Changes in version 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). Changes in version 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). Changes in version 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. Changes in version 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). Changes in version 0.39.2 (2022-10-31) Miscellaneous - Fix NEWS.md version formatting. Changes in version 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, ) integer vector. Changes in version 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. Changes in version 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). Changes in version 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. Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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. Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 0.27.1 (2019-08-19) Software Quality - Update decryption code to address unused result warning. Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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. Changes in version 0.23.1 (2018-07-18) Software Quality - ROBUSTNESS: Now registering native routines. Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 0.15.1 (2016-08-27) New Features - Now the package DLL is unloaded when the package is unloaded. Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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). Changes in version 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) Changes in version 0.11.1 (2015-07-29) - Updated the BiocViews field of DESCRIPTION. Changes in version 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). Changes in version 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). Changes in version 0.9.1 (2015-02-25) New Features - Modified code for reading encrypted idat files to cope with VeraCode data. Changes in version 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). Changes in version 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). Changes in version 0.7.2 (2014-10-02) - Now on GitHub. Changes in version 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. Changes in version 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). Changes in version 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). Changes in version 0.5.6 (2014-03-10) New Features - Added a CITATION file, cf. citation("illuminaio"). Changes in version 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. Changes in version 0.5.2 (2013-11-05) CODE REFACTORING: - Moved test data to IlluminaDataTestFiles. Software Quality - Added unit tests for encrypted IDATs. Changes in version 0.5.1 (2013-11-04) CODE REFACTORING: - Resshuffled internal code in readIDAT_nonenc() so that seek() is always forward based. Changes in version 0.5.0 (2013-10-14) - The version number was bumped for the Bioconductor devel version 2.14. Changes in version 0.4.0 (2013-10-14) - The version number was bumped for the Bioconductor release version 2.13. Changes in version 0.3.9 (2013-09-13) Documentation - Added vignette giving examples of usage and demonstrating comparison with GenomeStudio output. Changes in version 0.3.8 (2013-09-12) Software Quality - Bug fixes, renaming of readIDAT_bin() to readIDAT_nonenc(). Changes in version 0.3.6 (2013-08-21) New Features - Added one parent function readIDAT() which checks file format and dispatches to the relevant subfunction. Changes in version 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. Changes in version 0.3.0 (2013-04-03) - The version number was bumped for the Bioconductor devel version 2.13. Changes in version 0.2.0 (2013-04-03) - The version number was bumped for the Bioconductor release version 2.12. Changes in version 0.1.5 (2012-11-28) Documentation - Fixed typos in help for readBPM() and readIDAT(). Changes in version 0.1.4 (2012-11-27) New Features - Add/exporting readBPM(). Changes in version 0.1.3 (2012-11-12) Software Quality - Added system tests for readIDAT() on example files from the hapmap370k package. Changes in version 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. Changes in version 0.1.1 Software Quality - Added system tests for readIDAT() on example files from the minfiData package. Changes in version 0.1.0 (2012-10-09) Significant Changes - Package added to the Bioconductor repository. - Created.