Back to Long Tests report for BioC 3.18

This page was generated on 2024-03-02 23:55:03 -0500 (Sat, 02 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 13/30HostnameOS / ArchCHECK
biodbNci 1.6.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-03-02 09:55:02 -0500 (Sat, 02 Mar 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_18
git_last_commit: f5993f4
git_last_commit_date: 2023-10-24 11:40:20 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows 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: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.6.0.tar.gz
StartedAt: 2024-03-02 15:00:58 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 15:01:55 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 57.5 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-03-02 15:01:52.947][biodb::testContext]
biodb.INFO [2024-03-02 15:01:52.951][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:52.952][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-03-02 15:01:52.952][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:52.953][biodb::testContext]
biodb.INFO [2024-03-02 15:01:52.959][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:52.961][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:52.967][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:52.968][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 15:01:52.969][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 15:01:52.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:52.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:52.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:52.972][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 15:01:52.988][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 15:01:52.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:52.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:52.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:52.991][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 15:01:52.992][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 15:01:52.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:52.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:52.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:52.995][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 15:01:52.996][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 15:01:52.997][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 15:01:52.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:52.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:52.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.000][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 15:01:53.001][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 15:01:53.002][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 15:01:53.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.005][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 15:01:53.006][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 15:01:53.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.009][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 15:01:53.010][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 15:01:53.011][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 15:01:53.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.014][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 15:01:53.015][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 15:01:53.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.018][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 15:01:53.018][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 15:01:53.019][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 15:01:53.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.022][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:53.023][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 15:01:53.024][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 15:01:53.025][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 15:01:53.026][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 15:01:53.027][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 15:01:53.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.030][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 15:01:53.031][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 15:01:53.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.043][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 15:01:53.045][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 15:01:53.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.048][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 15:01:53.048][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 15:01:53.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.051][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 15:01:53.052][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 15:01:53.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.055][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 15:01:53.056][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 15:01:53.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.059][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:53.060][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 15:01:53.082][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 15:01:53.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.085][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 15:01:53.086][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 15:01:53.086][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 15:01:53.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.092][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 15:01:53.119][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.131][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 15:01:53.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:53.134][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.135][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.135][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.136][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.137][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:53.138][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:53.138][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.139][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 15:01:53.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:53.141][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.141][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.142][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:53.142][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:53.142][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:53.142][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:53.142][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:53.143][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:53.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.145][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:53.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.148][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.149][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:53.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:53.150][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.151][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.152][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 15:01:53.153][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.154][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:53.155][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.155][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:53.156][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.157][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.158][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.158][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.159][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:53.160][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:53.161][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.161][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 15:01:53.162][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:53.163][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.164][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.165][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:53.165][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:53.165][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:53.165][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:53.165][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:53.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:53.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.168][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:53.168][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.171][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.172][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:53.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:53.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.174][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.175][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 15:01:53.176][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.177][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 15:01:53.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.178][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:53.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.180][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.181][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.182][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:53.183][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:53.183][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.184][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 15:01:53.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:53.185][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.186][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.187][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.188][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:53.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.190][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:53.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.192][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.193][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.193][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:53.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:53.195][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.196][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.196][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 15:01:53.198][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.199][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:53.199][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.200][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:53.201][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.202][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.202][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.203][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.204][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:53.205][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:53.205][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.206][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 15:01:53.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:53.208][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.209][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.209][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.210][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:53.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:53.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.215][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.216][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:53.217][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:53.218][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.218][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.222][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:53.222][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.235][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[2024-03-02 15:01:53.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.239][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[2024-03-02 15:01:53.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.242][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[2024-03-02 15:01:53.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.253][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[2024-03-02 15:01:53.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.256][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[2024-03-02 15:01:53.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.288][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 15:01:53.292][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 15:01:53.293][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 15:01:53.294][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 15:01:53.296][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 15:01:53.297][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 15:01:53.298][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:53.299][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:53.300][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 15:01:53.301][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 15:01:53.302][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 15:01:53.303][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 15:01:53.304][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:53.305][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:53.306][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 15:01:53.307][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 15:01:53.308][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 15:01:53.309][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 15:01:53.310][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 15:01:53.311][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 15:01:53.312][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 15:01:53.314][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 15:01:53.315][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 15:01:53.316][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 15:01:53.317][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 15:01:53.318][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 15:01:53.319][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 15:01:53.320][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 15:01:53.321][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 15:01:53.322][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 15:01:53.323][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 15:01:53.324][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 15:01:53.325][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 15:01:53.326][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 15:01:53.327][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 15:01:53.328][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 15:01:53.330][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 15:01:53.331][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 15:01:53.332][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 15:01:53.333][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 15:01:53.334][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 15:01:53.335][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 15:01:53.336][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 15:01:53.337][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 15:01:53.338][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 15:01:53.339][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 15:01:53.340][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 15:01:53.341][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 15:01:53.342][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 15:01:53.343][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 15:01:53.344][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 15:01:53.345][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 15:01:53.346][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 15:01:53.347][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 15:01:53.348][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 15:01:53.349][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 15:01:53.350][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 15:01:53.351][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 15:01:53.352][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 15:01:53.353][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 15:01:53.354][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 15:01:53.355][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 15:01:53.356][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 15:01:53.357][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 15:01:53.358][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 15:01:53.359][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 15:01:53.360][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 15:01:53.361][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 15:01:53.362][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 15:01:53.363][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 15:01:53.364][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 15:01:53.365][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 15:01:53.366][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 15:01:53.367][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 15:01:53.368][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 15:01:53.369][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 15:01:53.370][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 15:01:53.371][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 15:01:53.373][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 15:01:53.374][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 15:01:53.375][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 15:01:53.376][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 15:01:53.377][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 15:01:53.381][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 15:01:53.383][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:53.385][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:53.386][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.388][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.388][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[2024-03-02 15:01:53.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.401][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[2024-03-02 15:01:53.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.410][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[2024-03-02 15:01:53.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.419][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[2024-03-02 15:01:53.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:53.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:53.478][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:53.485][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-03-02 15:01:53.486][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.487][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-03-02 15:01:53.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:53.489][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.490][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-03-02 15:01:53.491][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.492][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.492][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-03-02 15:01:53.493][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:53.494][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.494][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-03-02 15:01:53.495][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:53.496][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-03-02 15:01:53.496][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-03-02 15:01:53.496][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-03-02 15:01:53.496][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-03-02 15:01:53.496][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-03-02 15:01:53.496][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-03-02 15:01:53.496][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-03-02 15:01:53.497][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:53.498][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.498][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 15:01:53.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:53.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:53.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:53.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:53.503][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 15:01:53.503][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 15:01:53.503][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-03-02 15:01:53.503][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-03-02 15:01:53.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:53.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:53.506][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:53.506][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:53.511][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-03-02 15:01:53.530][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-03-02 15:01:53.531][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-03-02 15:01:53.534][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-03-02 15:01:53.538][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-03-02 15:01:53.541][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:53.542][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:53.543][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 15:01:53.544][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 15:01:53.545][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 15:01:53.546][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-03-02 15:01:53.554][biodb::testThat]
biodb.INFO [2024-03-02 15:01:53.555][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-03-02 15:01:53.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:53.556][biodb::testThat]
biodb.TRACE[2024-03-02 15:01:53.559][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-03-02 15:01:53.560][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-03-02 15:01:53.563][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-03-02 15:01:53.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:53.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:53.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:53.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:53.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:53.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:53.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 15:01:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.620][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.664][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.666][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:53.750][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-03-02 15:01:53.752][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:53.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:53.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.755][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:53.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:53.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:53.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.790][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.817][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.820][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.823][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:53.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.842][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.844][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.866][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.867][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.869][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.895][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.896][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.898][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.917][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.918][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.920][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.940][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.941][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.942][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.953][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:53.953][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:53.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.955][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.959][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:53.960][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:53.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.961][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.965][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:53.966][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:53.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.967][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:53.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.973][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.978][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.978][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:53.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:53.980][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:53.993][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-03-02 15:01:54.017][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-03-02 15:01:54.019][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-03-02 15:01:54.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:54.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:54.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:54.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:54.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:54.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.032][FUN] Functions in observer BiodbConfig: [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[2024-03-02 15:01:54.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.058][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.061][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.065][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.114][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.117][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.122][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:54.144][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-03-02 15:01:54.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.166][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:54.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:54.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.172][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:54.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:54.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.183][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.208][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.211][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.214][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.239][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.240][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.241][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.252][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.255][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.258][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.260][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.261][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.263][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.282][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.284][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.309][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.309][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.311][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.331][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.332][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.334][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.353][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.354][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.356][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.376][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.376][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.378][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.389][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.391][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.395][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.396][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.397][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.402][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.403][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.405][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.409][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.410][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.411][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.416][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.416][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.418][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.422][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.423][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.424][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.429][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.429][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.431][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 15:01:54.438][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.439][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-02 15:01:54.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.440][biodb::testThat]
biodb.DEBUG[2024-03-02 15:01:54.446][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-03-02 15:01:54.452][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-03-02 15:01:54.455][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-03-02 15:01:54.456][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-03-02 15:01:54.457][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-03-02 15:01:54.458][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-03-02 15:01:54.465][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[2024-03-02 15:01:54.466][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 15:01:54.467][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-03-02 15:01:54.468][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-03-02 15:01:54.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:54.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:54.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:54.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:54.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:54.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 15:01:54.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.517][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.520][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.526][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:54.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:54.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:54.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:54.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:54.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:54.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 15:01:54.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.562][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.566][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 15:01:54.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 15:01:54.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 15:01:54.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 15:01:54.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:54.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:54.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 15:01:54.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 15:01:54.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 15:01:54.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.625][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.634][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 15:01:54.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:54.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:54.665][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-03-02 15:01:54.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:54.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:54.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:54.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:54.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:54.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:54.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:54.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:54.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:54.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:54.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:54.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 15:01:54.696][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.696][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-02 15:01:54.697][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.698][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.704][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.704][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-03-02 15:01:54.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.706][biodb::testThat]
biodb.WARN [2024-03-02 15:01:54.722][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-03-02 15:01:54.741][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-03-02 15:01:54.750][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.751][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-03-02 15:01:54.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.752][biodb::testThat]
biodb.TRACE[2024-03-02 15:01:54.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:54.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:54.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.781][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:54.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:54.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.809][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:54.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.816][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:54.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:54.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:54.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:54.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:54.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:54.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 15:01:54.828][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.828][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-02 15:01:54.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.830][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.837][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.837][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-02 15:01:54.838][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.839][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.845][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.846][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-02 15:01:54.847][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.848][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.853][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.854][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-02 15:01:54.855][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:54.855][biodb::testThat]
biodb.INFO [2024-03-02 15:01:54.861][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 15:01:54.862][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-03-02 15:01:54.863][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-03-02 15:01:54.863][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 15:01:54.864][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:54.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:54.865][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:54.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:54.867][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.868][FUN] Functions in observer BiodbConfig: [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 [2024-03-02 15:01:54.879][biodb::testContext]
biodb.INFO [2024-03-02 15:01:54.880][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:54.881][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-03-02 15:01:54.882][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:54.882][biodb::testContext]
biodb.INFO [2024-03-02 15:01:54.884][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:54.885][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:54.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:54.890][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 15:01:54.890][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 15:01:54.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.893][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 15:01:54.894][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 15:01:54.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.896][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[2024-03-02 15:01:54.897][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 15:01:54.898][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 15:01:54.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.901][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 15:01:54.902][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 15:01:54.902][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 15:01:54.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.905][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[2024-03-02 15:01:54.905][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 15:01:54.906][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 15:01:54.907][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 15:01:54.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.910][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 15:01:54.911][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 15:01:54.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.914][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 15:01:54.915][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 15:01:54.916][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 15:01:54.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.919][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 15:01:54.919][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 15:01:54.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.922][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 15:01:54.923][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 15:01:54.924][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 15:01:54.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.927][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:54.928][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 15:01:54.928][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 15:01:54.929][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 15:01:54.930][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 15:01:54.931][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 15:01:54.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.933][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 15:01:54.934][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 15:01:54.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.937][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 15:01:54.938][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 15:01:54.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.941][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 15:01:54.942][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 15:01:54.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.944][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 15:01:54.945][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 15:01:54.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.948][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 15:01:54.949][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 15:01:54.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.952][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:54.953][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 15:01:54.969][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 15:01:54.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.973][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 15:01:54.973][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 15:01:54.974][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 15:01:54.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:54.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:54.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:54.978][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 15:01:54.979][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:54.980][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 15:01:54.981][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:54.982][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:54.983][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:54.983][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:54.984][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:54.985][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:54.986][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:54.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:54.987][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:54.988][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 15:01:54.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:54.990][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:54.990][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:54.991][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:54.991][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:54.991][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:54.991][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:54.991][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:54.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:54.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:54.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:54.994][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:54.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:54.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:54.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:54.997][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:54.998][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:54.999][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:55.000][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.000][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.001][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 15:01:55.003][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.004][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:55.004][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:55.006][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.007][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.008][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.009][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:55.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:55.011][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.012][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 15:01:55.012][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:55.013][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.014][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.015][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:55.015][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:55.015][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:55.015][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:55.015][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:55.016][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:55.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.018][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:55.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.021][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:55.022][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:55.023][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.024][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.029][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 15:01:55.031][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.031][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 15:01:55.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:55.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.035][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.036][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.037][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:55.038][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:55.038][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.039][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 15:01:55.040][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:55.041][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.042][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.042][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:55.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.045][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:55.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.048][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.048][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.049][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:55.050][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:55.051][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.052][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.053][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 15:01:55.054][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.055][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:55.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.057][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:55.057][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.058][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.059][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.061][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:55.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:55.062][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.063][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 15:01:55.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:55.065][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.066][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.067][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.068][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:55.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.070][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:55.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.072][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.073][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.074][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:55.075][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:55.075][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.076][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.077][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:55.078][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.137][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 15:01:55.139][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 15:01:55.140][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 15:01:55.141][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 15:01:55.142][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 15:01:55.143][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 15:01:55.144][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:55.145][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:55.146][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 15:01:55.147][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 15:01:55.148][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 15:01:55.149][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 15:01:55.150][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:55.151][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:55.152][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 15:01:55.153][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 15:01:55.154][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 15:01:55.159][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 15:01:55.161][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 15:01:55.162][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 15:01:55.163][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 15:01:55.164][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 15:01:55.165][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 15:01:55.166][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 15:01:55.167][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 15:01:55.168][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 15:01:55.169][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 15:01:55.170][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 15:01:55.171][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 15:01:55.172][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 15:01:55.173][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 15:01:55.174][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 15:01:55.175][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 15:01:55.176][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 15:01:55.177][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 15:01:55.178][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 15:01:55.179][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 15:01:55.180][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 15:01:55.181][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 15:01:55.182][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 15:01:55.183][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 15:01:55.184][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 15:01:55.185][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 15:01:55.186][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 15:01:55.187][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 15:01:55.188][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 15:01:55.189][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 15:01:55.190][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 15:01:55.192][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 15:01:55.193][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 15:01:55.194][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 15:01:55.195][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 15:01:55.196][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 15:01:55.197][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 15:01:55.198][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 15:01:55.199][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 15:01:55.200][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 15:01:55.201][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 15:01:55.202][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 15:01:55.203][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 15:01:55.204][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 15:01:55.205][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 15:01:55.206][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 15:01:55.207][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 15:01:55.208][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 15:01:55.209][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 15:01:55.211][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 15:01:55.212][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 15:01:55.213][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 15:01:55.214][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 15:01:55.215][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 15:01:55.216][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 15:01:55.217][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 15:01:55.218][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 15:01:55.219][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 15:01:55.220][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 15:01:55.221][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 15:01:55.223][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 15:01:55.224][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 15:01:55.225][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 15:01:55.226][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 15:01:55.227][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 15:01:55.228][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 15:01:55.229][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 15:01:55.230][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:55.231][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:55.232][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.233][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.239][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[2024-03-02 15:01:55.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.253][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[2024-03-02 15:01:55.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.262][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[2024-03-02 15:01:55.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:55.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:55.320][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:55.321][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-03-02 15:01:55.322][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.323][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-03-02 15:01:55.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.325][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:55.325][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.326][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-03-02 15:01:55.327][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.328][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.328][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-03-02 15:01:55.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:55.330][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.331][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-03-02 15:01:55.332][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-03-02 15:01:55.333][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:55.334][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.335][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 15:01:55.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.337][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:55.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:55.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:55.339][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:55.339][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 15:01:55.339][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 15:01:55.339][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-03-02 15:01:55.339][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-03-02 15:01:55.340][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:55.341][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:55.342][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:55.342][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:55.343][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-03-02 15:01:55.346][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-03-02 15:01:55.346][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-03-02 15:01:55.347][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-03-02 15:01:55.348][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-03-02 15:01:55.349][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:55.350][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:55.351][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 15:01:55.352][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 15:01:55.353][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 15:01:55.354][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-03-02 15:01:55.354][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 15:01:55.355][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-03-02 15:01:55.356][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-03-02 15:01:55.357][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 15:01:55.357][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:55.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:55.359][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:55.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:55.360][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:55.361][FUN] Functions in observer 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 
  3.718   0.265   4.019

'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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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-3.18-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)