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removed change history from vignette; version number bumped to 1.17.2

UBodenhofer authored on 18/10/2019 13:53:51
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@@ -1,8 +1,8 @@
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.17.1
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-Date: 2019-09-12
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+Version: 1.17.2
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+Date: 2019-10-17
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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@@ -4,7 +4,10 @@ Change history of package msa:
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 Version 1.18.0:
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 - release as part of Bioconductor 3.10
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-Version 1.7.1:
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+Version 1.17.2:
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+- removed change history from package vignette for easier maintenance
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+
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+Version 1.17.1:
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 - fixed regular expression to comply with PCRE2
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 - fixed Windows makefile for gc lib
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 - fixed Windows cleanup script
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@@ -6,12 +6,12 @@
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 \hypersetup{colorlinks=false,
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     pdfborder=0 0 0,
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     pdftitle={msa - An R Package for Multiple Sequence Alignment},
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-    pdfauthor={Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer}}
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+    pdfauthor={Enrico Bonatesta, Christoph Kainrath, and Ulrich Bodenhofer}}
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 \usepackage[OT1]{fontenc}
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 \title{{\Huge msa}\\[5mm] An R Package for Multiple Sequence Alignment}
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-\author{Enrico Bonatesta, Christoph Horej\v{s}-Kainrath, and Ulrich Bodenhofer}
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+\author{Enrico Bonatesta, Christoph Kainrath, and Ulrich Bodenhofer}
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 \affiliation{Institute of Bioinformatics, Johannes Kepler University
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 Linz\\Altenberger Str. 69, 4040 Linz, Austria\\
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 \email{msa@bioinf.jku.at}}
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@@ -887,126 +887,6 @@ Moreover, we insist that, any time you cite the package, you also cite
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 the original paper in which the original algorithm has been introduced (see
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 bibliography below).
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-\section{Change Log}
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-
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-\begin{description}
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-\item[Version 1.18.0:] release as part of Bioconductor 3.10
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-\item[Version 1.17.1:] \mbox{ }  \begin{itemize}
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-   \item fixed regular expression to comply with PCRE2
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-   \item fixed Windows makefile for gc lib
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-   \item fixed Windows cleanup script
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-   \item fixed\verb+ src/Makevars.win+
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-  \end{itemize}
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-\item[Version 1.17.0:] new branch for Bioconductor 3.10 devel
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-\item[Version 1.16.0:] release as part of Bioconductor 3.9
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-\item[Version 1.15.0:] new branch for Bioconductor 3.9 devel
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-\item[Version 1.14.0:] release as part of Bioconductor 3.8
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-\item[Version 1.13.0:] new branch for Bioconductor 3.8 devel
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-\item[Version 1.12.0:] release as part of Bioconductor 3.7
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-\item[Version 1.11.2:] \mbox{ }  \begin{itemize}
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-   \item minor fix in ClustalW
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-  \end{itemize}
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-\item[Version 1.11.1:] \mbox{ }  \begin{itemize}
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-   \item fix of code for using custom substitution matrices in ClustalW
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-  \end{itemize}
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-\item[Version 1.11.0:] new branch for Bioconductor 3.7 devel
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-\item[Version 1.10.0:] release as part of Bioconductor 3.56
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-\item[Version 1.9.0:] new branch for Bioconductor 3.6 devel
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-\item[Version 1.8.0:] release as part of Bioconductor 3.5
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-\item[Version 1.7.2:] \mbox{ }  \begin{itemize}
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-   \item fix for new \verb+clang+ 4 compiler on Mac OS
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-  \end{itemize}
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-\item[Version 1.7.1:] \mbox{ }  \begin{itemize}
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-   \item additional conversions implemented for \verb+msaConvert()+ function
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-   \item added a new method \verb+msaConsensusSequence()+ that extends the
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-     functionality provided by \verb+Biostring+'s \verb+consensusString()+ method
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-   \item added a new method \verb+msaConservationScore()+
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-   \item \verb+print()+ method extended such that it now also allows for
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-     customization of the consensus sequence (via the new
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-     \verb+msaConsensusSequence()+ method)
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-   \item package now depends on \verb+Biostrings+ version $\geq$2.40.0 in order
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-     to make sure that \verb+consensusMatrix()+ also works correctly
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-     for masked alignments
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-   \item corresponding changes in documentation and vignette
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-  \end{itemize}
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-\item[Version 1.7.0:] new branch for Bioconductor 3.5 devel
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-\item[Version 1.6.0:] release as part of Bioconductor 3.4
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-\item[Version 1.5.5:] \mbox{ }  \begin{itemize}
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-   \item fixes in ClustalOmega source code to ensure Windows compatibility of
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-   GCC6 compatibility fix
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-   \end{itemize}
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-\item[Version 1.5.4:] \mbox{ }  \begin{itemize}
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-   \item bug fix in \verb+msaClustalW()+: unsupported parameter `\verb+tree+' deactivated
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-   \item fixes in ClustalOmega source code to ensure GCC 6 compatibility
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-   \item fix in \verb+msaConvert()+ function to improve safety of call to suggested
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-  package \verb+phangorn+
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-  \end{itemize}
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-\item[Version 1.5.3:] \mbox{ }  \begin{itemize}
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-   \item additional conversions implemented for \verb+msaConvert()+ function
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-   \item corresponding changes in documentation
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-  \end{itemize}
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-\item[Versions 1.5.1 and 1.5.2:] version number bumps for technical reasons
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-  related to Bioconductor build servers
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-\item[Version 1.5.0:] new branch for Bioconductor 3.4 devel
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-\item[Version 1.4.0:] release as part of Bioconductor 3.3
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-\item[Version 1.3.7:] \mbox{ }  \begin{itemize}
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-   \item fixes in \verb+msaPrettyPrint()+ function
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-  \end{itemize}
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-\item[Version 1.3.6:] \mbox) { }  \begin{itemize}
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-   \item \verb+msaPrettyPrint()+ now also accepts dashes in file names
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-   \item added section about pretty-printing wide alignments to package vignette
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-  \end{itemize}
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-\item[Version 1.3.5:] \mbox{ }  \begin{itemize}
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-   \item adaptation of displaying help text by \verb+msa()+ function
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-  \end{itemize}
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-\item[Version 1.3.4:] \mbox{ }  \begin{itemize}
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-   \item added function for checking and fixing sequence names for
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-     possibly problematic characters that could lead to \LaTeX\ errors
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-     when using \verb+msaPrettyPrint()+
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-   \item corresponding changes in documentation
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-   \item minor namespace fix
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-  \end{itemize}
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-\item[Version 1.3.3:] \mbox{ }  \begin{itemize}
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-   \item added function for converting multiple sequence alignments for
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-     use with other sequence alignment packages
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-   \item corresponding changes in documentation
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-  \end{itemize}
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-\item[Version 1.3.2:] \mbox{ }  \begin{itemize}
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-   \item further fixes in Makefiles and Makevars files to account for changes in build system
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-   \item update of citation information
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-  \end{itemize}
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-\item[Version 1.3.1:] \mbox{ }  \begin{itemize}
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-   \item fixes in Makefiles and Makevars files to account for changes in build system
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-  \end{itemize}
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-\item[Version 1.3.0:] new branch for Bioconductor 3.3 devel
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-\item[Version 1.2.0:] release as part of Bioconductor 3.2
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-\item[Version 1.1.3:] \mbox{ }  \begin{itemize}
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-    \item bug fix related to custom substitution matrices
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-      in the MUSCLE interface
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-    \item corrections and updates of documentation
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-  \end{itemize}
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-\item[Version 1.1.2:] \mbox{ }  \begin{itemize}
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-    \item new \verb+print()+ function for multiple alignments that also
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-      allows for displaying alignments in their entirety (plus additional
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-      customizations)
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-    \item strongly improved handling of custom substitution matrices by
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-      \verb+msaClustalW()+: now custom matrices can also be supplied for nucleotide
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-      sequences which can also be passed via the \verb+substitutionMatrix+ argument.
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-      The \verb+dnamatrix+ argument is still available for the sake of backwards
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-      compatibility.
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-    \item strongly improved handling of custom substitution matrices by
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-      \verb+msaMuscle()+
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-    \item fix of improperly aligned sequence logos produced by
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-      \verb+msaPrettyPrint()+
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-    \item updated citation information
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-  \end{itemize}
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-\item[Version 1.1.1:]  \mbox{ }  \begin{itemize}
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-    \item fix of \verb+msa()+ function
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-  \end{itemize}
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-\item[Version 1.1.0:] new branch for Bioconductor 3.2 devel
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-\item[Version 1.0.0:] first official release as part of Bioconductor 3.1
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-\end{description}
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-
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 \bibliographystyle{plain}
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 \bibliography{lit}
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