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bug fixes; version number bumped to 1.20.1

UBodenhofer authored on 01/09/2020 08:26:45
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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: 1.20.0
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-Date: 2019-10-17
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+Version: 1.20.1
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+Date: 2020-09-01
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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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 Change history of package msa:
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 ==============================
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+Version 1.20.1:
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+- changed msaClustalW() examples to run smoothly on Windows with R 4.0.x
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+- added warning to msaClustalW() help page regarding cluster="upgma" on
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+  Windows
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+
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+Version 1.20.0:
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+- release as part of Bioconductor 3.11
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+
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+Version 1.19.0:
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+- new branch for Bioconductor 3.11 devel
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+
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 Version 1.18.0:
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 - release as part of Bioconductor 3.10
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@@ -19,7 +19,9 @@
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   \item{cluster}{The clustering method which should be used.
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     Possible values are \code{"nj"} (default) and \code{"upgma"}.
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     In the original ClustalW implementation, this parameter is called 
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-    \code{clustering}.}
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+    \code{clustering}. Please note that \code{cluster="upgma"} leads
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+    to an unidentified error on Windows with R 4.0.x that even crashes
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+    the entire R session.}
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   \item{gapOpening}{gap opening penalty; the default value for
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     nucleotide sequences is 15.0, the default value for 
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     amino acid sequences is 10.0.}
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@@ -111,6 +113,6 @@ msaClustalW(mySeqs)
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 ## call msaClustalW with custom parameters
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 msaClustalW(mySeqs, gapOpening=1, gapExtension=1, maxiters=16,
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-            cluster="upgma", kimura=FALSE, order="input", maxdiv=23)
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+            kimura=FALSE, order="input", maxdiv=23)
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 }
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 \keyword{manip}
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@@ -1630,7 +1630,7 @@ bool SubMatrix::commentline(char* line)
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  * @param temp 
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  * @param name 
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  */
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-void SubMatrix::printInFormat(vector<short>& temp, char* name)
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+void SubMatrix::printInFormat(vector<short>& temp, const char* name)
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 {
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     char nameOfFile[30];
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     strcpy(nameOfFile, name);
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@@ -1693,7 +1693,7 @@ void SubMatrix::printInFormat(vector<short>& temp, char* name)
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  * @param temp 
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  * @param name 
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  */
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-void SubMatrix::printVectorToFile(vector<short>& temp, char* name)
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+void SubMatrix::printVectorToFile(vector<short>& temp, const char* name)
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 {
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     char nameOfFile[30];
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     strcpy(nameOfFile, name);
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@@ -103,8 +103,8 @@ class SubMatrix
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         // The functions below are purely for testing purposes.
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         void printGetMatrixResults(int mat[NUMRES][NUMRES]); 
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         void compareMatrices(int mat1[NUMRES][NUMRES], int mat2[NUMRES][NUMRES]); 
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-        void printInFormat(vector<short>& temp, char* name = "tempfile.out");
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-        void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
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+        void printInFormat(vector<short>& temp, const char* name = "tempfile.out");
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+        void printVectorToFile(vector<short>& temp, const char* name = "tempfile.out");
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         Matrix* getUserMatAddress(int alignResidueType, int alignType);
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         Xref* getUserXrefAddress(int alignResidueType, int alignType);
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         void checkResidueAndAlignType(int alignResidueType, int alignType);