Back to Long Tests report for BioC 3.17

This page was generated on 2023-10-14 21:30:02 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 11/31HostnameOS / ArchCHECK
biodbMirbase 1.4.1  (landing page)
Pierrick Roger
Snapshot Date: 2023-10-14 09:55:02 -0400 (Sat, 14 Oct 2023)
git_url: https://git.bioconductor.org/packages/biodbMirbase
git_branch: RELEASE_3_17
git_last_commit: 8807efc
git_last_commit_date: 2023-08-11 08:53:35 -0400 (Fri, 11 Aug 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.6.4 Monterey / x86_64  ERROR  

CHECK results for biodbMirbase on palomino3


To the developers/maintainers of the biodbMirbase 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: biodbMirbase
Version: 1.4.1
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbMirbase_1.4.1.tar.gz
StartedAt: 2023-10-14 11:07:34 -0400 (Sat, 14 Oct 2023)
EndedAt: 2023-10-14 11:08:18 -0400 (Sat, 14 Oct 2023)
EllapsedTime: 44.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbMirbase.Rcheck
Warnings: NA

Tests output

biodbMirbase.Rcheck/tests/testthat.Rout.fail


R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbMirbase)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbMirbase")
biodb.INFO [2023-10-14 11:08:13.000][biodb::testContext]
biodb.INFO [2023-10-14 11:08:13.004][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:08:13.006][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-10-14 11:08:13.007][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:08:13.009][biodb::testContext]
biodb.INFO [2023-10-14 11:08:13.017][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:08:13.020][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:08:13.030][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:08:13.031][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:08:13.033][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:08:13.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.039][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:08:13.062][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:08:13.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.068][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:08:13.069][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:08:13.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.075][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:08:13.076][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:08:13.078][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:08:13.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.082][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[2023-10-14 11:08:13.083][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:08:13.085][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:08:13.086][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:08:13.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.092][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:08:13.093][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:08:13.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.098][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:08:13.100][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:08:13.101][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:08:13.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.106][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:08:13.108][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:08:13.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.114][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:08:13.115][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:08:13.117][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:08:13.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.122][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:08:13.124][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:08:13.125][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:08:13.126][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:08:13.128][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:08:13.129][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:08:13.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.134][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:08:13.136][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:08:13.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.141][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:08:13.143][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:08:13.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.148][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:08:13.149][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:08:13.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.155][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:08:13.156][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:08:13.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.162][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:08:13.163][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:08:13.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.168][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:08:13.170][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:08:13.174][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:08:13.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.180][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:08:13.181][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:08:13.183][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:08:13.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.191][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:08:13.241][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.255][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-14 11:08:13.257][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.258][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:13.259][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.260][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.262][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.263][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.264][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:08:13.265][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:13.267][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.268][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:08:13.269][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:13.270][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.271][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.273][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:08:13.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:08:13.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:08:13.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:08:13.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:08:13.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:13.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.277][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:13.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.282][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.283][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:13.284][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:13.285][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.287][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.288][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:08:13.290][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.291][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:08:13.292][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.294][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:13.295][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.298][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.301][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:08:13.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:13.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.305][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:08:13.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:13.308][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.309][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:08:13.311][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:13.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.315][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:13.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.319][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.320][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.321][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:13.322][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:13.323][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.325][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.326][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:08:13.328][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.329][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-14 11:08:13.331][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.332][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:13.333][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.334][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.335][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.337][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.338][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:08:13.339][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:13.340][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.342][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:08:13.343][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:13.344][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.345][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.347][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.348][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:13.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:13.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.355][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.356][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:13.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:13.359][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.361][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.362][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:08:13.364][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.365][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:08:13.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:13.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.374][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:08:13.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:13.377][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.378][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:08:13.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:13.381][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.382][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.383][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.384][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:13.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:13.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.392][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.393][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.394][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:13.395][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:13.396][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.397][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.401][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:08:13.402][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.474][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[2023-10-14 11:08:13.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.503][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:08:13.507][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:08:13.509][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:08:13.510][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:08:13.512][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:08:13.514][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:08:13.515][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:08:13.517][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:08:13.518][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:08:13.520][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:08:13.522][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:08:13.523][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:08:13.525][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:08:13.526][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:08:13.528][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:08:13.530][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:08:13.532][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:08:13.534][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:08:13.540][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:08:13.542][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:08:13.544][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:08:13.545][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:08:13.547][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:08:13.548][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:08:13.550][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:08:13.552][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:08:13.553][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:08:13.555][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:08:13.556][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:08:13.558][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:08:13.560][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:08:13.561][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:08:13.563][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:08:13.564][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:08:13.566][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:08:13.568][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:08:13.569][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:08:13.571][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:08:13.572][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:08:13.574][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:08:13.575][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:08:13.577][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:08:13.579][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:08:13.580][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:08:13.582][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:08:13.583][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:08:13.585][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:08:13.587][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:08:13.588][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:08:13.590][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:08:13.591][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:08:13.593][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:08:13.594][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:08:13.596][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:08:13.597][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:08:13.599][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:08:13.601][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:08:13.602][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:08:13.604][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:08:13.606][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:08:13.607][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:08:13.609][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:08:13.610][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:08:13.612][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:08:13.614][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:08:13.615][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:08:13.617][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:08:13.618][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:08:13.620][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:08:13.622][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:08:13.623][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:08:13.625][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:08:13.626][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:08:13.628][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:08:13.629][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:08:13.631][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:08:13.632][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:08:13.634][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:08:13.636][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:08:13.637][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:08:13.639][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:08:13.640][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:08:13.642][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:08:13.675][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:08:13.678][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:08:13.681][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:08:13.682][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.685][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:13.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:13.825][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-10-14 11:08:13.835][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:13.837][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.838][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:08:13.839][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.841][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:13.842][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.843][self$setPropertyValue] Setting property "dwnld.ext" to "txt".
biodb.DEBUG[2023-10-14 11:08:13.849][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.851][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.852][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:08:13.853][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:13.854][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.856][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-10-14 11:08:13.857][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:13.858][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-10-14 11:08:13.858][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-10-14 11:08:13.858][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-10-14 11:08:13.858][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-10-14 11:08:13.859][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:13.861][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.862][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:08:13.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:13.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:13.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:13.869][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:13.870][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/".
biodb.DEBUG[2023-10-14 11:08:13.870][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/download/CURRENT/mature.fa".
biodb.DEBUG[2023-10-14 11:08:13.871][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:13.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:13.873][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:13.875][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:13.880][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-10-14 11:08:13.904][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:13.905][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-10-14 11:08:13.909][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:13.914][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-10-14 11:08:13.918][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:08:13.919][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:08:13.921][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-10-14 11:08:13.922][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-10-14 11:08:13.933][biodb::testThat]
biodb.INFO [2023-10-14 11:08:13.934][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-14 11:08:13.936][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:13.937][biodb::testThat]
biodb.TRACE[2023-10-14 11:08:13.943][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000433-content.txt".
biodb.DEBUG[2023-10-14 11:08:13.945][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:08:13.949][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-10-14 11:08:13.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:08:13.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:13.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:13.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:13.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:13.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:13.981][FUN] Functions in observer BiodbConfig: [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[2023-10-14 11:08:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:13.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:13.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:13.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.018][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.039][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.044][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.049][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.059][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:08:14.131][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000433.
biodb.TRACE[2023-10-14 11:08:14.134][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.144][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:08:14.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:08:14.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.149][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:08:14.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:08:14.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.194][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.237][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.242][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.247][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.278][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.281][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.313][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.316][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.317][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.334][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.340][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.344][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.350][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.351][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.354][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.355][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.371][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.376][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.381][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.386][ef$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.393][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.395][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.397][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.413][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.415][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.417][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.425][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.427][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.428][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.430][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.437][ef$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.439][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.441][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.449][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.451][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.452][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.454][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.473][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/testref/entry-mirbase.mature-MIMAT0000434-content.txt".
biodb.DEBUG[2023-10-14 11:08:14.504][biodb$getFactory()$createEntryFromCo ...] Creating miRBase mature database entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:08:14.505][biodb$getFactory()$createEntryFromCo ...] Parsing 1 miRBase mature database entries.
biodb.DEBUG[2023-10-14 11:08:14.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:08:14.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:14.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:14.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:14.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:14.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:14.521][FUN] Functions in observer BiodbConfig: [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[2023-10-14 11:08:14.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.542][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.552][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.562][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.572][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:08:14.606][biodb$getFactory()$createEntryFromCo ...] Accession numbers: MIMAT0000434.
biodb.TRACE[2023-10-14 11:08:14.651][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.656][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:08:14.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.661][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:08:14.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:08:14.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.666][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:08:14.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:08:14.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.683][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.727][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.732][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.737][self$getBiodb()$getEntryFields()$get] Asked field names are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mirbase.mature.id.
biodb.TRACE[2023-10-14 11:08:14.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.776][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.778][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.779][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.780][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.811][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.813][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.815][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.832][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.837][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.842][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.847][ef$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.848][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.849][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.851][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.852][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2023-10-14 11:08:14.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.867][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.872][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.882][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.887][ef$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.889][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.891][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.892][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.908][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.909][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2023-10-14 11:08:14.910][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.912][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.919][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:08:14.921][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:08:14.922][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.923][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.931][ef$get] Asked field names are: description.
biodb.TRACE[2023-10-14 11:08:14.932][ef$get] Realnames of fields are: description.
biodb.TRACE[2023-10-14 11:08:14.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.934][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:08:14.942][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:08:14.944][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:08:14.945][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:08:14.946][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:08:14.960][biodb::testThat]
biodb.INFO [2023-10-14 11:08:14.961][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-14 11:08:14.963][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:14.964][biodb::testThat]
biodb.DEBUG[2023-10-14 11:08:14.967][private$loadEntries] Creating entries from ids [2]: "MIMAT0000433, MIMAT0000434".
biodb.DEBUG[2023-10-14 11:08:14.974][conn$getEntryContent] Get miRBase mature database entry content(s) for 2 id(s)...
biodb.INFO [2023-10-14 11:08:14.981][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ee3c16b1e67d439324a1d7fe34666ec8" for "mirbase.mature-ee3c16b1e67d439324a1d7fe34666ec8".
biodb.DEBUG[2023-10-14 11:08:14.983][self$isDownloaded] Database mirbase.mature has not yet been downloaded.
biodb.INFO [2023-10-14 11:08:14.984][self$download] Downloading whole database of mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:14.987][self$getDownloadPath] Download path of mirbase.mature is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ee3c16b1e67d439324a1d7fe34666ec8/download.txt".
biodb.DEBUG[2023-10-14 11:08:14.988][sched$downloadFile] Downloading file "https://www.mirbase.org/download/CURRENT/mature.fa".
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
biodb.INFO [2023-10-14 11:08:15.461][biodb::testThat]
biodb.INFO [2023-10-14 11:08:15.463][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-14 11:08:15.464][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:15.465][biodb::testThat]
biodb.INFO [2023-10-14 11:08:15.475][biodb::testThat]
biodb.INFO [2023-10-14 11:08:15.477][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-14 11:08:15.478][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:15.480][biodb::testThat]
biodb.WARN [2023-10-14 11:08:15.504][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2023-10-14 11:08:15.524][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2023-10-14 11:08:15.540][biodb::testThat]
biodb.INFO [2023-10-14 11:08:15.541][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-14 11:08:15.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:15.544][biodb::testThat]
biodb.DEBUG[2023-10-14 11:08:15.568][private$loadEntries] Creating entries from ids [1]: "MIMAT0000433".
biodb.DEBUG[2023-10-14 11:08:15.621][conn$getEntryContent] Get miRBase mature database entry content(s) for 1 id(s)...
biodb.DEBUG[2023-10-14 11:08:15.624][self$isDownloaded] Database mirbase.mature has not yet been downloaded.
biodb.INFO [2023-10-14 11:08:15.626][self$download] Downloading whole database of mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:15.647][self$getDownloadPath] Download path of mirbase.mature is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/mirbase.mature-ee3c16b1e67d439324a1d7fe34666ec8/download.txt".
biodb.DEBUG[2023-10-14 11:08:15.649][sched$downloadFile] Downloading file "https://www.mirbase.org/download/CURRENT/mature.fa".
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
biodb.INFO [2023-10-14 11:08:16.124][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.125][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-14 11:08:16.126][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:16.127][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.138][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.139][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-14 11:08:16.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:16.142][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.153][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.154][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-14 11:08:16.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:16.157][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.168][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.169][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-14 11:08:16.170][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:08:16.171][biodb::testThat]
biodb.INFO [2023-10-14 11:08:16.181][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:08:16.182][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-10-14 11:08:16.184][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-10-14 11:08:16.185][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:08:16.186][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.188][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.190][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-14 11:08:16.201][biodb::testContext]
biodb.INFO [2023-10-14 11:08:16.202][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:08:16.204][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-10-14 11:08:16.205][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:08:16.206][biodb::testContext]
biodb.INFO [2023-10-14 11:08:16.209][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:08:16.216][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:08:16.221][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:08:16.223][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:08:16.224][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:08:16.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.228][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:08:16.229][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:08:16.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.234][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:08:16.235][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:08:16.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.239][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:08:16.240][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:08:16.241][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:08:16.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.246][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:08:16.247][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:08:16.248][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:08:16.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.253][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:08:16.254][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:08:16.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.259][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:08:16.260][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:08:16.261][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:08:16.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.266][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:08:16.267][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:08:16.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.272][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:08:16.273][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:08:16.274][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:08:16.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.278][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:08:16.280][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:08:16.281][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:08:16.282][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:08:16.283][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:08:16.285][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:08:16.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.289][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:08:16.290][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:08:16.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.293][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[2023-10-14 11:08:16.295][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:08:16.296][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:08:16.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.300][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:08:16.302][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:08:16.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.305][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[2023-10-14 11:08:16.306][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:08:16.307][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:08:16.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.312][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:08:16.313][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:08:16.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.316][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[2023-10-14 11:08:16.318][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:08:16.319][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:08:16.323][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:08:16.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.327][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:08:16.328][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:08:16.330][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:08:16.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.334][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:08:16.336][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.337][self$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[2023-10-14 11:08:16.339][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:16.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.342][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.343][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.346][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:08:16.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:16.348][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.349][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:08:16.351][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:16.352][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.353][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.354][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:08:16.354][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:08:16.354][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:08:16.354][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:08:16.354][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:08:16.355][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:16.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.359][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:16.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.363][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:16.366][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:16.367][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.368][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.369][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:08:16.371][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.372][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:08:16.374][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.375][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:16.376][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.377][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.378][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.379][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.381][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:08:16.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:16.383][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.384][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:08:16.385][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:16.387][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.388][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.389][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:08:16.389][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:08:16.389][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:08:16.389][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:08:16.389][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:08:16.390][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:16.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.394][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:16.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.397][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.398][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:16.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:16.402][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.403][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.404][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:08:16.406][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.407][self$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[2023-10-14 11:08:16.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.410][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:16.411][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.412][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.413][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.414][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.416][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:08:16.417][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:16.418][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.419][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:08:16.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:16.421][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.423][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.424][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.425][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:16.426][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:16.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.432][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.433][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:16.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:16.437][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.438][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.439][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:08:16.441][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.443][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:08:16.444][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.445][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:16.446][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.447][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.448][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.450][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.451][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:08:16.452][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:16.453][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.459][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:08:16.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:16.462][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.463][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.464][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.465][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:08:16.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:16.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.473][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.474][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:16.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:16.477][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.478][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.479][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:08:16.480][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.487][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[2023-10-14 11:08:16.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.492][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[2023-10-14 11:08:16.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.498][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[2023-10-14 11:08:16.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.503][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[2023-10-14 11:08:16.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.514][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[2023-10-14 11:08:16.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.525][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[2023-10-14 11:08:16.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.530][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[2023-10-14 11:08:16.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.536][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[2023-10-14 11:08:16.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.541][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[2023-10-14 11:08:16.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.547][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[2023-10-14 11:08:16.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.552][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[2023-10-14 11:08:16.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.563][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[2023-10-14 11:08:16.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.568][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[2023-10-14 11:08:16.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.574][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[2023-10-14 11:08:16.575][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:08:16.577][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:08:16.578][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:08:16.580][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:08:16.582][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:08:16.583][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:08:16.585][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:08:16.586][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:08:16.588][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:08:16.589][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:08:16.591][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:08:16.592][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:08:16.594][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:08:16.596][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:08:16.597][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:08:16.599][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:08:16.600][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:08:16.602][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:08:16.603][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:08:16.605][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:08:16.606][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:08:16.608][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:08:16.610][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:08:16.611][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:08:16.613][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:08:16.614][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:08:16.616][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:08:16.617][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:08:16.619][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:08:16.620][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:08:16.622][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:08:16.623][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:08:16.625][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:08:16.627][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:08:16.628][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:08:16.630][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:08:16.631][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:08:16.633][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:08:16.634][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:08:16.636][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:08:16.637][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:08:16.639][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:08:16.641][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:08:16.642][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:08:16.644][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:08:16.645][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:08:16.647][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:08:16.648][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:08:16.650][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:08:16.651][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:08:16.653][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:08:16.654][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:08:16.656][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:08:16.658][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:08:16.660][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:08:16.662][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:08:16.663][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:08:16.665][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:08:16.666][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:08:16.668][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:08:16.669][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:08:16.671][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:08:16.672][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:08:16.674][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:08:16.676][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:08:16.677][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:08:16.679][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:08:16.680][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:08:16.682][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:08:16.688][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:08:16.690][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:08:16.692][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:08:16.693][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:08:16.695][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:08:16.696][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:08:16.698][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:08:16.700][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:08:16.701][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:08:16.703][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:08:16.704][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:08:16.706][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:08:16.707][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:08:16.709][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:08:16.711][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:08:16.713][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:08:16.714][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:08:16.715][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.717][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:08:16.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:08:16.882][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbMirbase.Rcheck/biodbMirbase/definitions.yml".
biodb.DEBUG[2023-10-14 11:08:16.885][self$getDbsInfo()$define] Define connector mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:16.888][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.890][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2023-10-14 11:08:16.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.895][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:08:16.897][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.899][self$setPropertyValue] Setting property "dwnld.ext" to "txt".
biodb.DEBUG[2023-10-14 11:08:16.901][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.905][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2023-10-14 11:08:16.907][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:08:16.909][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.911][self$setPropertyValue] Setting property "name" to "miRBase mature database".
biodb.DEBUG[2023-10-14 11:08:16.913][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:08:16.915][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *(MIMAT[0-9]+) .*$".
biodb.DEBUG[2023-10-14 11:08:16.915][self$setPropertyValue] Setting property "parsing.expr" to "^>[^ ]+ *MIMAT[0-9]+ (.*)$".
biodb.DEBUG[2023-10-14 11:08:16.915][self$setPropertyValue] Setting property "parsing.expr" to "^>([^ ]+) *MIMAT[0-9]+ .*$".
biodb.DEBUG[2023-10-14 11:08:16.915][self$setPropertyValue] Setting property "parsing.expr" to "^([ACGU]+)$".
biodb.DEBUG[2023-10-14 11:08:16.918][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:08:16.920][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.922][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:08:16.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:08:16.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:08:16.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:08:16.933][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:08:16.935][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/".
biodb.DEBUG[2023-10-14 11:08:16.935][self$setPropertyValue] Setting property "urls" to "https://www.mirbase.org/download/CURRENT/mature.fa".
biodb.DEBUG[2023-10-14 11:08:16.938][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:08:16.939][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:08:16.941][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:08:16.943][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:08:16.946][self$getEntryFields()$define] Define field mirbase.mature.id.
biodb.DEBUG[2023-10-14 11:08:16.951][initialize] Initialize connector mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:16.954][initialize] Register connector mirbase.mature with the request scheduler
biodb.DEBUG[2023-10-14 11:08:16.956][private$bdb$getRequestScheduler()$re ...] Register connector mirbase.mature.
biodb.DEBUG[2023-10-14 11:08:16.960][private$addConnectorRules] Create new rule for URL "www.mirbase.org" of connector "mirbase.mature".
biodb.DEBUG[2023-10-14 11:08:16.962][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:08:16.965][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:08:16.968][rule$addConnector] Connector "mirbase.mature" is already listed in rule "www.mirbase.org".
biodb.DEBUG[2023-10-14 11:08:16.970][biodb$getFactory()$createConn] Creating new connector mirbase.mature for database class mirbase.mature .
biodb.INFO [2023-10-14 11:08:16.972][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:08:16.974][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector mirbase.mature from the request scheduler
biodb.INFO [2023-10-14 11:08:16.977][self$deleteConn] Connector "mirbase.mature" deleted.
biodb.DEBUG[2023-10-14 11:08:16.979][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:08:16.980][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:08:16.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:08:16.984][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:08:16.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:08:16.988][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:08:16.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 65 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$download()
  9.               └─private$doDownload()
 10.                 └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
 11.                   └─utils::download.file(...)

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 65 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbMirbase_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbMirbase.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbMirbase/DESCRIPTION' ... OK
* this is package 'biodbMirbase' version '1.4.1'
* 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 whether package 'biodbMirbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'MirbaseMatureConn' 'MirbaseMatureEntry'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
    3.   └─opt$refEntries$getRealEntry(id)
    4.     └─self$getRealEntries(ids = id)
    5.       └─private$bdb$getFactory()$getEntry(...)
    6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    7.           └─conn$getEntryContent(ids)
    8.             └─self$download()
    9.               └─private$doDownload()
   10.                 └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
   11.                   └─utils::download.file(...)
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 65 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING
See
  'F:/biocbuild/bbs-3.17-bioc-longtests/meat/biodbMirbase.Rcheck/00check.log'
for details.

Installation output

biodbMirbase.Rcheck/00install.out

* installing *source* package 'biodbMirbase' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'biodbMirbase' 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbMirbase)