Back to Long Tests report for BioC 3.18

This page was generated on 2024-04-13 23:55:02 -0400 (Sat, 13 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4675
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4413
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4436
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 13/30HostnameOS / ArchCHECK
biodbNci 1.6.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-04-13 09:55:01 -0400 (Sat, 13 Apr 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_18
git_last_commit: f5993f4
git_last_commit_date: 2023-10-24 11:40:20 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on nebbiolo2


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

raw results

Summary

Package: biodbNci
Version: 1.6.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.6.0.tar.gz
StartedAt: 2024-04-13 16:07:17 -0400 (Sat, 13 Apr 2024)
EndedAt: 2024-04-13 16:08:21 -0400 (Sat, 13 Apr 2024)
EllapsedTime: 64.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-04-13 16:08:18.094][biodb::testContext]
biodb.INFO [2024-04-13 16:08:18.096][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:08:18.097][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-04-13 16:08:18.098][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:08:18.099][biodb::testContext]
biodb.INFO [2024-04-13 16:08:18.106][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:08:18.108][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:08:18.116][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:08:18.117][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:08:18.118][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:08:18.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.122][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:08:18.141][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:08:18.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.145][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:08:18.146][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:08:18.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.149][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:08:18.150][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:08:18.152][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:08:18.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.154][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[2024-04-13 16:08:18.155][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:08:18.156][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:08:18.157][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:08:18.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.161][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:08:18.162][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:08:18.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.175][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:08:18.176][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:08:18.177][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:08:18.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:08:18.181][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:08:18.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.184][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:08:18.185][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:08:18.186][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:08:18.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.189][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:08:18.190][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:08:18.191][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:08:18.192][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:08:18.193][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:08:18.194][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:08:18.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.197][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:08:18.198][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:08:18.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.201][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:08:18.202][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:08:18.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.205][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:08:18.206][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:08:18.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.209][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:08:18.210][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:08:18.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.214][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:08:18.215][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:08:18.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.218][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:08:18.219][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:08:18.223][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:08:18.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.226][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:08:18.227][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:08:18.228][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:08:18.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.234][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:08:18.264][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.278][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:08:18.279][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.280][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:18.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.282][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.283][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.284][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.284][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:08:18.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:18.286][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.287][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:08:18.288][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:18.289][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.290][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.291][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:08:18.291][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:08:18.291][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:08:18.291][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:08:18.291][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:08:18.292][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:18.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.294][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:18.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.297][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.298][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.299][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:18.299][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:18.300][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.301][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.302][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:08:18.304][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.305][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:08:18.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.306][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:18.307][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.309][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.310][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.311][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:08:18.312][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:18.313][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.314][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:08:18.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:18.315][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.316][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.317][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:08:18.317][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:08:18.317][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:08:18.317][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:08:18.317][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:08:18.318][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:18.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:18.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.324][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.325][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:18.326][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:18.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.327][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.329][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:08:18.330][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.331][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:08:18.332][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.333][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:18.334][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.335][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.335][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.337][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:08:18.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:18.339][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.340][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:08:18.341][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:18.342][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.343][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.344][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.344][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:18.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.347][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:18.348][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.349][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.350][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.351][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:18.352][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:18.353][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.354][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.359][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:08:18.361][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.362][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:08:18.363][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.363][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:18.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.368][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:08:18.369][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:18.370][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.371][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:08:18.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:18.372][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.373][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.374][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:18.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.377][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:18.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.381][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:18.382][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:18.383][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.384][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.388][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:08:18.389][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.458][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:08:18.463][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:08:18.464][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:08:18.466][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:08:18.467][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:08:18.468][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:08:18.469][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:08:18.471][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:08:18.472][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:08:18.473][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:08:18.474][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:08:18.476][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:08:18.477][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:08:18.482][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:08:18.484][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:08:18.485][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:08:18.487][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:08:18.488][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:08:18.490][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:08:18.491][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:08:18.493][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:08:18.494][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:08:18.495][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:08:18.497][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:08:18.498][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:08:18.500][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:08:18.501][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:08:18.502][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:08:18.504][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:08:18.505][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:08:18.507][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:08:18.508][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:08:18.509][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:08:18.511][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:08:18.512][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:08:18.513][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:08:18.515][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:08:18.516][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:08:18.518][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:08:18.519][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:08:18.520][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:08:18.522][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:08:18.523][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:08:18.525][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:08:18.526][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:08:18.527][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:08:18.529][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:08:18.530][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:08:18.532][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:08:18.533][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:08:18.534][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:08:18.536][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:08:18.537][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:08:18.538][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:08:18.540][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:08:18.541][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:08:18.543][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:08:18.544][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:08:18.545][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:08:18.547][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:08:18.548][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:08:18.550][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:08:18.565][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:08:18.566][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:08:18.568][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:08:18.569][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:08:18.570][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:08:18.572][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:08:18.573][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:08:18.574][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:08:18.575][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:08:18.577][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:08:18.578][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:08:18.580][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:08:18.581][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:08:18.582][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:08:18.584][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:08:18.585][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:08:18.586][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:08:18.588][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:08:18.589][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:08:18.591][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:08:18.592][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:08:18.598][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:08:18.600][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:08:18.603][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:08:18.604][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.606][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.647][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[2024-04-13 16:08:18.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.677][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[2024-04-13 16:08:18.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:18.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:18.713][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-04-13 16:08:18.721][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-04-13 16:08:18.723][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.724][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-04-13 16:08:18.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:18.727][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.728][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-04-13 16:08:18.728][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.729][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.730][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-04-13 16:08:18.731][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:18.732][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.733][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-04-13 16:08:18.734][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:18.735][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-04-13 16:08:18.735][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-04-13 16:08:18.735][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-04-13 16:08:18.735][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-04-13 16:08:18.735][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-04-13 16:08:18.735][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-04-13 16:08:18.735][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-04-13 16:08:18.736][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:18.737][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.738][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:08:18.739][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:18.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:18.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:18.743][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:18.744][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-04-13 16:08:18.744][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-04-13 16:08:18.744][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-04-13 16:08:18.744][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-04-13 16:08:18.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:18.745][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:18.746][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:18.751][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:18.756][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-04-13 16:08:18.779][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-04-13 16:08:18.780][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-04-13 16:08:18.784][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-04-13 16:08:18.788][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-04-13 16:08:18.792][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:08:18.793][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:08:18.794][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-04-13 16:08:18.795][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-04-13 16:08:18.796][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-04-13 16:08:18.797][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-04-13 16:08:18.806][biodb::testThat]
biodb.INFO [2024-04-13 16:08:18.807][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-13 16:08:18.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:18.809][biodb::testThat]
biodb.TRACE[2024-04-13 16:08:18.812][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-04-13 16:08:18.814][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:08:18.817][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-04-13 16:08:18.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:08:18.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:18.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:18.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:18.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:18.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:18.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:08:18.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:18.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:18.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:18.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:18.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:18.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:18.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:18.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:18.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:18.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:18.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:18.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:18.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:18.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:18.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.931][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:18.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:18.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.934][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:18.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:18.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.941][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:18.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:18.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:18.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:18.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:18.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:18.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:08:19.004][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-04-13 16:08:19.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:19.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:19.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.016][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:19.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:19.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.047][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.077][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.080][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.084][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.135][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.135][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.137][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.148][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.152][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.159][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.160][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.162][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.163][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.183][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.184][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.186][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.207][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.208][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.210][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.232][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.233][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.234][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.245][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.246][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.248][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.251][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.252][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.254][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.258][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.259][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.261][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.267][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.271][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.272][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.273][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.292][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-04-13 16:08:19.323][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:08:19.324][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-04-13 16:08:19.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:08:19.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:19.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:19.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:19.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:19.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:19.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:08:19.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.364][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.368][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.372][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.376][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.436][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.440][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.448][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:08:19.476][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-04-13 16:08:19.496][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.500][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:19.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.504][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:19.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:19.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.508][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:19.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:19.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.520][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.552][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.556][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.560][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.595][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.596][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.598][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.610][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.614][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.617][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.621][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.622][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.624][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.625][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.647][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.648][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.650][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.661][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.665][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.669][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.673][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.676][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.699][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.700][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.701][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.724][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.725][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.732][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.755][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.757][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.769][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.772][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.775][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.776][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.778][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.782][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.783][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.785][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.789][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.790][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.792][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.796][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.797][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.799][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.802][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.803][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.805][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.809][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.812][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:08:19.819][biodb::testThat]
biodb.INFO [2024-04-13 16:08:19.819][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-13 16:08:19.820][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:19.821][biodb::testThat]
biodb.DEBUG[2024-04-13 16:08:19.823][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-04-13 16:08:19.831][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-04-13 16:08:19.835][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-04-13 16:08:19.837][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-04-13 16:08:19.839][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-04-13 16:08:19.840][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-04-13 16:08:19.842][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-04-13 16:08:19.843][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-04-13 16:08:19.844][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-04-13 16:08:19.845][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-04-13 16:08:19.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:08:19.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:19.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:19.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:19.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:19.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:19.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:08:19.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:19.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:19.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:19.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.908][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.912][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.919][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:19.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:08:19.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:08:19.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:19.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:19.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:19.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:19.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:19.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:08:19.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:19.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:19.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.960][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.964][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:08:19.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.968][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.972][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:08:19.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:08:19.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-13 16:08:19.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:19.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:19.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:19.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:19.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:20.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:20.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:20.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:20.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:08:20.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:08:20.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:20.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:20.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:08:20.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:08:20.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:20.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:20.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:08:20.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:08:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.028][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:20.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.039][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:20.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-04-13 16:08:20.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:08:20.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:08:20.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:08:20.081][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-04-13 16:08:20.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:08:20.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:08:20.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:08:20.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:08:20.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:08:20.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:08:20.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:08:20.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:08:20.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:08:20.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:08:20.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:08:20.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:08:20.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:08:20.114][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.115][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-13 16:08:20.116][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:20.117][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.122][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.123][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-13 16:08:20.124][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:20.124][biodb::testThat]
biodb.WARN [2024-04-13 16:08:20.144][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-04-13 16:08:20.162][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-04-13 16:08:20.170][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.171][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-13 16:08:20.172][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:20.173][biodb::testThat]
biodb.TRACE[2024-04-13 16:08:20.193][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.202][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.206][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:20.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:20.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:20.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:20.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.242][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.246][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:08:20.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.250][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:20.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:08:20.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:08:20.254][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:20.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:08:20.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:08:20.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:08:20.262][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.263][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-13 16:08:20.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:20.264][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.271][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.272][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-13 16:08:20.273][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:20.273][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.280][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.281][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-13 16:08:20.282][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:20.282][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.288][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.289][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-13 16:08:20.290][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:08:20.290][biodb::testThat]
biodb.INFO [2024-04-13 16:08:20.296][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:08:20.297][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-04-13 16:08:20.298][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-04-13 16:08:20.299][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:08:20.299][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.301][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.303][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-13 16:08:20.312][biodb::testContext]
biodb.INFO [2024-04-13 16:08:20.313][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:08:20.314][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-04-13 16:08:20.315][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:08:20.316][biodb::testContext]
biodb.INFO [2024-04-13 16:08:20.318][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:08:20.320][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:08:20.323][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:08:20.324][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:08:20.325][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:08:20.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.329][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:08:20.330][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:08:20.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.333][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:08:20.334][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:08:20.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.342][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:08:20.343][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:08:20.344][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:08:20.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.347][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:08:20.348][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:08:20.349][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:08:20.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.353][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:08:20.354][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:08:20.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.356][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[2024-04-13 16:08:20.357][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:08:20.358][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:08:20.359][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:08:20.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.362][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:08:20.363][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:08:20.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.367][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:08:20.368][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:08:20.369][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:08:20.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.372][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:08:20.373][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:08:20.374][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:08:20.375][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:08:20.376][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:08:20.377][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:08:20.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.381][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:08:20.382][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:08:20.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.385][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:08:20.386][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:08:20.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.390][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:08:20.391][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:08:20.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.394][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:08:20.395][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:08:20.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.399][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:08:20.400][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:08:20.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.403][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:08:20.404][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:08:20.407][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:08:20.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.411][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:08:20.412][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:08:20.413][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:08:20.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.417][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:08:20.418][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.419][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:08:20.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:20.422][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.423][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.425][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.426][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:08:20.427][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:20.428][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.429][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:08:20.430][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:20.431][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.432][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.433][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:08:20.433][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:08:20.433][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:08:20.433][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:08:20.433][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:08:20.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:20.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:20.437][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.439][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.440][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.441][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:20.442][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:20.443][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.444][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.445][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:08:20.447][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.448][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:08:20.449][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:20.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.452][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.453][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.454][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:08:20.455][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:20.456][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.457][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:08:20.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:20.459][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.460][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.461][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:08:20.461][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:08:20.461][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:08:20.461][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:08:20.461][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:08:20.462][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:20.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.465][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:20.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.467][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.468][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.469][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:20.470][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:20.471][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.472][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.473][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:08:20.475][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.476][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:08:20.477][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.478][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:20.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.480][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.480][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.481][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.482][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:08:20.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:20.484][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.485][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:08:20.486][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:20.487][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.488][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.489][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.490][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:20.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.497][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:20.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.500][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.500][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:20.502][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:20.503][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.504][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.505][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:08:20.507][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.508][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:08:20.509][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.510][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:20.510][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.511][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.512][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.513][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.514][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:08:20.515][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:20.516][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.517][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:08:20.518][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:20.519][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.520][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.521][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.522][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:08:20.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.525][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:20.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.527][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.528][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.529][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:20.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:20.531][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.532][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.533][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:08:20.534][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.608][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:08:20.609][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:08:20.610][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:08:20.612][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:08:20.613][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:08:20.614][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:08:20.616][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:08:20.617][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:08:20.618][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:08:20.620][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:08:20.621][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:08:20.622][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:08:20.624][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:08:20.625][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:08:20.626][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:08:20.628][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:08:20.629][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:08:20.630][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:08:20.632][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:08:20.633][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:08:20.634][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:08:20.636][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:08:20.637][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:08:20.642][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:08:20.644][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:08:20.645][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:08:20.646][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:08:20.647][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:08:20.649][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:08:20.650][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:08:20.651][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:08:20.653][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:08:20.654][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:08:20.655][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:08:20.657][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:08:20.658][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:08:20.659][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:08:20.660][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:08:20.662][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:08:20.663][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:08:20.664][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:08:20.666][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:08:20.667][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:08:20.668][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:08:20.670][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:08:20.671][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:08:20.672][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:08:20.674][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:08:20.675][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:08:20.676][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:08:20.678][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:08:20.679][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:08:20.680][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:08:20.682][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:08:20.683][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:08:20.684][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:08:20.686][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:08:20.687][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:08:20.688][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:08:20.690][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:08:20.691][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:08:20.692][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:08:20.694][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:08:20.695][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:08:20.696][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:08:20.697][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:08:20.699][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:08:20.700][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:08:20.701][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:08:20.703][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:08:20.704][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:08:20.705][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:08:20.707][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:08:20.708][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:08:20.709][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:08:20.711][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:08:20.712][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:08:20.713][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:08:20.714][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:08:20.716][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:08:20.717][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:08:20.718][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:08:20.720][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:08:20.721][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:08:20.723][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:08:20.724][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:08:20.724][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.726][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.745][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[2024-04-13 16:08:20.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.768][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[2024-04-13 16:08:20.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.813][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[2024-04-13 16:08:20.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:08:20.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:08:20.833][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-04-13 16:08:20.834][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-04-13 16:08:20.836][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.837][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-04-13 16:08:20.838][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.839][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:08:20.840][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.841][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-04-13 16:08:20.842][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.843][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.844][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-04-13 16:08:20.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:08:20.846][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.846][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-04-13 16:08:20.847][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:08:20.848][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-04-13 16:08:20.848][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-04-13 16:08:20.848][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-04-13 16:08:20.848][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-04-13 16:08:20.848][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-04-13 16:08:20.848][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-04-13 16:08:20.848][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-04-13 16:08:20.849][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:08:20.850][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.851][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:08:20.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.854][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:08:20.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:08:20.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:08:20.857][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:08:20.858][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-04-13 16:08:20.858][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-04-13 16:08:20.858][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-04-13 16:08:20.858][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-04-13 16:08:20.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:08:20.859][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:08:20.860][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:08:20.861][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:08:20.863][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-04-13 16:08:20.865][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-04-13 16:08:20.866][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-04-13 16:08:20.868][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-04-13 16:08:20.869][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-04-13 16:08:20.870][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:08:20.871][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:08:20.872][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-04-13 16:08:20.874][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-04-13 16:08:20.875][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-04-13 16:08:20.876][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-04-13 16:08:20.877][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:08:20.878][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-04-13 16:08:20.879][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-04-13 16:08:20.880][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:08:20.880][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:08:20.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:08:20.882][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:08:20.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:08:20.884][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:08:20.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  4.220   0.232   4.441

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)