Changes in version 1.3.3 (2022-04-02) o Explain how to use custom CSV file in vignette. Changes in version 1.3.2 (2022-03-11) o Correct ext pkg upgrade: do not generate C++ example files again. o Change default vignette name to package name. o When upgrading a extension package, do not generate C++ files again. o Accept an unknown total in Progress class. o isSearchableByField() accepts field.type param now. Changes in version 1.3.1 (2021-12-10) o Remove custom cache folder setting in vignette. Changes in version 1.1.17 (2021-10-22) o Correct running of long tests. Changes in version 1.1.16 (2021-10-19) o Update documentation. o Add ORCID for Alexis. Changes in version 1.1.15 (2021-10-18) o Correct getUrlContent() to handle binary files. Changes in version 1.1.14 (2021-10-17) o Factorize RCurl calls into global functions. o Disable warnings in calls to readLines() when using base::url(). o Catch errors when trying to set locale. o Correct some tests. Changes in version 1.1.13 (2021-10-12) o Make custom persistent the cache the default, following slowness with BiocFileCache in biodbHmdb. o Remove useless bib refs in vignettes/references.bib. o Add session info in vignettes. o Add ORCID, URL and BugReports. o Add an install section in main vignette. Changes in version 1.1.12 (2021-10-09) o Switch back to custom implementation of persistent cache, following errors with BiocFileCache on Windows and also slowness with HMDB. Changes in version 1.1.11 (2021-10-07) o Decompose test test.collapseRows() because of error on Bioconductor not reproduced on local computer. Changes in version 1.1.10 (2021-09-30) o Disable UniProt request test: it fails (result is NA) for reason unknown only on Bioconductor Linux server during "R CMD check". Works fine on local computer. Changes in version 1.1.9 (2021-09-28) o Correct handling of wrong URL with base::url(). Changes in version 1.1.8 (2021-09-28) o Correct bug of UniProt request on Windows. Changes in version 1.1.7 (2021-09-23) o Ignore build folder when building package. o Update documentation. o Correct setting of R_ENVIRON_USER when building. Changes in version 1.1.6 (2021-09-14) o Update documentation. Changes in version 1.1.5 (2021-09-13) o Correct bug in return type of BiodbRequestScheduler::sendRequest(). o Correct encoding of test reference filenames. Changes in version 1.1.4 (2021-09-12) o Allow to set the test reference folder directly into runGenericTests(). This is now necessary for running generic tests in extension packages. Changes in version 1.1.3 (2021-09-12) o Set package name when calling runGenericTests() in order to find test ref files the correct way, by calling system.file(). Changes in version 1.1.2 (2021-09-09) o Use BiocFileCache for the persistent cache system. o Switch to R6. o Define do...() private methods to be redefined in subclasses, instead of redefining public methods defined inside super class. o Use now local entry files for testing parsing of entry fields. Changes in version 1.1.1 (2021-06-10) o Allow skipping of some fields when testing searchForEntries(). o Move test reference entries folder from tests/testthat/res to inst/testref. o Move long tests folder from tests/long to longtests and enable Bioconductor long tests. Changes in version 1.0.4 (2021-06-09) o Bug fix: correct call to logger in BiodbPersitentCache class. Changes in version 1.0.3 (2021-05-26) o Bug fix: correct generic test of searchForEntries(), allowing testing with NA value. Changes in version 1.0.2 (2021-05-23) o Bug fix: correct return type of searchForEntries(), which now returns always a character vector and never NULL. Changes in version 1.0.1 (2021-05-20) o Bug fix: correct some calls to logging functions that raised a warning. Changes in version 0.99.11 (2021-05-17) o Change example inside BiodbConfig to avoid misinterpretation of `set('cache.directory', '~/my.biodb.cache')`, leading to believe that some files are written inside USER HOME folder when running the example. Changes in version 0.99.10 (2021-05-07) o Correct documentation of C++ function. Changes in version 0.99.9 (2021-05-07) o Solving some NOTES from BiocCheck. o Correct example in Progress class. Changes in version 0.99.8 (2021-05-06) o Correct template travis.yml for extensions: missing deps install, run all checks. o Improve template Makefile for extensions. o Add missing test-cpp.R template file for running C++ tests from testthat. o Limit by default the entries to test to one entry inside generic tests. o Improve vignettes. o Rename default vignette into "biodb.Rmd". Changes in version 0.99.7 (2021-04-27) o Renamed Biodb class into BiodbMain in order to avoid "Rd warning: Previous alias or file overwritten by alias: biodb" on Windows platform. o Implement newInst() global function for creating new BiodbMain instance. Changes in version 0.99.6 (2021-04-27) o Rebuilding doc. Changes in version 0.99.5 (2021-04-27) o Add missing parameters documentation for runGenericTests(). Changes in version 0.99.4 (2021-04-27) o Move long tests to separate directory "long". Changes in version 0.99.3 (2021-04-27) o Added "biodb" as watched tag on my profile on support site https://support.bioconductor.org/. Changes in version 0.99.2 (2021-04-27) o Switch to MassBank extract for testing MassCsvFile and MassSqlite connectors. Changes in version 0.99.1 (2021-04-26) o Remove Git files refused by BiocCheckGitClone. o Use CHECK_RENVIRON in local tests. o Correct condition in BiodbEntryFields::getRealName() that did not pass check. o Add all doc files man/*.Rd for BiocCheck run on http://bioconductor.org. Changes in version 0.99.0 (2021-04-22) o Submitted to Bioconductor