NEWS

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biodb 1.3.3 (2022-04-02)

• Explain how to use custom CSV file in vignette.

biodb 1.3.2 (2022-03-11)

• Correct ext pkg upgrade: do not generate C++ example files again.
• Change default vignette name to package name.
• When upgrading a extension package, do not generate C++ files again.
• Accept an unknown total in Progress class.
• isSearchableByField() accepts field.type param now.

biodb 1.3.1 (2021-12-10)

• Remove custom cache folder setting in vignette.

biodb 1.1.17 (2021-10-22)

• Correct running of long tests.

biodb 1.1.16 (2021-10-19)

• Update documentation.
• Add ORCID for Alexis.

biodb 1.1.15 (2021-10-18)

• Correct getUrlContent() to handle binary files.

biodb 1.1.14 (2021-10-17)

• Factorize RCurl calls into global functions.
• Disable warnings in calls to readLines() when using base::url().
• Catch errors when trying to set locale.
• Correct some tests.

biodb 1.1.13 (2021-10-12)

• Make custom persistent the cache the default, following slowness with BiocFileCache in biodbHmdb.
• Remove useless bib refs in vignettes/references.bib.
• Add session info in vignettes.
• Add ORCID, URL and BugReports.
• Add an install section in main vignette.

biodb 1.1.12 (2021-10-09)

• Switch back to custom implementation of persistent cache, following errors with BiocFileCache on Windows and also slowness with HMDB.

biodb 1.1.11 (2021-10-07)

• Decompose test test.collapseRows() because of error on Bioconductor not reproduced on local computer.

biodb 1.1.10 (2021-09-30)

• 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.

biodb 1.1.9 (2021-09-28)

• Correct handling of wrong URL with base::url().

biodb 1.1.8 (2021-09-28)

• Correct bug of UniProt request on Windows.

biodb 1.1.7 (2021-09-23)

• Ignore build folder when building package.
• Update documentation.
• Correct setting of R_ENVIRON_USER when building.

biodb 1.1.6 (2021-09-14)

• Update documentation.

biodb 1.1.5 (2021-09-13)

• Correct bug in return type of BiodbRequestScheduler::sendRequest().
• Correct encoding of test reference filenames.

biodb 1.1.4 (2021-09-12)

• Allow to set the test reference folder directly into runGenericTests(). This is now necessary for running generic tests in extension packages.

biodb 1.1.3 (2021-09-12)

• Set package name when calling runGenericTests() in order to find test ref files the correct way, by calling system.file().

biodb 1.1.2 (2021-09-09)

• Use BiocFileCache for the persistent cache system.
• Switch to R6.
• Define do...() private methods to be redefined in subclasses, instead of redefining public methods defined inside super class.
• Use now local entry files for testing parsing of entry fields.

biodb 1.1.1 (2021-06-10)

• Allow skipping of some fields when testing searchForEntries().
• Move test reference entries folder from tests/testthat/res to inst/testref.
• Move long tests folder from tests/long to longtests and enable Bioconductor long tests.

biodb 1.0.4 (2021-06-09)

• Bug fix: correct call to logger in BiodbPersitentCache class.

biodb 1.0.3 (2021-05-26)

• Bug fix: correct generic test of searchForEntries(), allowing testing with NA value.

biodb 1.0.2 (2021-05-23)

• Bug fix: correct return type of searchForEntries(), which now returns always a character vector and never NULL.

biodb 1.0.1 (2021-05-20)

• Bug fix: correct some calls to logging functions that raised a warning.

biodb 0.99.11 (2021-05-17)

• 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.

biodb 0.99.10 (2021-05-07)

• Correct documentation of C++ function.

biodb 0.99.9 (2021-05-07)

• Solving some NOTES from BiocCheck.
• Correct example in Progress class.

biodb 0.99.8 (2021-05-06)

• Correct template travis.yml for extensions: missing deps install, run all checks.
• Improve template Makefile for extensions.
• Add missing test-cpp.R template file for running C++ tests from testthat.
• Limit by default the entries to test to one entry inside generic tests.
• Improve vignettes.
• Rename default vignette into "biodb.Rmd".

biodb 0.99.7 (2021-04-27)

• Renamed Biodb class into BiodbMain in order to avoid "Rd warning: Previous alias or file overwritten by alias: biodb" on Windows platform.
• Implement newInst() global function for creating new BiodbMain instance.

biodb 0.99.6 (2021-04-27)

• Rebuilding doc.

biodb 0.99.5 (2021-04-27)

• Add missing parameters documentation for runGenericTests().

biodb 0.99.4 (2021-04-27)

• Move long tests to separate directory "long".

biodb 0.99.3 (2021-04-27)

• Added "biodb" as watched tag on my profile on support site https://support.bioconductor.org/.

biodb 0.99.2 (2021-04-27)

• Switch to MassBank extract for testing MassCsvFile and MassSqlite connectors.

biodb 0.99.1 (2021-04-26)

• Remove Git files refused by BiocCheckGitClone.
• Use CHECK_RENVIRON in local tests.
• Correct condition in BiodbEntryFields::getRealName() that did not pass check.
• Add all doc files man/*.Rd for BiocCheck run on http://bioconductor.org.

biodb 0.99.0 (2021-04-22)

• Submitted to Bioconductor