Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-01 23:55 -0500 (Sat, 01 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4768
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4503
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4526
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 11/32HostnameOS / ArchCHECK
biodbNci 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-01 09:55 -0500 (Sat, 01 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_20
git_last_commit: d666b49
git_last_commit_date: 2024-10-29 11:09:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows 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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2025-03-01 16:02:26 -0500 (Sat, 01 Mar 2025)
EndedAt: 2025-03-01 16:03:41 -0500 (Sat, 01 Mar 2025)
EllapsedTime: 74.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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Type 'contributors()' for more information and
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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 [2025-03-01 16:03:37.026][biodb::testContext]
biodb.INFO [2025-03-01 16:03:37.030][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:03:37.031][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-01 16:03:37.032][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:03:37.033][biodb::testContext]
biodb.INFO [2025-03-01 16:03:37.040][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:03:37.043][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:03:37.051][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:03:37.052][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:03:37.054][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:03:37.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.058][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:03:37.083][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:03:37.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.088][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:03:37.089][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:03:37.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.094][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:03:37.095][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:03:37.096][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:03:37.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.101][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:03:37.102][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:03:37.103][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:03:37.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.108][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:03:37.109][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:03:37.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.113][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:03:37.115][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:03:37.116][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:03:37.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.120][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:03:37.122][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:03:37.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.126][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:03:37.127][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:03:37.129][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:03:37.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.133][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:03:37.134][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:03:37.136][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:03:37.137][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:03:37.138][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:03:37.139][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:03:37.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.144][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:03:37.145][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:03:37.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.150][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:03:37.151][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:03:37.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.155][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:03:37.157][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:03:37.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.161][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:03:37.162][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:03:37.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.167][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:03:37.168][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:03:37.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.173][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:03:37.174][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:03:37.185][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:03:37.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.190][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:03:37.191][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:03:37.192][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:03:37.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.199][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:03:37.243][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.270][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:03:37.272][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.273][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:37.274][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.275][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.277][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.278][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.279][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:03:37.281][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:37.282][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.283][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:03:37.284][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:37.286][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.287][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.288][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:03:37.288][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:03:37.288][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:03:37.288][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:03:37.288][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:03:37.290][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:37.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.294][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:37.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.297][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.298][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.300][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:37.301][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:37.302][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.303][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.305][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:03:37.307][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.308][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:03:37.309][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.311][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:37.312][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.313][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.314][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.316][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.317][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:03:37.318][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:37.320][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.321][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:03:37.322][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:37.323][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.325][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.326][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:03:37.326][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:03:37.326][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:03:37.326][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:03:37.326][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:03:37.327][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:37.328][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.331][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:37.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.334][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.336][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.337][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:37.338][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:37.339][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.340][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.342][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:03:37.344][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.345][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:03:37.347][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.348][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:37.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.352][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.353][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.354][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:03:37.356][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:37.357][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.358][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:03:37.359][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:37.361][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.362][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.363][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.364][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:37.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.368][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:37.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.371][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.373][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.374][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:37.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:37.376][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.378][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.379][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:03:37.381][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.383][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:03:37.384][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.385][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:37.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.389][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.390][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.391][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:03:37.393][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:37.394][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.395][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:03:37.396][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:37.398][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.399][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.400][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.402][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:37.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:37.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.409][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.410][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.411][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:37.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:37.413][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.415][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.419][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:03:37.420][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.460][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[2025-03-01 16:03:37.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.518][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:03:37.523][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:03:37.525][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:03:37.526][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:03:37.528][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:03:37.530][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:03:37.531][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:03:37.533][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:03:37.535][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:03:37.536][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:03:37.538][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:03:37.540][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:03:37.541][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:03:37.543][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:03:37.545][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:03:37.546][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:03:37.548][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:03:37.550][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:03:37.551][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:03:37.553][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:03:37.555][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:03:37.556][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:03:37.558][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:03:37.560][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:03:37.561][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:03:37.563][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:03:37.565][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:03:37.566][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:03:37.568][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:03:37.570][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:03:37.571][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:03:37.573][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:03:37.575][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:03:37.576][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:03:37.578][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:03:37.580][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:03:37.581][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:03:37.583][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:03:37.585][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:03:37.586][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:03:37.588][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:03:37.590][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:03:37.591][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:03:37.593][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:03:37.595][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:03:37.596][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:03:37.598][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:03:37.600][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:03:37.601][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:03:37.603][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:03:37.605][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:03:37.606][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:03:37.608][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:03:37.610][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:03:37.611][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:03:37.613][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:03:37.615][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:03:37.616][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:03:37.618][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:03:37.620][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:03:37.622][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:03:37.623][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:03:37.625][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:03:37.627][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:03:37.628][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:03:37.630][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:03:37.632][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:03:37.633][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:03:37.635][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:03:37.637][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:03:37.638][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:03:37.640][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:03:37.642][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:03:37.643][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:03:37.645][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:03:37.647][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:03:37.648][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:03:37.650][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:03:37.652][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:03:37.653][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:03:37.655][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:03:37.657][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:03:37.658][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:03:37.666][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:03:37.668][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:03:37.671][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:03:37.672][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.674][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:37.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:37.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:37.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:37.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:37.816][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-01 16:03:37.828][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-01 16:03:37.831][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.832][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-01 16:03:37.833][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.835][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:37.836][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.837][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-01 16:03:37.838][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.839][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.841][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-01 16:03:37.842][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:37.843][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.844][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-01 16:03:37.846][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:37.847][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-01 16:03:37.847][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-01 16:03:37.847][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-01 16:03:37.847][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-01 16:03:37.847][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-01 16:03:37.847][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-01 16:03:37.847][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-01 16:03:37.848][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:37.850][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.851][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:03:37.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.854][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:37.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:37.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:37.858][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:37.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:03:37.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:03:37.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-01 16:03:37.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-01 16:03:37.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:37.861][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:37.863][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:37.864][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:37.872][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-01 16:03:37.896][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-01 16:03:37.897][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-01 16:03:37.901][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-01 16:03:37.906][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-01 16:03:37.910][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:03:37.912][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:03:37.913][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:03:37.915][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:03:37.917][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:03:37.918][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-01 16:03:37.958][biodb::testThat]
biodb.INFO [2025-03-01 16:03:37.960][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:03:37.961][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:37.962][biodb::testThat]
biodb.TRACE[2025-03-01 16:03:37.966][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-03-01 16:03:37.968][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:03:37.972][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:03:37.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:03:37.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:37.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:37.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:38.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:38.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:38.003][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.TRACE[2025-03-01 16:03:38.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.134][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.139][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.149][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:03:38.236][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-03-01 16:03:38.239][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.244][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.249][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:38.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:38.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.254][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:38.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:38.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.297][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.339][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.344][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.383][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.385][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.417][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.418][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.421][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.422][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.451][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.452][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.484][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.486][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.518][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.519][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.542][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.543][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.561][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.571][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.573][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.581][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.582][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.608][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-03-01 16:03:38.657][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:03:38.659][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:03:38.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:03:38.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:38.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:38.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:38.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:38.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:38.672][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.TRACE[2025-03-01 16:03:38.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.726][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:38.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:38.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.732][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:38.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.737][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:38.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:38.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:38.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:38.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:38.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:38.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:38.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:38.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:38.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:38.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:38.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:38.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:38.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:38.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:38.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:38.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:38.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:38.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:38.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:38.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.815][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.820][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.829][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:03:38.864][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-03-01 16:03:38.892][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.901][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:38.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.905][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:38.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:38.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:38.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:38.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.926][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:38.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:38.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.968][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.972][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.019][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.020][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.022][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.038][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.043][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.048][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.053][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.054][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.057][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.058][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.092][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.093][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.095][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.121][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.126][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.127][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.131][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.160][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.162][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.180][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.195][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.231][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.251][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.253][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.261][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.263][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.276][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.277][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.286][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.288][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.296][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.298][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.306][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.308][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.310][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.316][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.318][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.320][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:03:39.330][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.332][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:03:39.333][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.334][biodb::testThat]
biodb.DEBUG[2025-03-01 16:03:39.337][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-03-01 16:03:39.344][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-03-01 16:03:39.349][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-03-01 16:03:39.351][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-03-01 16:03:39.353][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-03-01 16:03:39.355][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-01 16:03:39.357][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[2025-03-01 16:03:39.359][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:03:39.360][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-03-01 16:03:39.362][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:03:39.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:03:39.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:39.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:39.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:39.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:39.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:39.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:03:39.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.436][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.442][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.447][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.457][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:03:39.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:03:39.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:39.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:39.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:39.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:39.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:39.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:03:39.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.521][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.527][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:03:39.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:03:39.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:03:39.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:03:39.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:03:39.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:03:39.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:03:39.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:03:39.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:03:39.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.611][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.616][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.626][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:03:39.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:03:39.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:03:39.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:03:39.683][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-03-01 16:03:39.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:03:39.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:03:39.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:03:39.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:03:39.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:03:39.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:03:39.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:03:39.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:03:39.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:03:39.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:03:39.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:03:39.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:03:39.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:03:39.729][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.731][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:03:39.732][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.733][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.740][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.742][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:03:39.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.744][biodb::testThat]
biodb.WARN [2025-03-01 16:03:39.769][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-01 16:03:39.794][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-01 16:03:39.805][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.807][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:03:39.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.809][biodb::testThat]
biodb.TRACE[2025-03-01 16:03:39.844][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.849][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:39.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:39.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:39.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:39.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.912][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:03:39.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.917][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:39.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:03:39.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:03:39.922][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:39.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:03:39.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:03:39.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:03:39.953][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.955][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:03:39.956][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.957][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.966][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.967][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:03:39.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.970][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.979][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.980][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:03:39.981][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.982][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.990][biodb::testThat]
biodb.INFO [2025-03-01 16:03:39.991][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:03:39.992][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:03:39.993][biodb::testThat]
biodb.INFO [2025-03-01 16:03:40.001][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:03:40.002][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-01 16:03:40.004][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-01 16:03:40.005][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:03:40.006][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.008][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.010][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-01 16:03:40.027][biodb::testContext]
biodb.INFO [2025-03-01 16:03:40.028][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:03:40.029][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-01 16:03:40.031][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:03:40.032][biodb::testContext]
biodb.INFO [2025-03-01 16:03:40.034][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:03:40.036][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:03:40.040][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:03:40.041][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:03:40.042][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:03:40.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.047][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:03:40.048][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:03:40.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.052][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:03:40.054][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:03:40.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.058][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:03:40.059][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:03:40.061][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:03:40.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.065][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:03:40.066][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:03:40.068][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:03:40.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.072][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:03:40.073][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:03:40.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.078][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:03:40.079][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:03:40.080][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:03:40.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.085][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:03:40.086][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:03:40.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.090][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:03:40.092][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:03:40.093][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:03:40.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.097][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:03:40.099][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:03:40.100][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:03:40.101][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:03:40.102][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:03:40.104][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:03:40.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.108][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:03:40.110][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:03:40.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.114][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:03:40.115][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:03:40.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.120][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:03:40.121][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:03:40.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.126][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:03:40.127][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:03:40.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.132][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:03:40.133][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:03:40.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.138][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:03:40.139][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:03:40.149][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:03:40.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.154][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:03:40.155][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:03:40.156][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:03:40.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.161][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:03:40.163][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.164][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:03:40.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:40.168][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.169][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.172][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.173][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:03:40.174][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:40.176][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.177][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:03:40.178][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:40.179][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.180][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.182][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:03:40.182][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:03:40.182][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:03:40.182][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:03:40.182][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:03:40.183][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:40.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:40.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.190][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.191][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:40.193][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:40.195][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.196][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.201][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:03:40.203][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.205][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:03:40.206][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.207][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:40.208][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.209][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.211][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.212][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.213][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:03:40.214][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:40.216][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.217][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:03:40.218][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:40.219][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.220][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.222][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:03:40.222][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:03:40.222][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:03:40.222][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:03:40.222][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:03:40.223][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:40.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.226][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:40.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.229][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.230][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.231][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.232][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:40.234][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:40.235][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.236][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.238][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:03:40.240][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.241][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:03:40.242][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.244][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:40.245][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.247][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.248][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.250][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:03:40.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:40.252][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.254][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:03:40.255][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:40.256][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.257][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.258][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.260][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:40.261][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.263][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:40.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.268][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:40.270][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:40.271][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.273][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.274][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:03:40.276][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.277][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:03:40.279][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.280][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:40.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.282][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.284][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.285][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.286][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:03:40.287][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:40.288][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.290][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:03:40.291][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:40.292][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.293][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.295][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.296][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:03:40.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.299][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:40.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.303][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.304][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.305][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:40.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:40.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.309][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.310][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:03:40.311][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.410][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:03:40.412][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:03:40.414][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:03:40.415][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:03:40.417][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:03:40.419][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:03:40.420][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:03:40.422][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:03:40.424][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:03:40.426][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:03:40.427][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:03:40.429][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:03:40.431][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:03:40.432][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:03:40.434][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:03:40.436][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:03:40.437][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:03:40.439][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:03:40.441][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:03:40.442][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:03:40.444][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:03:40.446][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:03:40.448][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:03:40.449][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:03:40.451][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:03:40.453][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:03:40.454][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:03:40.456][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:03:40.457][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:03:40.459][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:03:40.461][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:03:40.462][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:03:40.464][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:03:40.466][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:03:40.467][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:03:40.469][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:03:40.471][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:03:40.472][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:03:40.474][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:03:40.476][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:03:40.477][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:03:40.479][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:03:40.481][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:03:40.483][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:03:40.484][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:03:40.486][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:03:40.488][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:03:40.489][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:03:40.491][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:03:40.493][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:03:40.495][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:03:40.496][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:03:40.498][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:03:40.500][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:03:40.501][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:03:40.503][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:03:40.505][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:03:40.507][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:03:40.508][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:03:40.510][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:03:40.512][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:03:40.513][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:03:40.515][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:03:40.517][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:03:40.518][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:03:40.520][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:03:40.522][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:03:40.524][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:03:40.530][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:03:40.531][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:03:40.533][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:03:40.535][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:03:40.537][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:03:40.538][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:03:40.540][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:03:40.542][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:03:40.543][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:03:40.545][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:03:40.547][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:03:40.548][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:03:40.550][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:03:40.552][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:03:40.553][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:03:40.555][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:03:40.557][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:03:40.558][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:03:40.559][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.561][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.639][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[2025-03-01 16:03:40.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:03:40.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:03:40.699][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-01 16:03:40.701][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-01 16:03:40.704][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.705][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-01 16:03:40.706][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.707][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:03:40.709][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.710][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-01 16:03:40.711][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.712][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.713][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-01 16:03:40.715][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:03:40.716][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.717][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-01 16:03:40.718][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:03:40.720][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-01 16:03:40.720][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-01 16:03:40.720][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-01 16:03:40.720][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-01 16:03:40.720][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-01 16:03:40.720][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-01 16:03:40.720][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-01 16:03:40.721][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:03:40.723][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.724][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:03:40.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.728][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:03:40.729][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:03:40.730][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:03:40.731][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:03:40.732][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:03:40.732][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:03:40.732][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-01 16:03:40.732][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-01 16:03:40.734][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:03:40.735][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:03:40.736][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:03:40.737][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:03:40.739][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-01 16:03:40.743][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-01 16:03:40.744][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-01 16:03:40.745][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-01 16:03:40.747][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-01 16:03:40.749][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:03:40.750][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:03:40.751][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:03:40.753][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:03:40.755][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:03:40.756][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-01 16:03:40.757][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:03:40.758][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-01 16:03:40.760][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-01 16:03:40.761][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:03:40.762][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:03:40.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:03:40.764][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:03:40.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:03:40.766][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:03:40.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  5.699   0.328   6.029

'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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-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)