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.388][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.388][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.390][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.402][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-06-08 16:05:02.425][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:05:02.426][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:05:02.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:05:02.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:02.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:02.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:02.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:02.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:02.434][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.TRACE[2024-06-08 16:05:02.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.458][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.461][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.512][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.515][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.521][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:05:02.541][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-06-08 16:05:02.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.558][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:02.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:02.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:02.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:02.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:02.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.576][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.601][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.607][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.630][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.631][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.632][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.642][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.644][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.650][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.651][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.652][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.653][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.670][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.671][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.672][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.685][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.690][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.693][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.694][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.713][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.714][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.715][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.733][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.735][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.752][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.753][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.754][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.764][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.765][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.766][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.769][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.770][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.772][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.775][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.777][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.781][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.781][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.783][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.790][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.791][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.792][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.796][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.796][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.801][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.802][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.803][ef$get] fields variable is a list.
biodb.INFO [2024-06-08 16:05:02.809][biodb::testThat]
biodb.INFO [2024-06-08 16:05:02.810][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-08 16:05:02.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:02.811][biodb::testThat]
biodb.DEBUG[2024-06-08 16:05:02.813][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-06-08 16:05:02.818][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-06-08 16:05:02.820][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-06-08 16:05:02.821][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-06-08 16:05:02.823][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-06-08 16:05:02.824][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-08 16:05:02.825][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-06-08 16:05:02.826][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-06-08 16:05:02.827][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-06-08 16:05:02.828][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:05:02.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:05:02.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:02.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:02.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:02.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:02.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:02.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:05:02.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.847][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.872][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.880][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:05:02.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:05:02.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:02.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:02.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:02.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:02.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:02.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:05:02.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.916][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.919][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:05:02.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:05:02.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:05:02.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:05:02.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:02.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:02.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.954][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:05:02.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:05:02.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:05:02.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.966][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.968][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.974][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:05:02.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:02.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:02.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:02.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:02.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:05:03.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:05:03.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:05:03.002][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-06-08 16:05:03.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:05:03.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:05:03.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:05:03.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:05:03.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:05:03.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:05:03.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:05:03.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:05:03.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:05:03.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:05:03.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:05:03.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:05:03.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:05:03.032][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.033][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-08 16:05:03.034][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:03.035][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.039][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.040][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-08 16:05:03.041][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:03.041][biodb::testThat]
biodb.WARN [2024-06-08 16:05:03.055][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-06-08 16:05:03.067][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-06-08 16:05:03.074][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.075][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-08 16:05:03.075][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:03.076][biodb::testThat]
biodb.TRACE[2024-06-08 16:05:03.092][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:03.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:03.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:03.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:03.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.145][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:05:03.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:05:03.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:03.153][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:03.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:05:03.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:03.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:05:03.161][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.161][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-08 16:05:03.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:03.163][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.168][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.169][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-08 16:05:03.170][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:03.170][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.176][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.177][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-08 16:05:03.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:03.178][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.183][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.183][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-08 16:05:03.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:03.185][biodb::testThat]
biodb.INFO [2024-06-08 16:05:03.190][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:05:03.190][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-08 16:05:03.191][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-08 16:05:03.192][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:05:03.192][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.194][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.195][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-08 16:05:03.202][biodb::testContext]
biodb.INFO [2024-06-08 16:05:03.203][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:05:03.204][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-08 16:05:03.204][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:05:03.205][biodb::testContext]
biodb.INFO [2024-06-08 16:05:03.206][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:05:03.208][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:05:03.211][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:03.211][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:05:03.212][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:05:03.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.215][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:05:03.215][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:05:03.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.218][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:05:03.222][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:05:03.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.225][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:05:03.225][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:05:03.226][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:05:03.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.229][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:05:03.229][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:05:03.230][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:05:03.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.233][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:05:03.233][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:05:03.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.236][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:05:03.237][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:05:03.237][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:05:03.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.240][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:05:03.241][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:05:03.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.243][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:05:03.244][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:05:03.245][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:05:03.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.247][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:05:03.248][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:05:03.249][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:05:03.249][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:05:03.250][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:05:03.251][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:05:03.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.253][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:05:03.254][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:05:03.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.257][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:05:03.257][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:05:03.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.260][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:05:03.261][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:05:03.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.263][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:05:03.264][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:05:03.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.266][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:05:03.267][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:05:03.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.270][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:05:03.271][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:05:03.285][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:05:03.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.288][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:05:03.288][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:05:03.289][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:05:03.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.292][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:05:03.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.294][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:05:03.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.295][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:03.296][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.297][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.298][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.299][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:05:03.300][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:03.300][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.301][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:05:03.302][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:03.302][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.304][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:05:03.304][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:05:03.304][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:05:03.304][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:05:03.304][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:05:03.305][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:03.305][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.307][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:03.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.309][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.309][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.310][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:03.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:03.311][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.312][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.313][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:05:03.314][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.315][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:05:03.315][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.316][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:03.317][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.317][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.318][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.319][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.319][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:05:03.320][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:03.321][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.322][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:05:03.322][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:03.323][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.324][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.324][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:05:03.324][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:05:03.324][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:05:03.324][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:05:03.324][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:05:03.325][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:03.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.327][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:03.328][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.329][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.330][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.334][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:03.334][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:03.335][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.336][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.337][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:05:03.338][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.339][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:05:03.339][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:03.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.341][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.342][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.343][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.343][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:05:03.344][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:03.345][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.345][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:05:03.346][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:03.347][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.348][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.348][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:03.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:03.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.353][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.354][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.354][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:03.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:03.355][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.356][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.357][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:05:03.358][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.359][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:05:03.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.360][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:03.361][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.362][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.362][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.363][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.364][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:05:03.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:03.365][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.366][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:05:03.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:03.367][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.368][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.369][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.369][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:03.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.371][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:03.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.373][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.374][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:03.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:03.376][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.377][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.378][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:03.378][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.419][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[2024-06-08 16:05:03.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.425][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[2024-06-08 16:05:03.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.435][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[2024-06-08 16:05:03.435][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:05:03.436][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:05:03.437][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:05:03.438][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:05:03.439][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:05:03.440][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:05:03.441][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:05:03.442][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:05:03.443][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:05:03.444][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:05:03.445][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:05:03.446][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:05:03.447][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:05:03.448][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:05:03.449][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:05:03.450][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:05:03.451][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:05:03.452][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:05:03.453][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:05:03.454][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:05:03.455][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:05:03.456][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:05:03.457][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:05:03.458][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:05:03.459][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:05:03.460][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:05:03.461][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:05:03.462][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:05:03.463][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:05:03.464][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:05:03.465][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:05:03.466][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:05:03.466][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:05:03.467][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:05:03.468][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:05:03.469][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:05:03.470][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:05:03.471][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:05:03.472][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:05:03.473][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:05:03.474][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:05:03.475][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:05:03.476][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:05:03.477][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:05:03.478][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:05:03.479][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:05:03.480][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:05:03.481][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:05:03.482][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:05:03.483][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:05:03.484][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:05:03.485][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:05:03.486][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:05:03.487][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:05:03.488][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:05:03.489][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:05:03.490][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:05:03.491][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:05:03.492][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:05:03.493][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:05:03.494][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:05:03.494][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:05:03.495][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:05:03.496][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:05:03.497][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:05:03.498][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:05:03.499][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:05:03.500][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:05:03.501][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:05:03.502][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:05:03.503][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:05:03.504][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:05:03.505][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:05:03.506][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:05:03.507][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:05:03.508][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:05:03.509][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:05:03.510][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:05:03.511][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:05:03.512][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:05:03.513][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:05:03.514][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:05:03.515][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:05:03.516][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:05:03.517][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:05:03.518][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:03.518][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.519][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:03.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:03.599][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-08 16:05:03.600][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-08 16:05:03.602][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.602][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-08 16:05:03.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.604][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:03.605][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.605][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-08 16:05:03.606][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.607][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-08 16:05:03.608][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:03.609][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.609][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-08 16:05:03.610][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:03.611][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-08 16:05:03.611][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-08 16:05:03.611][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-08 16:05:03.611][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-08 16:05:03.611][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-08 16:05:03.611][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-08 16:05:03.611][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-08 16:05:03.612][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:03.612][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.613][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:05:03.614][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.615][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:03.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:03.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:03.617][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:03.618][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:05:03.618][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:05:03.618][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-08 16:05:03.618][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-08 16:05:03.618][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:03.622][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:03.623][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:03.624][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:03.625][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-08 16:05:03.627][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-08 16:05:03.627][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-08 16:05:03.628][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-08 16:05:03.629][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-08 16:05:03.630][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:05:03.631][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:05:03.632][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:05:03.633][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:05:03.633][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:05:03.634][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-08 16:05:03.635][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:05:03.636][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-08 16:05:03.636][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-08 16:05:03.637][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:05:03.638][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:03.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:03.639][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:03.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:03.640][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:03.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  3.330   0.232   3.623

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)