Change history of package msa: ============================== Version 1.31.7: - changes of Version 1.31.6 undone (fix did not work on Mac OS) - update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17: added -std=c++14 Version 1.31.6: - update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17: added -D_HAS_AUTO_PTR_ETC=1 Version 1.31.5: - update of Muscle source code to avoid problems arising from compiling Muscle with C++ 17: renamed type 'byte' to 'MByte' Version 1.31.4: - updated src/Muscle/subfams.cpp to avoid conflicting definitions of INFINITY on some Mac systems Version 1.31.3: - updated config.sub and config.guess in source code of ClustalW and ClustalOmega to solve compilation issues on aarch64 (thanks to Yikun Jiang for contributing this fix!) Version 1.31.2: - msa() function changed such that it also works if the package is not attached to the workspace Version 1.31.1: - update of gc Version 1.31.0: - new branch for Bioconductor 3.17 devel Version 1.30.0: - release as part of Bioconductor 3.16 Version 1.29.3: - fix for possibly malformed inputs: all sequences are forced to uppercase characters (previously, ClustalW and ClustalOmega produced wrong results when called with lowercase sequences) Version 1.29.2: - fix in texshade.sty as suggested on TeXshade homepage at CTAN Version 1.29.1: - fix in argtable library (ClustalOmega) to avoid compilation errors on newest Mac OS Version 1.29.0: - new branch for Bioconductor 3.16 devel Version 1.28.0: - release as part of Bioconductor 3.15 Version 1.27.2: - applied patch to allow msa to work with the new Windows UCRT toolchain Version 1.27.1: - workaround for problems running texi2dvi() on R 4.2.0; those occurred during package checks when running some examples and the vignette code - updated URLs and DOIs (now requires R version >= 3.3.0) - fixed msaConvert() function to now work well with newer versions of the 'ape' package (now requires at least version 5.2) Version 1.27.0: - new branch for Bioconductor 3.15 devel Version 1.26.0: - release as part of Bioconductor 3.14 Version 1.25.3: - further changes to get rid of compiler warnings Version 1.25.2: - removed build/ directory from repo to avoid installation problems Version 1.25.1: - update of gc - minor changes to get rid of compiler warnings Version 1.25.0: - new branch for Bioconductor 3.14 devel Version 1.24.0: - release as part of Bioconductor 3.13 Version 1.23.1: - updated texshade.sty to newest version Version 1.23.0: - new branch for Bioconductor 3.13 devel Version 1.22.0: - release as part of Bioconductor 3.12 Version 1.21.1: - changed msaClustalW() examples to run smoothly on Windows with R 4.0.x - added warning to msaClustalW() help page regarding cluster="upgma" on Windows Version 1.21.0: - new branch for Bioconductor 3.12 devel Version 1.20.0: - release as part of Bioconductor 3.11 Version 1.19.0: - new branch for Bioconductor 3.11 devel Version 1.18.0: - release as part of Bioconductor 3.10 Version 1.17.2: - removed change history from package vignette for easier maintenance Version 1.17.1: - fixed regular expression to comply with PCRE2 - fixed Windows makefile for gc lib - fixed Windows cleanup script - fixed src/Makevars.win Version 1.17.0: - new branch for Bioconductor 3.10 devel Version 1.16.0: - release as part of Bioconductor 3.9 Version 1.15.0: - new branch for Bioconductor 3.9 devel Version 1.14.0: - release as part of Bioconductor 3.8 Version 1.13.0: - new branch for Bioconductor 3.8 devel Version 1.12.0: - release as part of Bioconductor 3.7 Version 1.11.1: - minor fix in ClustalW Version 1.11.2: - fix of code for using custom substitution matrices in ClustalW Version 1.11.0: - new branch for Bioconductor 3.7 devel Version 1.10.0: - release as part of Bioconductor 3.6 Version 1.9.0: - new branch for Bioconductor 3.6 devel Version 1.8.0: - release as part of Bioconductor 3.5 Version 1.7.2: - fix for new clang 4 compiler on Mac OS Version 1.7.1: - additional conversions implemented for msaConvert() function - added a new method msaConsensusSequence() that extends the functionality provided by Biostring's consensusString() method - added a new method msaConservationScore() - print() method extended such that it now also allows for customization of the consensus sequence (via the new msaConsensusSequence() method) - package now depends on Biostrings version >= 2.40.0 in order to make sure that consensusMatrix() also works correctly for masked alignments - corresponding changes in documentation and vignette Version 1.7.0: - new branch for Bioconductor 3.5 devel Version 1.6.0: - release as part of Bioconductor 3.4 Version 1.5.5: - fixes in ClustalOmega source code to ensure Windows compatibility of GCC6 compatibility fix Version 1.5.4: - bug fix in msaClustalW(): unsupported parameter 'tree' deactivated - fixes in ClustalOmega source code to ensure GCC6 compatibility - fix in msaConvert() function to improve safety of call to suggested package 'phangorn' Version 1.5.3: - additional conversions implemented for msaConvert() function - corresponding changes in documentation Versions 1.5.1 / 1.5.2: - version number bumps for technical reasons related to Bioconductor build servers Version 1.5.0: - new branch for Bioconductor 3.4 devel Version 1.4.0: - release as part of Bioconductor 3.3 Version 1.3.7: - fixes in msaPrettyPrint() function Version 1.3.6: - msaPrettyPrint() now also accepts dashes in file names - added section about pretty-printing wide alignments to package vignette Version 1.3.5: - adaptation of displaying help text by msa() function Version 1.3.4: - added function for checking and fixing sequence names for possibly problematic characters that could lead to LaTeX errors when using msaPrettyPrint() - corresponding changes in documentation - minor namespace fix Version 1.3.3: - added function for converting multiple sequence alignments for use with other sequence alignment packages - corresponding changes in documentation Version 1.3.2: - further fixes in Makefiles and Makevars files to account for changes in build system - update of citation information Version 1.3.1: - fixes in Makefiles and Makevars files to account for changes in build system Version 1.3.0: - new branch for Bioconductor 3.3 devel Version 1.2.0: - release as part of Bioconductor 3.2 Version 1.1.3: - bug fix related to custom substitution matrices in the MUSCLE interface - correction and updates of documentation Version 1.1.2: - new print() function for multiple alignments that also allows for displaying alignments in their entirety (plus additional customizations) - strongly improved handling of custom substitution matrices by msaClustalW(): now custom matrices can also be supplied for nucleotide sequences which can also be passed via the 'substitutionMatrix' argument. The 'dnamatrix' argument is still available for the sake of backwards compatibility. - strongly improved handling of custom substitution matrices by msaMuscle() - fix of improperly aligned sequence logos produced by msaPrettyPrint() - updated citation information Version 1.1.1: - fix of msa() function Version 1.1.0: - new branch for Bioconductor 3.2 devel Version 1.0.0: - first official release as part of Bioconductor 3.1