Back to Long Tests report for BioC 3.21

This page was generated on 2025-05-24 23:55 -0400 (Sat, 24 May 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4836
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4577
merida1macOS 12.7.5 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4601
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 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-05-24 09:55 -0400 (Sat, 24 May 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1

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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2025-05-24 16:01:23 -0400 (Sat, 24 May 2025)
EndedAt: 2025-05-24 16:35:56 -0400 (Sat, 24 May 2025)
EllapsedTime: 2073.5 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-05-24 16:02:34.781][biodb::testContext]
biodb.INFO [2025-05-24 16:02:34.784][biodb::testContext] ********************************************************************************
biodb.INFO [2025-05-24 16:02:34.786][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-05-24 16:02:34.787][biodb::testContext] ********************************************************************************
biodb.INFO [2025-05-24 16:02:34.788][biodb::testContext]
biodb.INFO [2025-05-24 16:02:34.795][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-05-24 16:02:34.797][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-05-24 16:02:34.805][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-05-24 16:02:34.806][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-05-24 16:02:34.807][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-05-24 16:02:34.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.812][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-05-24 16:02:34.837][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-05-24 16:02:34.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.842][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-05-24 16:02:34.843][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-05-24 16:02:34.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.848][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-05-24 16:02:34.849][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-05-24 16:02:34.850][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-05-24 16:02:34.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.855][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-05-24 16:02:34.856][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-05-24 16:02:34.857][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-05-24 16:02:34.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.861][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-05-24 16:02:34.863][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-05-24 16:02:34.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.867][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-05-24 16:02:34.868][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-05-24 16:02:34.870][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-05-24 16:02:34.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.874][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-05-24 16:02:34.875][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-05-24 16:02:34.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.880][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-05-24 16:02:34.881][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-05-24 16:02:34.882][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-05-24 16:02:34.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.887][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-05-24 16:02:34.888][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-05-24 16:02:34.889][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-05-24 16:02:34.890][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-05-24 16:02:34.892][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-05-24 16:02:34.893][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-05-24 16:02:34.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.896][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[2025-05-24 16:02:34.897][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-05-24 16:02:34.899][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-05-24 16:02:34.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.903][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-05-24 16:02:34.904][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-05-24 16:02:34.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.909][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-05-24 16:02:34.910][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-05-24 16:02:34.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.915][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-05-24 16:02:34.916][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-05-24 16:02:34.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.920][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-05-24 16:02:34.922][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-05-24 16:02:34.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.926][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-05-24 16:02:34.927][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-05-24 16:02:34.945][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-05-24 16:02:34.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.950][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-05-24 16:02:34.951][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-05-24 16:02:34.953][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-05-24 16:02:34.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:34.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:34.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:34.960][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-05-24 16:02:35.003][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.030][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-05-24 16:02:35.031][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:02:35.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.039][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-05-24 16:02:35.040][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:02:35.041][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.042][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-05-24 16:02:35.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:02:35.045][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.046][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.047][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-05-24 16:02:35.047][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-05-24 16:02:35.047][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-05-24 16:02:35.047][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-05-24 16:02:35.047][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-05-24 16:02:35.048][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:02:35.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:02:35.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.056][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.058][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:02:35.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:02:35.060][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.061][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.062][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-05-24 16:02:35.065][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.066][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-05-24 16:02:35.067][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.068][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:02:35.070][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.072][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.073][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.075][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-05-24 16:02:35.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:02:35.077][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.078][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-05-24 16:02:35.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:02:35.081][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.082][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.083][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-05-24 16:02:35.083][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-05-24 16:02:35.083][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-05-24 16:02:35.083][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-05-24 16:02:35.083][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-05-24 16:02:35.084][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:02:35.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:02:35.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.093][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:02:35.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:02:35.096][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.097][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.099][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-05-24 16:02:35.101][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.102][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-05-24 16:02:35.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:02:35.106][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.107][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.108][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.110][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-05-24 16:02:35.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:02:35.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.114][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-05-24 16:02:35.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:02:35.117][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.119][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.120][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:02:35.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:02:35.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.128][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:02:35.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:02:35.132][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.133][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.134][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-05-24 16:02:35.136][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.138][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-05-24 16:02:35.139][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.140][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:02:35.141][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.142][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.144][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.145][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.146][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-05-24 16:02:35.147][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:02:35.149][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.150][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-05-24 16:02:35.151][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:02:35.153][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.154][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.155][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.156][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:02:35.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:02:35.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.163][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.164][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.166][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:02:35.167][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:02:35.168][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.169][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.173][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-05-24 16:02:35.174][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.257][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[2025-05-24 16:02:35.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.262][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[2025-05-24 16:02:35.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.267][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[2025-05-24 16:02:35.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.274][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-05-24 16:02:35.279][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-05-24 16:02:35.281][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-05-24 16:02:35.282][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-05-24 16:02:35.284][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-05-24 16:02:35.286][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-05-24 16:02:35.287][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-05-24 16:02:35.289][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-05-24 16:02:35.291][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-05-24 16:02:35.292][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-05-24 16:02:35.294][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-05-24 16:02:35.296][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-05-24 16:02:35.297][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-05-24 16:02:35.299][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-05-24 16:02:35.301][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-05-24 16:02:35.302][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-05-24 16:02:35.304][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-05-24 16:02:35.306][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-05-24 16:02:35.307][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-05-24 16:02:35.309][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-05-24 16:02:35.311][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-05-24 16:02:35.312][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-05-24 16:02:35.314][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-05-24 16:02:35.316][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-05-24 16:02:35.318][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-05-24 16:02:35.319][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-05-24 16:02:35.321][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-05-24 16:02:35.323][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-05-24 16:02:35.324][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-05-24 16:02:35.326][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-05-24 16:02:35.328][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-05-24 16:02:35.329][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-05-24 16:02:35.331][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-05-24 16:02:35.333][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-05-24 16:02:35.335][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-05-24 16:02:35.336][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-05-24 16:02:35.338][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-05-24 16:02:35.340][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-05-24 16:02:35.341][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-05-24 16:02:35.343][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-05-24 16:02:35.345][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-05-24 16:02:35.346][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-05-24 16:02:35.348][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-05-24 16:02:35.350][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-05-24 16:02:35.352][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-05-24 16:02:35.353][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-05-24 16:02:35.355][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-05-24 16:02:35.357][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-05-24 16:02:35.358][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-05-24 16:02:35.360][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-05-24 16:02:35.362][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-05-24 16:02:35.364][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-05-24 16:02:35.365][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-05-24 16:02:35.367][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-05-24 16:02:35.369][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-05-24 16:02:35.370][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-05-24 16:02:35.372][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-05-24 16:02:35.374][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-05-24 16:02:35.375][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-05-24 16:02:35.377][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-05-24 16:02:35.379][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-05-24 16:02:35.381][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-05-24 16:02:35.382][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-05-24 16:02:35.384][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-05-24 16:02:35.386][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-05-24 16:02:35.388][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-05-24 16:02:35.389][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-05-24 16:02:35.391][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-05-24 16:02:35.393][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-05-24 16:02:35.395][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-05-24 16:02:35.396][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-05-24 16:02:35.398][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-05-24 16:02:35.400][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-05-24 16:02:35.401][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-05-24 16:02:35.403][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-05-24 16:02:35.405][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-05-24 16:02:35.407][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-05-24 16:02:35.408][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-05-24 16:02:35.410][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-05-24 16:02:35.412][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-05-24 16:02:35.414][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-05-24 16:02:35.415][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-05-24 16:02:35.417][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-05-24 16:02:35.425][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-05-24 16:02:35.427][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-05-24 16:02:35.430][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-05-24 16:02:35.431][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.433][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:02:35.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:02:35.578][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-05-24 16:02:35.590][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-05-24 16:02:35.593][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.594][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-05-24 16:02:35.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.597][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:02:35.598][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.599][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-05-24 16:02:35.600][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.602][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.603][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-05-24 16:02:35.604][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:02:35.605][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.606][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-05-24 16:02:35.608][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:02:35.609][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-05-24 16:02:35.609][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-05-24 16:02:35.609][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-05-24 16:02:35.609][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-05-24 16:02:35.609][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-05-24 16:02:35.609][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-05-24 16:02:35.609][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-05-24 16:02:35.610][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-05-24 16:02:35.611][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.613][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-05-24 16:02:35.614][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.615][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.616][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:02:35.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:02:35.618][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:02:35.620][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:02:35.621][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-05-24 16:02:35.621][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-05-24 16:02:35.621][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-05-24 16:02:35.621][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-05-24 16:02:35.622][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:02:35.623][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:02:35.624][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-05-24 16:02:35.626][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:02:35.634][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-05-24 16:02:35.656][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-05-24 16:02:35.658][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-05-24 16:02:35.662][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-05-24 16:02:35.666][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-05-24 16:02:35.671][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-05-24 16:02:35.672][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-05-24 16:02:35.674][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-05-24 16:02:35.675][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-05-24 16:02:35.677][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-05-24 16:02:35.678][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-05-24 16:02:35.716][biodb::testThat]
biodb.INFO [2025-05-24 16:02:35.718][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-05-24 16:02:35.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:02:35.720][biodb::testThat]
biodb.TRACE[2025-05-24 16:02:35.724][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-05-24 16:02:35.726][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-05-24 16:02:35.729][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-05-24 16:02:35.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-05-24 16:02:35.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:35.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:35.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:35.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:35.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:35.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-05-24 16:02:35.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:35.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:35.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.847][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:35.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:35.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:35.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:35.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:35.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:35.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:35.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:35.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:35.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:35.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:35.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:35.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:35.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:35.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.886][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:35.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:35.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.891][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:35.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:35.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.902][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:35.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:35.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:35.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:35.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-05-24 16:02:35.988][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-05-24 16:02:35.991][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:02:35.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:02:35.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:35.996][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:02:35.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:02:35.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:35.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.001][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-05-24 16:02:36.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-05-24 16:02:36.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-05-24 16:02:36.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-05-24 16:02:36.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.089][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.131][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.136][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.141][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.174][ef$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.178][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.194][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.199][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.209][ef$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.210][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.213][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.243][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.245][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.247][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.278][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.279][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.281][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.312][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.313][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.315][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.317][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.331][ef$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.333][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.339][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.346][ef$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.347][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.349][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.355][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.356][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.358][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.364][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.365][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.368][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.373][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.375][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.377][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.399][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-05-24 16:02:36.446][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-05-24 16:02:36.448][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-05-24 16:02:36.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-05-24 16:02:36.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:02:36.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:02:36.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:02:36.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:02:36.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:02:36.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-05-24 16:02:36.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.514][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.518][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:36.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.601][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.606][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-05-24 16:02:36.650][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-05-24 16:02:36.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:02:36.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:02:36.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:02:36.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:02:36.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.690][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-05-24 16:02:36.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-05-24 16:02:36.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.695][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-05-24 16:02:36.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-05-24 16:02:36.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.711][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.752][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.757][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.762][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:02:36.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.803][ef$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.804][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.806][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:36.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:36.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.822][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.828][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.833][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.838][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.839][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.842][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.843][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:36.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.878][ef$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.879][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.881][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:36.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:36.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.912][ef$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.914][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.916][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.917][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:36.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:36.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.948][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.949][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.952][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:36.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.983][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.985][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.987][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:36.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:36.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:36.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:36.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.019][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.020][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.023][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.040][ef$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:02:37.041][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:02:37.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.044][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.050][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:02:37.052][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:02:37.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.054][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.064][ef$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:02:37.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:02:37.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.068][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.074][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:02:37.075][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:02:37.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.078][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.085][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:02:37.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.087][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.093][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:37.095][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:02:37.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.097][ef$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:02:37.103][ef$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:02:37.105][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:02:37.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:02:37.107][ef$get] fields variable is a list.
biodb.INFO [2025-05-24 16:02:37.117][biodb::testThat]
biodb.INFO [2025-05-24 16:02:37.118][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-05-24 16:02:37.120][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:02:37.121][biodb::testThat]
biodb.DEBUG[2025-05-24 16:02:37.123][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-05-24 16:02:37.130][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-05-24 16:02:37.135][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-05-24 16:02:37.136][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-05-24 16:02:37.138][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-05-24 16:02:37.139][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2025-05-24 16:03:16.268][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactusd35d849369fgz".
biodb.TRACE[2025-05-24 16:03:16.270][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-05-24 16:03:16.271][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-05-24 16:03:16.273][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-05-24 16:03:16.274][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-05-24 16:03:16.276][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerd35d7ea104f8marker".
biodb.TRACE[2025-05-24 16:03:16.278][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-05-24 16:03:16.279][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-05-24 16:03:16.281][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-05-24 16:03:16.283][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-05-24 16:03:16.284][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-05-24 16:03:16.286][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-05-24 16:04:34.545][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-05-24 16:04:34.547][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2025-05-24 16:33:46.521][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-05-24 16:33:46.997][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2025-05-24 16:35:52.566][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-05-24 16:35:52.569][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-05-24 16:35:53.390][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerd35d7d4d76bamarker".
biodb.TRACE[2025-05-24 16:35:53.392][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-05-24 16:35:53.394][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-05-24 16:35:53.398][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-05-24 16:35:53.400][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-05-24 16:35:53.404][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-05-24 16:35:53.406][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-05-24 16:35:53.410][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-05-24 16:35:53.412][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-05-24 16:35:53.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-05-24 16:35:53.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:53.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:53.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:53.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:53.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:53.443][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.TRACE[2025-05-24 16:35:53.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:35:53.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:35:53.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.491][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:35:53.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:35:53.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:35:53.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:35:53.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:35:53.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:35:53.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.544][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.550][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.561][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-05-24 16:35:53.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-05-24 16:35:53.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:53.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:53.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:53.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:53.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:53.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-05-24 16:35:53.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.631][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:35:53.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:35:53.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.637][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-05-24 16:35:53.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-05-24 16:35:53.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.644][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:35:53.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:35:53.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-05-24 16:35:53.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-05-24 16:35:53.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-05-24 16:35:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:35:53.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:35:53.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:35:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:35:53.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:35:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:35:53.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:35:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:35:53.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:35:53.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:35:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:35:53.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:35:53.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-05-24 16:35:53.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-05-24 16:35:53.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:35:53.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:35:53.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-05-24 16:35:53.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-05-24 16:35:53.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-05-24 16:35:53.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.737][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.743][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.755][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-05-24 16:35:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-05-24 16:35:53.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-05-24 16:35:53.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-05-24 16:35:53.814][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-05-24 16:35:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-05-24 16:35:53.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-05-24 16:35:53.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-05-24 16:35:53.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-05-24 16:35:53.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-05-24 16:35:53.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-05-24 16:35:53.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-05-24 16:35:53.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-05-24 16:35:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-05-24 16:35:53.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-05-24 16:35:53.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:53.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-05-24 16:35:53.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-05-24 16:35:53.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:53.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-05-24 16:35:53.869][biodb::testThat]
biodb.INFO [2025-05-24 16:35:53.870][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-05-24 16:35:53.872][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:35:53.873][biodb::testThat]
biodb.INFO [2025-05-24 16:35:53.883][biodb::testThat]
biodb.INFO [2025-05-24 16:35:53.884][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-05-24 16:35:53.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:35:53.887][biodb::testThat]
biodb.WARN [2025-05-24 16:35:53.924][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-05-24 16:35:53.956][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-05-24 16:35:53.970][biodb::testThat]
biodb.INFO [2025-05-24 16:35:53.972][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-05-24 16:35:53.973][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:35:53.974][biodb::testThat]
biodb.TRACE[2025-05-24 16:35:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:54.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:54.028][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-05-24 16:35:54.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-05-24 16:35:54.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:54.034][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-05-24 16:35:54.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-05-24 16:35:54.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:54.096][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:54.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-05-24 16:35:54.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:54.109][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-05-24 16:35:54.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-05-24 16:35:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-05-24 16:35:54.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-05-24 16:35:54.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-05-24 16:35:54.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-05-24 16:35:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-05-24 16:35:54.132][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.134][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-05-24 16:35:54.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:35:54.138][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.151][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.152][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-05-24 16:35:54.154][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:35:54.155][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.167][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.168][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-05-24 16:35:54.170][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:35:54.171][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.181][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.183][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-05-24 16:35:54.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-05-24 16:35:54.186][biodb::testThat]
biodb.INFO [2025-05-24 16:35:54.195][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-05-24 16:35:54.197][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-05-24 16:35:54.199][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-05-24 16:35:54.201][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-05-24 16:35:54.202][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.206][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.209][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-05-24 16:35:54.233][biodb::testContext]
biodb.INFO [2025-05-24 16:35:54.234][biodb::testContext] ********************************************************************************
biodb.INFO [2025-05-24 16:35:54.236][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-05-24 16:35:54.238][biodb::testContext] ********************************************************************************
biodb.INFO [2025-05-24 16:35:54.240][biodb::testContext]
biodb.INFO [2025-05-24 16:35:54.245][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-05-24 16:35:54.248][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-05-24 16:35:54.255][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-05-24 16:35:54.256][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-05-24 16:35:54.258][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-05-24 16:35:54.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.262][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[2025-05-24 16:35:54.263][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-05-24 16:35:54.265][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-05-24 16:35:54.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.271][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-05-24 16:35:54.272][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-05-24 16:35:54.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.276][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[2025-05-24 16:35:54.278][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-05-24 16:35:54.279][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-05-24 16:35:54.281][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-05-24 16:35:54.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.286][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-05-24 16:35:54.288][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-05-24 16:35:54.289][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-05-24 16:35:54.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.295][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-05-24 16:35:54.296][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-05-24 16:35:54.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.302][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-05-24 16:35:54.303][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-05-24 16:35:54.305][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-05-24 16:35:54.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.309][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[2025-05-24 16:35:54.310][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-05-24 16:35:54.311][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-05-24 16:35:54.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.317][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-05-24 16:35:54.319][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-05-24 16:35:54.320][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-05-24 16:35:54.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.325][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-05-24 16:35:54.327][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-05-24 16:35:54.329][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-05-24 16:35:54.330][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-05-24 16:35:54.332][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-05-24 16:35:54.333][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-05-24 16:35:54.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.339][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-05-24 16:35:54.340][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-05-24 16:35:54.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.346][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-05-24 16:35:54.347][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-05-24 16:35:54.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.353][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-05-24 16:35:54.354][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-05-24 16:35:54.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.360][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-05-24 16:35:54.361][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-05-24 16:35:54.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.367][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-05-24 16:35:54.368][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-05-24 16:35:54.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.374][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-05-24 16:35:54.375][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-05-24 16:35:54.401][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-05-24 16:35:54.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.407][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-05-24 16:35:54.408][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-05-24 16:35:54.410][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-05-24 16:35:54.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.416][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-05-24 16:35:54.419][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.421][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-05-24 16:35:54.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.424][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:35:54.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.428][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.430][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.431][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-05-24 16:35:54.433][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:35:54.434][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.436][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-05-24 16:35:54.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:35:54.439][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.440][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.442][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-05-24 16:35:54.442][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-05-24 16:35:54.442][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-05-24 16:35:54.442][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-05-24 16:35:54.442][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-05-24 16:35:54.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:35:54.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:35:54.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.453][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.454][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:35:54.456][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:35:54.457][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.459][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.460][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-05-24 16:35:54.463][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.464][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-05-24 16:35:54.466][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.467][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:35:54.469][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.470][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.472][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.473][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.475][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-05-24 16:35:54.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:35:54.478][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.479][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-05-24 16:35:54.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:35:54.482][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.484][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.485][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-05-24 16:35:54.485][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-05-24 16:35:54.485][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-05-24 16:35:54.485][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-05-24 16:35:54.485][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-05-24 16:35:54.487][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:35:54.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.491][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:35:54.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.495][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.496][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.498][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:35:54.499][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:35:54.501][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.502][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.504][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-05-24 16:35:54.507][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.508][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-05-24 16:35:54.510][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.511][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:35:54.513][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.514][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.515][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.517][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.518][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-05-24 16:35:54.520][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:35:54.521][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.523][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-05-24 16:35:54.524][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:35:54.526][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.527][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.529][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.530][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:35:54.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.534][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:35:54.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.538][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.540][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.542][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:35:54.543][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:35:54.544][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.546][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.547][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-05-24 16:35:54.550][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.552][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-05-24 16:35:54.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.555][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:35:54.556][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.562][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-05-24 16:35:54.563][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:35:54.565][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.566][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-05-24 16:35:54.568][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:35:54.569][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.571][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:54.572][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.574][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-05-24 16:35:54.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:35:54.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:54.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:54.582][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:35:54.583][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.585][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:35:54.586][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:35:54.587][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:54.589][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:54.591][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-05-24 16:35:54.592][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.706][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-05-24 16:35:54.709][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-05-24 16:35:54.711][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-05-24 16:35:54.713][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-05-24 16:35:54.715][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-05-24 16:35:54.717][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-05-24 16:35:54.719][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-05-24 16:35:54.721][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-05-24 16:35:54.723][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-05-24 16:35:54.725][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-05-24 16:35:54.727][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-05-24 16:35:54.729][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-05-24 16:35:54.731][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-05-24 16:35:54.733][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-05-24 16:35:54.735][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-05-24 16:35:54.737][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-05-24 16:35:54.739][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-05-24 16:35:54.741][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-05-24 16:35:54.743][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-05-24 16:35:54.745][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-05-24 16:35:54.747][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-05-24 16:35:54.749][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-05-24 16:35:54.752][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-05-24 16:35:54.754][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-05-24 16:35:54.756][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-05-24 16:35:54.758][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-05-24 16:35:54.760][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-05-24 16:35:54.762][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-05-24 16:35:54.764][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-05-24 16:35:54.766][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-05-24 16:35:54.768][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-05-24 16:35:54.770][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-05-24 16:35:54.772][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-05-24 16:35:54.774][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-05-24 16:35:54.776][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-05-24 16:35:54.778][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-05-24 16:35:54.780][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-05-24 16:35:54.782][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-05-24 16:35:54.784][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-05-24 16:35:54.786][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-05-24 16:35:54.789][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-05-24 16:35:54.791][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-05-24 16:35:54.793][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-05-24 16:35:54.795][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-05-24 16:35:54.797][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-05-24 16:35:54.799][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-05-24 16:35:54.801][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-05-24 16:35:54.803][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-05-24 16:35:54.805][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-05-24 16:35:54.807][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-05-24 16:35:54.809][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-05-24 16:35:54.811][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-05-24 16:35:54.813][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-05-24 16:35:54.815][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-05-24 16:35:54.817][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-05-24 16:35:54.819][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-05-24 16:35:54.821][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-05-24 16:35:54.823][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-05-24 16:35:54.825][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-05-24 16:35:54.827][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-05-24 16:35:54.830][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-05-24 16:35:54.832][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-05-24 16:35:54.834][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-05-24 16:35:54.836][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-05-24 16:35:54.838][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-05-24 16:35:54.840][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-05-24 16:35:54.842][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-05-24 16:35:54.844][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-05-24 16:35:54.846][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-05-24 16:35:54.848][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-05-24 16:35:54.850][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-05-24 16:35:54.852][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-05-24 16:35:54.854][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-05-24 16:35:54.856][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-05-24 16:35:54.858][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-05-24 16:35:54.860][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-05-24 16:35:54.862][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-05-24 16:35:54.864][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-05-24 16:35:54.866][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-05-24 16:35:54.868][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-05-24 16:35:54.870][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-05-24 16:35:54.872][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-05-24 16:35:54.874][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-05-24 16:35:54.876][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-05-24 16:35:54.878][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-05-24 16:35:54.880][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-05-24 16:35:54.881][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.884][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.922][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[2025-05-24 16:35:54.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.940][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[2025-05-24 16:35:54.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:54.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:54.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:54.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:54.994][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[2025-05-24 16:35:54.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:54.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:54.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:54.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:55.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:55.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:55.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:55.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:55.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:55.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:55.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:55.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:55.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:55.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:55.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:55.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:55.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:55.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:55.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:55.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:55.021][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[2025-05-24 16:35:55.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:55.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:55.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:55.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:55.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:55.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:55.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:55.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-05-24 16:35:55.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:55.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:55.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:55.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:55.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:55.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-05-24 16:35:55.043][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-05-24 16:35:55.046][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-05-24 16:35:55.048][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:55.050][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-05-24 16:35:55.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:55.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-05-24 16:35:55.054][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:55.056][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-05-24 16:35:55.057][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:55.059][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-05-24 16:35:55.060][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-05-24 16:35:55.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-05-24 16:35:55.063][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:55.065][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-05-24 16:35:55.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-05-24 16:35:55.068][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-05-24 16:35:55.068][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-05-24 16:35:55.068][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-05-24 16:35:55.068][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-05-24 16:35:55.068][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-05-24 16:35:55.068][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-05-24 16:35:55.068][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-05-24 16:35:55.069][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-05-24 16:35:55.071][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:55.072][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-05-24 16:35:55.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:55.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:55.076][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-05-24 16:35:55.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-05-24 16:35:55.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-05-24 16:35:55.080][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-05-24 16:35:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-05-24 16:35:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-05-24 16:35:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-05-24 16:35:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-05-24 16:35:55.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-05-24 16:35:55.085][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-05-24 16:35:55.086][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-05-24 16:35:55.088][self$setPropertyValue]
biodb.DEBUG[2025-05-24 16:35:55.090][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-05-24 16:35:55.095][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-05-24 16:35:55.097][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-05-24 16:35:55.099][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-05-24 16:35:55.101][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-05-24 16:35:55.103][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-05-24 16:35:55.105][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-05-24 16:35:55.107][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-05-24 16:35:55.109][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-05-24 16:35:55.110][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-05-24 16:35:55.112][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-05-24 16:35:55.113][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-05-24 16:35:55.115][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-05-24 16:35:55.116][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-05-24 16:35:55.118][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-05-24 16:35:55.119][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-05-24 16:35:55.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-05-24 16:35:55.121][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-05-24 16:35:55.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-05-24 16:35:55.124][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-05-24 16:35:55.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
    user   system  elapsed 
1240.243  265.016 2002.591

'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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** 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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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
installing to /Users/biocbuild/bbs-3.21-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)