Back to Long Tests report for BioC 3.20

This page was generated on 2025-01-25 23:55 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 11/32HostnameOS / ArchCHECK
biodbNci 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-01-25 09:55 -0500 (Sat, 25 Jan 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_20
git_last_commit: d666b49
git_last_commit_date: 2024-10-29 11:09:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.5 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: 1.10.0
Command: /home/biocbuild/bbs-3.20-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_1.10.0.tar.gz
StartedAt: 2025-01-25 16:04:33 -0500 (Sat, 25 Jan 2025)
EndedAt: 2025-01-25 16:05:32 -0500 (Sat, 25 Jan 2025)
EllapsedTime: 59.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


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

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-01-25 16:05:30.001][biodb::testContext]
biodb.INFO [2025-01-25 16:05:30.002][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:05:30.003][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-25 16:05:30.004][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:05:30.005][biodb::testContext]
biodb.INFO [2025-01-25 16:05:30.010][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:05:30.012][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-25 16:05:30.018][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:30.019][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-25 16:05:30.020][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-25 16:05:30.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.023][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-25 16:05:30.040][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-25 16:05:30.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.043][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-25 16:05:30.044][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-25 16:05:30.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.047][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-25 16:05:30.048][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-25 16:05:30.049][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-25 16:05:30.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.052][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-25 16:05:30.053][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-25 16:05:30.054][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-25 16:05:30.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.057][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-25 16:05:30.058][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-25 16:05:30.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.061][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-25 16:05:30.062][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-25 16:05:30.063][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-25 16:05:30.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.066][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-25 16:05:30.067][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-25 16:05:30.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.070][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-25 16:05:30.071][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-25 16:05:30.072][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-25 16:05:30.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.075][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:05:30.076][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-25 16:05:30.077][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-25 16:05:30.078][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-25 16:05:30.079][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-25 16:05:30.079][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-25 16:05:30.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.083][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-25 16:05:30.084][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-25 16:05:30.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.087][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-25 16:05:30.088][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-25 16:05:30.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.091][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-25 16:05:30.092][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-25 16:05:30.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.095][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-25 16:05:30.096][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:05:30.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.099][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-25 16:05:30.100][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-25 16:05:30.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.103][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:05:30.104][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-25 16:05:30.108][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-25 16:05:30.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.112][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-25 16:05:30.113][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-25 16:05:30.113][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-25 16:05:30.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.119][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-25 16:05:30.148][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.167][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-25 16:05:30.168][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.169][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:30.170][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.171][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.172][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.173][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:05:30.174][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:30.175][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.176][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-25 16:05:30.177][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:30.178][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.179][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.180][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:05:30.180][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:05:30.180][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:05:30.180][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:05:30.180][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:05:30.180][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:30.181][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.182][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.183][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:30.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.185][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.186][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.187][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:30.188][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:30.189][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.190][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.191][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-25 16:05:30.192][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.193][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:05:30.194][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.195][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:30.196][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.198][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.198][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.199][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:05:30.200][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:30.201][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.202][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-25 16:05:30.203][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:30.204][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.205][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.206][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:05:30.206][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:05:30.206][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:05:30.206][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:05:30.206][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:05:30.206][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:30.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:30.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.211][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.212][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.213][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:30.214][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:30.215][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.216][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.217][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-25 16:05:30.218][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.219][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-25 16:05:30.220][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.221][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:30.222][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.223][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.223][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.224][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.225][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:05:30.226][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:30.227][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.228][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-25 16:05:30.229][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:30.230][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.230][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.231][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.232][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:30.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.235][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:30.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.237][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.238][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.239][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:30.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:30.240][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.241][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.242][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-25 16:05:30.244][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.245][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:05:30.246][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:30.247][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.248][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.249][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.250][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.251][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:05:30.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:30.253][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.254][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-25 16:05:30.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:30.255][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.257][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:30.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.260][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:30.261][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.264][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.265][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:30.265][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:30.266][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.267][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.270][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:30.271][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.343][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-25 16:05:30.347][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-25 16:05:30.348][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-25 16:05:30.349][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-25 16:05:30.351][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-25 16:05:30.352][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:05:30.353][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-25 16:05:30.354][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-25 16:05:30.356][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-25 16:05:30.357][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:05:30.358][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:05:30.359][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-25 16:05:30.361][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-25 16:05:30.362][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-25 16:05:30.363][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-25 16:05:30.364][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:05:30.366][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-25 16:05:30.367][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-25 16:05:30.368][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-25 16:05:30.369][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-25 16:05:30.371][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-25 16:05:30.372][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-25 16:05:30.373][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-25 16:05:30.374][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-25 16:05:30.376][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-25 16:05:30.377][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-25 16:05:30.378][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-25 16:05:30.379][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-25 16:05:30.381][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-25 16:05:30.382][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-25 16:05:30.383][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-25 16:05:30.384][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-25 16:05:30.386][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-25 16:05:30.387][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-25 16:05:30.388][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-25 16:05:30.389][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-25 16:05:30.390][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-25 16:05:30.392][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-25 16:05:30.393][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-25 16:05:30.394][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-25 16:05:30.395][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-25 16:05:30.397][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-25 16:05:30.398][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-25 16:05:30.399][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-25 16:05:30.400][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-25 16:05:30.402][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-25 16:05:30.403][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-25 16:05:30.404][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-25 16:05:30.405][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-25 16:05:30.407][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-25 16:05:30.408][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-25 16:05:30.409][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-25 16:05:30.410][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-25 16:05:30.411][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-25 16:05:30.413][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-25 16:05:30.414][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-25 16:05:30.415][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-25 16:05:30.416][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-25 16:05:30.418][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-25 16:05:30.419][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-25 16:05:30.420][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-25 16:05:30.421][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-25 16:05:30.423][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-25 16:05:30.424][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-25 16:05:30.425][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-25 16:05:30.426][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-25 16:05:30.428][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-25 16:05:30.429][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-25 16:05:30.430][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-25 16:05:30.431][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-25 16:05:30.432][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-25 16:05:30.434][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-25 16:05:30.435][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-25 16:05:30.436][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-25 16:05:30.437][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-25 16:05:30.439][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-25 16:05:30.440][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-25 16:05:30.441][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-25 16:05:30.442][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-25 16:05:30.444][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-25 16:05:30.445][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-25 16:05:30.446][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-25 16:05:30.447][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-25 16:05:30.453][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-25 16:05:30.454][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:05:30.457][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:30.457][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.459][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.556][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[2025-01-25 16:05:30.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:30.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:30.576][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-01-25 16:05:30.587][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-01-25 16:05:30.589][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.590][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-01-25 16:05:30.591][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.592][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:30.593][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.594][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-01-25 16:05:30.595][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.597][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-01-25 16:05:30.598][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:30.599][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.600][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-01-25 16:05:30.601][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:30.602][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-01-25 16:05:30.602][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-01-25 16:05:30.602][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-01-25 16:05:30.602][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-01-25 16:05:30.602][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-01-25 16:05:30.602][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-01-25 16:05:30.602][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-01-25 16:05:30.603][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:30.604][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.605][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-25 16:05:30.606][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.608][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:30.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:30.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:30.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:30.612][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:05:30.612][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:05:30.612][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-01-25 16:05:30.612][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-01-25 16:05:30.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:30.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:30.614][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:30.615][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:30.621][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-01-25 16:05:30.647][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-01-25 16:05:30.648][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-01-25 16:05:30.652][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-01-25 16:05:30.656][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-01-25 16:05:30.660][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:05:30.661][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:05:30.662][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:05:30.664][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:05:30.665][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:05:30.666][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-01-25 16:05:30.674][biodb::testThat]
biodb.INFO [2025-01-25 16:05:30.675][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-25 16:05:30.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:30.677][biodb::testThat]
biodb.TRACE[2025-01-25 16:05:30.711][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-01-25 16:05:30.713][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:05:30.716][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-01-25 16:05:30.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:05:30.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:30.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:30.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:30.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:30.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:30.739][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.TRACE[2025-01-25 16:05:30.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.773][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:30.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:30.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:30.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:30.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:30.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:30.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:30.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:30.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:30.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:30.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:30.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:30.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:30.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:30.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:30.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:30.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.825][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.829][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.836][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:05:30.895][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-01-25 16:05:30.897][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:30.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:30.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:30.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:30.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:30.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:30.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.907][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:30.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:30.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.937][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.966][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.969][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.995][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:30.996][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:30.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:30.998][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:30.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.019][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.020][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.022][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.043][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.044][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.045][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.066][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.067][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.069][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.090][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.091][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.092][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.103][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.105][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.109][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.113][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.115][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.118][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.119][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.121][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.125][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.127][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.131][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.132][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.133][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.148][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-01-25 16:05:31.179][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:05:31.180][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-01-25 16:05:31.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:05:31.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:31.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:31.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:31.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:31.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:31.189][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.TRACE[2025-01-25 16:05:31.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.220][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.227][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.286][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.289][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.296][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:05:31.321][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-01-25 16:05:31.339][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.342][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.346][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:31.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:31.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.352][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:31.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:31.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.363][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.392][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.399][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.426][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.427][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.429][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.439][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.442][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.446][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.449][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.450][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.452][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.453][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.473][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.474][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.479][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.489][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.499][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.500][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.502][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.523][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.526][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.547][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.547][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.549][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.573][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.583][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.584][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.586][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.589][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.590][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.592][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.595][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.596][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.598][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.605][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.606][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.608][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.611][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.612][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.614][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.618][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.619][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.620][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.624][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.625][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.627][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:05:31.632][biodb::testThat]
biodb.INFO [2025-01-25 16:05:31.633][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-25 16:05:31.634][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:31.635][biodb::testThat]
biodb.DEBUG[2025-01-25 16:05:31.637][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-01-25 16:05:31.643][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-01-25 16:05:31.647][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-01-25 16:05:31.648][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-01-25 16:05:31.650][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-01-25 16:05:31.651][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-01-25 16:05:31.653][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[2025-01-25 16:05:31.654][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-01-25 16:05:31.655][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-01-25 16:05:31.656][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-01-25 16:05:31.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:05:31.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:31.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:31.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:31.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:31.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:31.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-25 16:05:31.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.682][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.709][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.712][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.719][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:05:31.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:05:31.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:31.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:31.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:31.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:31.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:31.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-25 16:05:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.761][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.764][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:31.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.768][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:31.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:31.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:05:31.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:31.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:31.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:31.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:31.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:31.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.823][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.827][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.834][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:05:31.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:31.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:31.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:05:31.872][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-01-25 16:05:31.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-25 16:05:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-25 16:05:31.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:05:31.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:05:31.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:05:31.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:05:31.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-25 16:05:31.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-25 16:05:31.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:05:31.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:05:31.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:05:31.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:05:31.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:05:31.902][biodb::testThat]
biodb.INFO [2025-01-25 16:05:31.903][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-25 16:05:31.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:31.905][biodb::testThat]
biodb.INFO [2025-01-25 16:05:31.909][biodb::testThat]
biodb.INFO [2025-01-25 16:05:31.910][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-25 16:05:31.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:31.912][biodb::testThat]
biodb.WARN [2025-01-25 16:05:31.929][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-01-25 16:05:31.946][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-01-25 16:05:31.953][biodb::testThat]
biodb.INFO [2025-01-25 16:05:31.954][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-25 16:05:31.955][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:31.955][biodb::testThat]
biodb.TRACE[2025-01-25 16:05:31.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.978][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:31.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.985][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:31.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:31.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:31.989][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:31.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:31.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:31.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:32.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:32.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:32.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:32.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:32.024][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:32.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:32.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:32.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:32.028][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:32.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:32.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:32.031][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:32.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:32.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:32.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:05:32.039][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.039][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-25 16:05:32.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:32.041][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.047][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.048][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-25 16:05:32.049][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:32.049][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.055][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.056][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-25 16:05:32.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:32.058][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.062][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.063][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-25 16:05:32.064][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:32.065][biodb::testThat]
biodb.INFO [2025-01-25 16:05:32.070][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-25 16:05:32.071][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-01-25 16:05:32.072][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-01-25 16:05:32.072][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-25 16:05:32.073][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.075][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.076][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-25 16:05:32.085][biodb::testContext]
biodb.INFO [2025-01-25 16:05:32.086][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:05:32.087][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-01-25 16:05:32.087][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:05:32.088][biodb::testContext]
biodb.INFO [2025-01-25 16:05:32.090][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:05:32.092][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-25 16:05:32.098][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:32.099][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-25 16:05:32.100][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-25 16:05:32.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.103][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-25 16:05:32.104][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-25 16:05:32.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.107][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-25 16:05:32.108][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-25 16:05:32.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.111][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-25 16:05:32.112][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-25 16:05:32.113][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-25 16:05:32.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.116][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-25 16:05:32.117][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-25 16:05:32.118][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-25 16:05:32.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.121][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-25 16:05:32.122][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-25 16:05:32.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.126][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-25 16:05:32.126][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-25 16:05:32.127][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-25 16:05:32.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.130][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-25 16:05:32.131][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-25 16:05:32.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.135][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-25 16:05:32.135][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-25 16:05:32.136][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-25 16:05:32.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.140][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:05:32.140][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-25 16:05:32.141][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-25 16:05:32.142][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-25 16:05:32.143][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-25 16:05:32.144][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-25 16:05:32.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.147][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-25 16:05:32.148][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-25 16:05:32.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.151][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-25 16:05:32.152][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-25 16:05:32.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.155][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-25 16:05:32.156][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-25 16:05:32.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.160][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-25 16:05:32.160][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:05:32.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.164][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-25 16:05:32.165][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-25 16:05:32.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.168][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:05:32.169][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-25 16:05:32.172][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-25 16:05:32.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.176][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-25 16:05:32.177][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-25 16:05:32.178][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-25 16:05:32.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.181][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-25 16:05:32.182][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.183][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-25 16:05:32.184][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.185][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:32.186][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.187][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.188][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.190][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:05:32.190][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:32.191][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.192][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-25 16:05:32.193][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:32.194][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.195][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.196][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:05:32.196][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:05:32.196][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:05:32.196][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:05:32.196][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:05:32.197][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:32.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.199][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:32.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.202][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.202][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.203][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:32.204][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:32.205][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.206][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.207][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-25 16:05:32.208][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.209][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:05:32.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:32.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.213][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.214][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.215][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.215][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:05:32.216][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:32.217][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.218][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-25 16:05:32.222][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:32.223][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.224][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.225][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:05:32.225][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:05:32.225][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:05:32.225][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:05:32.225][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:05:32.226][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:32.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.228][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:32.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.231][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.231][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.232][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:32.233][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:32.234][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.235][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.236][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-25 16:05:32.237][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.238][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-25 16:05:32.239][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.240][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:32.241][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.242][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.243][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.243][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.244][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:05:32.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:32.246][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.247][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-25 16:05:32.248][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:32.249][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.250][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.250][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.251][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:32.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.254][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:32.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.256][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.257][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.258][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:32.259][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:32.260][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.260][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.261][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-25 16:05:32.263][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.264][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:05:32.265][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.266][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:32.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.267][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.268][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.269][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.270][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:05:32.271][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:32.272][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.273][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-25 16:05:32.274][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:32.274][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.275][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.276][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.277][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:32.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.279][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:32.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.282][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.283][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.284][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:32.284][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:32.285][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.286][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:32.288][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.328][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[2025-01-25 16:05:32.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.332][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[2025-01-25 16:05:32.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.359][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-25 16:05:32.361][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-25 16:05:32.362][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-25 16:05:32.363][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-25 16:05:32.364][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-25 16:05:32.366][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:05:32.367][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-25 16:05:32.368][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-25 16:05:32.369][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-25 16:05:32.370][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:05:32.372][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:05:32.373][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-25 16:05:32.374][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-25 16:05:32.375][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-25 16:05:32.377][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-25 16:05:32.378][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:05:32.379][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-25 16:05:32.380][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-25 16:05:32.382][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-25 16:05:32.383][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-25 16:05:32.384][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-25 16:05:32.385][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-25 16:05:32.386][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-25 16:05:32.388][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-25 16:05:32.389][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-25 16:05:32.390][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-25 16:05:32.391][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-25 16:05:32.393][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-25 16:05:32.394][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-25 16:05:32.395][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-25 16:05:32.396][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-25 16:05:32.398][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-25 16:05:32.399][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-25 16:05:32.400][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-25 16:05:32.401][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-25 16:05:32.402][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-25 16:05:32.404][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-25 16:05:32.405][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-25 16:05:32.406][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-25 16:05:32.407][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-25 16:05:32.409][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-25 16:05:32.410][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-25 16:05:32.411][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-25 16:05:32.412][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-25 16:05:32.414][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-25 16:05:32.415][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-25 16:05:32.416][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-25 16:05:32.417][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-25 16:05:32.418][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-25 16:05:32.420][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-25 16:05:32.421][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-25 16:05:32.422][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-25 16:05:32.423][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-25 16:05:32.425][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-25 16:05:32.426][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-25 16:05:32.427][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-25 16:05:32.428][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-25 16:05:32.430][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-25 16:05:32.431][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-25 16:05:32.432][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-25 16:05:32.433][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-25 16:05:32.434][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-25 16:05:32.436][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-25 16:05:32.437][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-25 16:05:32.438][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-25 16:05:32.439][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-25 16:05:32.441][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-25 16:05:32.442][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-25 16:05:32.443][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-25 16:05:32.444][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-25 16:05:32.445][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-25 16:05:32.447][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-25 16:05:32.448][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-25 16:05:32.449][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-25 16:05:32.450][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-25 16:05:32.452][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-25 16:05:32.453][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-25 16:05:32.454][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-25 16:05:32.455][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-25 16:05:32.460][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-25 16:05:32.461][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-25 16:05:32.462][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-25 16:05:32.464][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-25 16:05:32.465][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-25 16:05:32.466][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:05:32.467][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:32.468][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.470][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:32.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:32.564][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-01-25 16:05:32.566][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-01-25 16:05:32.567][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.568][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-01-25 16:05:32.569][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.570][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:32.571][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.572][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-01-25 16:05:32.573][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.573][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.577][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-01-25 16:05:32.578][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:32.579][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.580][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-01-25 16:05:32.581][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:32.582][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-01-25 16:05:32.582][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-01-25 16:05:32.582][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-01-25 16:05:32.582][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-01-25 16:05:32.582][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-01-25 16:05:32.582][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-01-25 16:05:32.582][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-01-25 16:05:32.583][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:32.584][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.584][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-25 16:05:32.585][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.586][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.587][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:32.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:32.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:32.589][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:32.590][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:05:32.590][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:05:32.590][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-01-25 16:05:32.590][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-01-25 16:05:32.591][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:32.592][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:32.593][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:32.594][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:32.595][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-01-25 16:05:32.597][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-01-25 16:05:32.598][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-01-25 16:05:32.599][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-01-25 16:05:32.601][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-01-25 16:05:32.602][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:05:32.603][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:05:32.604][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:05:32.605][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:05:32.606][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:05:32.607][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-01-25 16:05:32.608][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-25 16:05:32.609][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-01-25 16:05:32.610][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-01-25 16:05:32.610][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-25 16:05:32.611][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:32.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:32.613][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:32.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:32.614][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:32.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  3.936   0.204   4.130

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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-3.20-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 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)