NEWS

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illuminaio 0.43.0 (2023-04-25)

Notes

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.18 for R (>= 4.4.0).

illuminaio 0.42.0 (2023-04-25)

Notes

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0).

illuminaio 0.41.0 (2022-11-01)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.17 for R-devel.

illuminaio 0.40.0 (2022-11-01)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.16 for R (>= 4.2.2).

illuminaio 0.39.2 (2022-10-31)

Miscellaneous

• Fix NEWS.md version formatting.

illuminaio 0.39.1 (2022-09-23)

Bug Fixes

• readIDAT() would only return the first five Unknown.N fields. Additional ones would be dropped.

• readIDAT() could produce Warning message: In readChar(con, nchars = n) : truncating string with embedded nuls if the IDAT file had an Unknown.6 field. Until we know what that field represents, it is parsed as an (nbytes, <byte sequence>) integer vector.

illuminaio 0.39.0 (2022-04-26)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.16 for R-devel.

illuminaio 0.38.0 (2022-04-26)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.15 for R (>= 4.2.0).

illuminaio 0.37.0 (2021-10-27)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.15 for R-devel.

illuminaio 0.36.0 (2021-10-27)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.14 for R (>= 4.1.1).

illuminaio 0.34.0 (2021-05-19)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.13 for R (>= 4.0.3).

illuminaio 0.32.0 (2020-10-27)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.12 for R (>= 4.0.0).

illuminaio 0.31.1 (2020-07-15)

Updates

• Error messages produced by readIDAT() when failing decrypt no longer appends an extra newline at the end.

• readIDAT() uses explicit stringsAsFactors = FALSE internally.

• readIDAT() no longer keeps two file connections open at the same.

Documentation

• The BibTeX URL reported by citation(package = "illuminaio") was broken.

Bug Fixes

• readBGX() would leave an open connection if there was a file-reading error.

illuminaio 0.31.0 (2020-04-27)

• The version number was bumped for the Bioconductor develop version, which is now Bioconductor 3.12 for R (>= 4.0.0).

illuminaio 0.30.0 (2020-04-27)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.11 for R (>= 4.0.0).

illuminaio 0.28.0 (2019-10-29)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.10 for R (>= 3.6.1).

illuminaio 0.27.1 (2019-08-19)

Software Quality

• Update decryption code to address unused result warning.

illuminaio 0.27.0 (2019-05-02)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.10 for R (>= 3.6.0).

illuminaio 0.26.0 (2019-05-02)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.9 for R (>= 3.6.0).

illuminaio 0.25.0 (2018-10-30)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.9 for R (>= 3.6.0).

illuminaio 0.24.0 (2018-10-30)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.8 for R (>= 3.5.1).

illuminaio 0.23.2 (2018-07-18)

New Features

• The readIDAT() function gains a what argument (only for unencrypted IDAT files). This allows the fast return of the number of nSNPsRead (number of probes in file) and IlluminaID (probenames). This is to allow fast handling of IDAT files in the minfi package.

illuminaio 0.23.1 (2018-07-18)

Software Quality

• ROBUSTNESS: Now registering native routines.

illuminaio 0.23.0 (2018-05-01)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.8 for R (>= 3.5.0).

illuminaio 0.22.0 (2017-05-01)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.7 for R (>= 3.5.0).

illuminaio 0.21.0 (2017-10-31)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.7 for R (>= 3.5.0).

illuminaio 0.20.0 (2017-10-31)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.6 for R (>= 3.4.0).

illuminaio 0.19.0 (2017-04-25)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.6 for R (>= 3.4.0).

illuminaio 0.18.0 (2017-04-25)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.5 for R (>= 3.4.0).

illuminaio 0.17.0 (2016-10-18)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.5 for R (>= 3.4.0).

illuminaio 0.16.0 (2016-10-18)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.4 for R (>= 3.3.1).

illuminaio 0.15.1 (2016-08-27)

New Features

• Now the package DLL is unloaded when the package is unloaded.

illuminaio 0.15.0 (2015-05-03)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.4 for R (>= 3.3.0).

illuminaio 0.14.0 (2015-05-03)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.3 for R (>= 3.3.0).

illuminaio 0.13.1 (2016-01-12)

Deprecated and Defunct

• readBPM() is deprecated because it was only a stub that never really worked (Issues #5 and #6).

illuminaio 0.13.0 (2015-10-23)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.3 for R (>= 3.3.0).

illuminaio 0.12.0 (2015-10-13)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.2 for R (>= 3.2.2).

illuminaio 0.11.2 (2015-09-11)

Bug Fixes

• readIDAT() can now read non-encrypted IDAT files with strings longer than 127 characters.

• readIDAT() incorrectly assumed that there were exactly two blocks in RunInfo fields of non-encrypted (v3) IDAT files. Thanks to Gordon Bean (GitHub @brazilbean) for reporting on and contributing with code for the above two bugs. (Issue #2)

illuminaio 0.11.1 (2015-07-29)

• Updated the BiocViews field of DESCRIPTION.

illuminaio 0.11.0 (2015-04-16)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.2 for R (>= 3.3.0).

illuminaio 0.10.0 (2015-04-16)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.1 for R (>= 3.2.0).

illuminaio 0.9.1 (2015-02-25)

New Features

• Modified code for reading encrypted idat files to cope with VeraCode data.

illuminaio 0.9.0 (2014-10-13)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.1 for R (>= 3.2.0).

illuminaio 0.8.0 (2014-10-13)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.0 for R (>= 3.1.1).

illuminaio 0.7.2 (2014-10-02)

• Now on GitHub.

illuminaio 0.7.1 (2014-09-21)

Code Refactoring

• The vignette now reads the GenomeStudio example file from the IlluminaDataTestFiles package instead of the internet.

• Updated CITATION.

Documentation

• Added citation to vignette.

illuminaio 0.7.0 (2014-04-11)

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 2.15 for R (>= 3.1.0).

illuminaio 0.6.0 (2014-04-11)

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 2.14 for R (>= 3.1.0).

illuminaio 0.5.6 (2014-03-10)

New Features

• Added a CITATION file, cf. citation("illuminaio").

illuminaio 0.5.5 (2014-01-19)

• Added support for encrypted IDAT files where not all data fields are of the same length, e.g. HumanHap550 v1.

illuminaio 0.5.2 (2013-11-05)

CODE REFACTORING:

• Moved test data to IlluminaDataTestFiles.

Software Quality

• Added unit tests for encrypted IDATs.

illuminaio 0.5.1 (2013-11-04)

CODE REFACTORING:

• Resshuffled internal code in readIDAT_nonenc() so that seek() is always forward based.

illuminaio 0.5.0 (2013-10-14)

• The version number was bumped for the Bioconductor devel version 2.14.

illuminaio 0.4.0 (2013-10-14)

• The version number was bumped for the Bioconductor release version 2.13.

illuminaio 0.3.9 (2013-09-13)

Documentation

• Added vignette giving examples of usage and demonstrating comparison with GenomeStudio output.

illuminaio 0.3.8 (2013-09-12)

Software Quality

• Bug fixes, renaming of readIDAT_bin() to readIDAT_nonenc().

illuminaio 0.3.6 (2013-08-21)

New Features

• Added one parent function readIDAT() which checks file format and dispatches to the relevant subfunction.

illuminaio 0.3.5 (2013-08-02)

Code Refactoring

• Cleaned up internal code of readBPM().

Software Quality

• ROBUSTNESS: Added unit tests for readBPM(). Note that these are only run if environment variable _R_CHECK_FULL_ is set, i.e. they will not be performed on the Bioconductor servers.

illuminaio 0.3.0 (2013-04-03)

• The version number was bumped for the Bioconductor devel version 2.13.

illuminaio 0.2.0 (2013-04-03)

• The version number was bumped for the Bioconductor release version 2.12.

illuminaio 0.1.5 (2012-11-28)

Documentation

• Fixed typos in help for readBPM() and readIDAT().

illuminaio 0.1.4 (2012-11-27)

New Features

• Add/exporting readBPM().

illuminaio 0.1.3 (2012-11-12)

Software Quality

• Added system tests for readIDAT() on example files from the hapmap370k package.

illuminaio 0.1.2 (2012-11-07)

Bug Fixes

• readIDAT() would not close connections it opened if there was an error. Now it guarantees to close any connections it opens.

illuminaio 0.1.1

Software Quality

• Added system tests for readIDAT() on example files from the minfiData package.

illuminaio 0.1.0 (2012-10-09)

Significant Changes

• Package added to the Bioconductor repository.

• Created.