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NEWS
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NEWS
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Changes in version 1.6.1 (2022-11-22)
+ Upgrade deprecated methods.
+ Remove R_front script.
Changes in version 1.3.3 (2022-04-02)
+ Explain how to use custom CSV file in vignette.
Changes in version 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.
Changes in version 1.3.1 (2021-12-10)
+ Remove custom cache folder setting in vignette.
Changes in version 1.1.17 (2021-10-22)
+ Correct running of long tests.
Changes in version 1.1.16 (2021-10-19)
+ Update documentation.
+ Add ORCID for Alexis.
Changes in version 1.1.15 (2021-10-18)
+ Correct getUrlContent() to handle binary files.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 1.1.11 (2021-10-07)
+ Decompose test test.collapseRows() because of error on Bioconductor not reproduced on local computer.
Changes in version 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.
Changes in version 1.1.9 (2021-09-28)
+ Correct handling of wrong URL with base::url().
Changes in version 1.1.8 (2021-09-28)
+ Correct bug of UniProt request on Windows.
Changes in version 1.1.7 (2021-09-23)
+ Ignore build folder when building package.
+ Update documentation.
+ Correct setting of R_ENVIRON_USER when building.
Changes in version 1.1.6 (2021-09-14)
+ Update documentation.
Changes in version 1.1.5 (2021-09-13)
+ Correct bug in return type of BiodbRequestScheduler::sendRequest().
+ Correct encoding of test reference filenames.
Changes in version 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.
Changes in version 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().
Changes in version 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.
Changes in version 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.
Changes in version 1.0.4 (2021-06-09)
+ Bug fix: correct call to logger in BiodbPersitentCache class.
Changes in version 1.0.3 (2021-05-26)
+ Bug fix: correct generic test of searchForEntries(), allowing testing with NA
value.
Changes in version 1.0.2 (2021-05-23)
+ 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)
+ Bug fix: correct some calls to logging functions that raised a warning.
Changes in version 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.
Changes in version 0.99.10 (2021-05-07)
+ Correct documentation of C++ function.
Changes in version 0.99.9 (2021-05-07)
+ Solving some NOTES from BiocCheck.
+ Correct example in Progress class.
Changes in version 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".
Changes in version 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.
Changes in version 0.99.6 (2021-04-27)
+ Rebuilding doc.
Changes in version 0.99.5 (2021-04-27)
+ Add missing parameters documentation for runGenericTests().
Changes in version 0.99.4 (2021-04-27)
+ Move long tests to separate directory "long".
Changes in version 0.99.3 (2021-04-27)
+ Added "biodb" as watched tag on my profile on support site
https://support.bioconductor.org/.
Changes in version 0.99.2 (2021-04-27)
+ Switch to MassBank extract for testing MassCsvFile and MassSqlite connectors.
Changes in version 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.
Changes in version 0.99.0 (2021-04-22)
+ Submitted to Bioconductor