| Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-10-12 23:55 -0400 (Sat, 12 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
| 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 12/33 | Hostname | OS / Arch | CHECK | |||||||
| biodbNci 1.8.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ||||||||
|
To the developers/maintainers of the biodbNci package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbNci |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz |
| StartedAt: 2024-10-12 16:07:17 -0400 (Sat, 12 Oct 2024) |
| EndedAt: 2024-10-12 16:08:18 -0400 (Sat, 12 Oct 2024) |
| EllapsedTime: 61.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbNci.Rcheck |
| Warnings: 0 |
biodbNci.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-10-12 16:08:14.944][biodb::testContext]
biodb.INFO [2024-10-12 16:08:14.946][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:08:14.947][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-10-12 16:08:14.948][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:08:14.949][biodb::testContext]
biodb.INFO [2024-10-12 16:08:14.955][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:08:14.956][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:08:14.963][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:08:14.964][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:08:14.965][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:08:14.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:14.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:14.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:14.969][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:08:14.985][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:08:14.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:14.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:14.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:14.988][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:08:14.989][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:08:14.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:14.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:14.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:14.993][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:08:14.993][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:08:14.994][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:08:14.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:14.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:14.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:14.998][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:08:14.999][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:08:14.999][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:08:15.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.003][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:08:15.004][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:08:15.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.007][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:08:15.008][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:08:15.009][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:08:15.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.012][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:08:15.013][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:08:15.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.016][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:08:15.017][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:08:15.018][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:08:15.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.021][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:08:15.022][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:08:15.023][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:08:15.024][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:08:15.025][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:08:15.026][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:08:15.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.029][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:08:15.030][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:08:15.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.033][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:08:15.034][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:08:15.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.037][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[2024-10-12 16:08:15.037][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:08:15.038][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:08:15.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.042][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:08:15.043][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:08:15.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.046][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:08:15.047][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:08:15.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.050][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:08:15.051][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:08:15.055][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:08:15.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.059][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:08:15.059][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:08:15.060][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:08:15.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.066][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:08:15.102][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.115][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-12 16:08:15.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.117][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:15.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.120][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.122][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:08:15.123][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:15.124][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.124][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:08:15.125][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:15.126][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.127][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.128][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:08:15.128][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:08:15.128][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:08:15.128][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:08:15.128][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:08:15.129][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:15.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.131][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:15.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.134][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.135][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:15.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:15.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.138][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.139][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:08:15.141][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.142][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:08:15.143][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.144][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:15.144][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.146][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.147][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.148][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:08:15.149][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:15.150][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.151][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:08:15.152][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:15.152][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.153][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.154][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:08:15.154][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:08:15.154][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:08:15.154][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:08:15.154][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:08:15.155][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:15.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.158][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:15.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.160][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.161][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.162][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:15.163][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:15.164][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.165][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.166][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:08:15.167][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.168][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-12 16:08:15.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:15.171][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.172][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.173][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.174][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:08:15.175][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:15.176][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.177][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:08:15.178][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:15.179][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.180][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.181][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.182][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:15.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.184][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:15.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.187][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.187][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.188][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:15.189][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:15.190][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.191][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.192][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:08:15.194][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.194][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:08:15.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:15.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.199][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.201][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:08:15.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:15.203][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.203][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:08:15.204][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:15.205][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.206][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.207][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.208][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:15.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.210][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:15.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.213][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.214][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.215][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:15.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:15.216][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.217][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.221][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:08:15.222][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.227][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[2024-10-12 16:08:15.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.251][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[2024-10-12 16:08:15.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.270][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[2024-10-12 16:08:15.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.296][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:08:15.300][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:08:15.302][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:08:15.303][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:08:15.304][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:08:15.305][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:08:15.307][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:08:15.308][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:08:15.309][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:08:15.310][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:08:15.312][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:08:15.313][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:08:15.314][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:08:15.315][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:08:15.317][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:08:15.318][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:08:15.319][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:08:15.321][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:08:15.322][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:08:15.323][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:08:15.324][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:08:15.326][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:08:15.327][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:08:15.328][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:08:15.329][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:08:15.334][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:08:15.336][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:08:15.338][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:08:15.339][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:08:15.341][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:08:15.342][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:08:15.344][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:08:15.345][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:08:15.346][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:08:15.348][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:08:15.349][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:08:15.351][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:08:15.352][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:08:15.353][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:08:15.355][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:08:15.356][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:08:15.358][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:08:15.359][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:08:15.361][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:08:15.362][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:08:15.363][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:08:15.365][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:08:15.366][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:08:15.368][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:08:15.369][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:08:15.371][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:08:15.372][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:08:15.373][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:08:15.375][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:08:15.376][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:08:15.377][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:08:15.379][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:08:15.380][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:08:15.382][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:08:15.383][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:08:15.385][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:08:15.386][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:08:15.387][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:08:15.389][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:08:15.390][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:08:15.392][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:08:15.393][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:08:15.394][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:08:15.396][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:08:15.397][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:08:15.398][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:08:15.400][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:08:15.401][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:08:15.403][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:08:15.404][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:08:15.405][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:08:15.407][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:08:15.408][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:08:15.409][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:08:15.411][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:08:15.412][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:08:15.414][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:08:15.415][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:08:15.434][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:08:15.436][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:08:15.439][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:08:15.440][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.442][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.443][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[2024-10-12 16:08:15.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.490][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[2024-10-12 16:08:15.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.496][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[2024-10-12 16:08:15.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.514][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[2024-10-12 16:08:15.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.520][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[2024-10-12 16:08:15.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:15.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:15.550][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-10-12 16:08:15.558][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-10-12 16:08:15.560][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.561][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-10-12 16:08:15.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:15.564][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.564][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-10-12 16:08:15.565][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.567][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-10-12 16:08:15.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:15.569][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.570][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-10-12 16:08:15.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:15.572][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-10-12 16:08:15.572][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-10-12 16:08:15.572][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-10-12 16:08:15.572][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-10-12 16:08:15.572][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-10-12 16:08:15.572][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-10-12 16:08:15.572][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-10-12 16:08:15.573][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:15.574][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.575][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:08:15.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.577][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:15.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:15.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:15.580][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:15.580][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:08:15.580][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:08:15.580][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-10-12 16:08:15.580][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-10-12 16:08:15.581][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:15.582][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:15.583][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:15.584][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:15.589][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-10-12 16:08:15.615][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-10-12 16:08:15.616][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-10-12 16:08:15.620][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-10-12 16:08:15.624][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-10-12 16:08:15.628][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:08:15.629][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:08:15.630][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:08:15.632][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:08:15.633][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:08:15.634][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-10-12 16:08:15.643][biodb::testThat]
biodb.INFO [2024-10-12 16:08:15.644][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-10-12 16:08:15.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:15.646][biodb::testThat]
biodb.TRACE[2024-10-12 16:08:15.649][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-10-12 16:08:15.651][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:08:15.654][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-10-12 16:08:15.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:08:15.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:15.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:15.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:15.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:15.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:15.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:08:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:15.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:15.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:15.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:15.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:15.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:15.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:15.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:15.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:15.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:15.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:15.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:15.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:15.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:15.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:15.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:15.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.767][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.771][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.812][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:08:15.866][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-10-12 16:08:15.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:15.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:15.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:15.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:15.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.875][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:15.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:15.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.879][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:15.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:15.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.910][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.943][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.950][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:15.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.970][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.973][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:15.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:15.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:15.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:15.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:15.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:15.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:15.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:15.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.994][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:15.995][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:15.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:15.997][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:15.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:15.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.018][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.019][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.021][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.042][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.043][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.044][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.070][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.071][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.082][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.083][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.084][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.088][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.091][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.097][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.103][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.107][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.108][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.109][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.124][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-10-12 16:08:16.156][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:08:16.157][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-10-12 16:08:16.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:08:16.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:16.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:16.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:16.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:16.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:16.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:08:16.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.201][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.204][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.212][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.265][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.268][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.275][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:08:16.300][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-10-12 16:08:16.322][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.325][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.329][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:16.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.332][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:16.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.343][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.372][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.380][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.407][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.408][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.410][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.424][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.431][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.435][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.436][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.437][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.438][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.458][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.461][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.482][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.483][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.485][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.506][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.507][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.508][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.529][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.530][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.532][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.557][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.557][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.559][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.569][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.570][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.572][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.576][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.577][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.578][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.582][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.583][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.585][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.588][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.589][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.591][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.594][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.595][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.597][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.601][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.602][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.603][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.607][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.608][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.609][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:08:16.615][biodb::testThat]
biodb.INFO [2024-10-12 16:08:16.616][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-12 16:08:16.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:16.618][biodb::testThat]
biodb.DEBUG[2024-10-12 16:08:16.620][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-10-12 16:08:16.627][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-10-12 16:08:16.631][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-10-12 16:08:16.632][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-10-12 16:08:16.634][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-10-12 16:08:16.635][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-10-12 16:08:16.637][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-10-12 16:08:16.638][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-10-12 16:08:16.639][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-10-12 16:08:16.640][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-10-12 16:08:16.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:08:16.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:16.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:16.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:16.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:16.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:16.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:08:16.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.663][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.699][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.702][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.709][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:08:16.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:08:16.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:16.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:16.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:16.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:16.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:16.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:08:16.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.748][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.752][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:08:16.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.760][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:08:16.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:08:16.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:08:16.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:08:16.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:08:16.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:08:16.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:08:16.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:08:16.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.812][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.819][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.826][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:08:16.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:08:16.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:08:16.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:08:16.863][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-10-12 16:08:16.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:08:16.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:08:16.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:08:16.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:08:16.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:08:16.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:08:16.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:08:16.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:08:16.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:08:16.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:08:16.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:08:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:08:16.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:08:16.894][biodb::testThat]
biodb.INFO [2024-10-12 16:08:16.895][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-12 16:08:16.896][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:16.897][biodb::testThat]
biodb.INFO [2024-10-12 16:08:16.902][biodb::testThat]
biodb.INFO [2024-10-12 16:08:16.903][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-10-12 16:08:16.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:16.904][biodb::testThat]
biodb.WARN [2024-10-12 16:08:16.923][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-10-12 16:08:16.944][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-10-12 16:08:16.952][biodb::testThat]
biodb.INFO [2024-10-12 16:08:16.953][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-10-12 16:08:16.953][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:16.954][biodb::testThat]
biodb.TRACE[2024-10-12 16:08:16.974][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.978][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.982][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:16.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:16.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:16.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:16.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:17.018][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:17.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:17.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:17.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:17.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:08:17.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:08:17.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:17.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:17.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:17.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:08:17.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:17.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:08:17.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:17.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:08:17.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:08:17.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:08:17.036][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.037][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-12 16:08:17.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:17.039][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.045][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.046][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-12 16:08:17.047][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:17.047][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.057][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.058][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-12 16:08:17.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:17.060][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.064][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.065][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-12 16:08:17.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:08:17.067][biodb::testThat]
biodb.INFO [2024-10-12 16:08:17.072][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:08:17.073][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-10-12 16:08:17.074][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-10-12 16:08:17.074][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:08:17.075][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.077][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.078][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-12 16:08:17.087][biodb::testContext]
biodb.INFO [2024-10-12 16:08:17.088][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:08:17.089][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-10-12 16:08:17.090][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:08:17.091][biodb::testContext]
biodb.INFO [2024-10-12 16:08:17.093][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:08:17.094][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:08:17.097][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:08:17.098][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:08:17.099][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:08:17.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.103][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:08:17.104][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:08:17.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.107][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:08:17.108][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:08:17.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.111][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:08:17.112][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:08:17.113][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:08:17.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.116][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:08:17.117][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:08:17.118][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:08:17.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.121][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:08:17.122][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:08:17.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.125][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:08:17.126][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:08:17.127][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:08:17.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.130][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:08:17.131][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:08:17.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.135][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:08:17.136][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:08:17.137][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:08:17.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.140][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:08:17.141][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:08:17.142][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:08:17.143][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:08:17.143][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:08:17.144][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:08:17.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.147][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[2024-10-12 16:08:17.148][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:08:17.149][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:08:17.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.152][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:08:17.153][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:08:17.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.156][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:08:17.157][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:08:17.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.160][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:08:17.161][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:08:17.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.165][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:08:17.166][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:08:17.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.169][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:08:17.170][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:08:17.173][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:08:17.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.180][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:08:17.181][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:08:17.182][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:08:17.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.185][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:08:17.187][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.188][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-12 16:08:17.188][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.189][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:17.190][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.191][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.193][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.194][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:08:17.195][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:17.196][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.197][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:08:17.197][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:17.198][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.199][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.200][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:08:17.200][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:08:17.200][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:08:17.200][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:08:17.200][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:08:17.201][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:17.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:17.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.206][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.207][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:17.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:17.210][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.210][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.212][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:08:17.213][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.214][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:08:17.215][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.216][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:17.217][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.218][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.219][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.219][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.220][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:08:17.221][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:17.222][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.223][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:08:17.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:17.225][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.226][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.227][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:08:17.227][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:08:17.227][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:08:17.227][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:08:17.227][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:08:17.228][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:17.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.229][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.230][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:17.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.233][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.234][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.234][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:17.235][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:17.236][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.237][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.238][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:08:17.240][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.240][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-12 16:08:17.241][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:17.243][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.245][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.246][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.247][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:08:17.248][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:17.249][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.249][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:08:17.250][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:17.251][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.252][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.253][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.254][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:17.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.256][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:17.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.259][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.260][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.261][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:17.262][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:17.262][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.263][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.264][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:08:17.266][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.267][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:08:17.268][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.269][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:17.270][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.271][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.271][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.272][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.273][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:08:17.274][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:17.275][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.276][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:08:17.277][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:17.278][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.279][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.280][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:08:17.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:17.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.285][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.286][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.287][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:17.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:17.289][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.290][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.291][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:08:17.292][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.293][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[2024-10-12 16:08:17.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.316][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[2024-10-12 16:08:17.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.366][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:08:17.367][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:08:17.368][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:08:17.369][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:08:17.371][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:08:17.372][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:08:17.373][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:08:17.374][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:08:17.376][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:08:17.377][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:08:17.378][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:08:17.379][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:08:17.381][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:08:17.382][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:08:17.383][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:08:17.384][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:08:17.386][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:08:17.387][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:08:17.388][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:08:17.389][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:08:17.391][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:08:17.392][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:08:17.393][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:08:17.394][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:08:17.396][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:08:17.397][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:08:17.398][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:08:17.399][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:08:17.401][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:08:17.402][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:08:17.403][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:08:17.404][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:08:17.406][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:08:17.407][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:08:17.408][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:08:17.409][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:08:17.411][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:08:17.412][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:08:17.413][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:08:17.414][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:08:17.416][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:08:17.421][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:08:17.422][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:08:17.423][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:08:17.424][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:08:17.426][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:08:17.427][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:08:17.428][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:08:17.429][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:08:17.431][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:08:17.432][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:08:17.433][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:08:17.434][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:08:17.436][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:08:17.437][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:08:17.438][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:08:17.439][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:08:17.441][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:08:17.442][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:08:17.443][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:08:17.444][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:08:17.446][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:08:17.447][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:08:17.448][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:08:17.449][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:08:17.451][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:08:17.452][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:08:17.453][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:08:17.454][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:08:17.456][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:08:17.457][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:08:17.458][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:08:17.459][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:08:17.460][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:08:17.462][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:08:17.463][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:08:17.464][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:08:17.465][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:08:17.467][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:08:17.468][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:08:17.469][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:08:17.470][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:08:17.472][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:08:17.473][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:08:17.474][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:08:17.475][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:08:17.476][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.478][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.479][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[2024-10-12 16:08:17.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.490][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[2024-10-12 16:08:17.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.501][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[2024-10-12 16:08:17.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:08:17.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:08:17.580][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-10-12 16:08:17.581][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-10-12 16:08:17.583][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.583][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-10-12 16:08:17.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.585][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:08:17.586][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.587][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-10-12 16:08:17.588][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.589][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.590][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-10-12 16:08:17.591][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:08:17.592][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.592][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-10-12 16:08:17.593][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:08:17.594][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-10-12 16:08:17.594][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-10-12 16:08:17.594][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-10-12 16:08:17.594][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-10-12 16:08:17.594][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-10-12 16:08:17.594][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-10-12 16:08:17.594][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-10-12 16:08:17.595][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:08:17.596][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.597][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:08:17.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:08:17.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:08:17.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:08:17.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:08:17.603][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:08:17.603][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:08:17.603][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-10-12 16:08:17.603][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-10-12 16:08:17.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:08:17.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:08:17.606][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:08:17.607][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:08:17.608][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-10-12 16:08:17.610][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-10-12 16:08:17.611][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-10-12 16:08:17.612][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-10-12 16:08:17.614][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-10-12 16:08:17.615][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:08:17.616][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:08:17.617][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:08:17.618][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:08:17.619][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:08:17.620][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-10-12 16:08:17.621][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:08:17.622][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-10-12 16:08:17.623][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-10-12 16:08:17.624][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:08:17.625][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:08:17.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:08:17.626][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:08:17.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:08:17.628][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:08:17.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
>
> proc.time()
user system elapsed
4.118 0.228 4.334
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: OK
biodbNci.Rcheck/00install.out
* installing *source* package ‘biodbNci’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-example.cpp -o test-100-example.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)