@@ -1,8 +1,8 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.21.0

-Date: 2019-10-17

+Version: 1.21.1

+Date: 2020-08-12

 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer

 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

 Description: The 'msa' package provides a unified R/Bioconductor interface to

@@ -1,6 +1,20 @@

 Change history of package msa:

 ==============================

+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

@@ -19,7 +19,9 @@

   \item{cluster}{The clustering method which should be used.

     Possible values are \code{"nj"} (default) and \code{"upgma"}.

     In the original ClustalW implementation, this parameter is called 

-    \code{clustering}.}

+    \code{clustering}. Please note that \code{cluster="upgma"} leads

+    to an unidentified error on Windows with R 4.0.x that even crashes

+    the entire R session.}

   \item{gapOpening}{gap opening penalty; the default value for

     nucleotide sequences is 15.0, the default value for 

     amino acid sequences is 10.0.}

@@ -111,6 +113,6 @@ msaClustalW(mySeqs)

 ## call msaClustalW with custom parameters

 msaClustalW(mySeqs, gapOpening=1, gapExtension=1, maxiters=16,

-            cluster="upgma", kimura=FALSE, order="input", maxdiv=23)

+            kimura=FALSE, order="input", maxdiv=23)

 }

 \keyword{manip}

@@ -1630,7 +1630,7 @@ bool SubMatrix::commentline(char* line)

  * @param temp 

  * @param name 

  */

-void SubMatrix::printInFormat(vector<short>& temp, char* name)

+void SubMatrix::printInFormat(vector<short>& temp, const char* name)

 {

     char nameOfFile[30];

     strcpy(nameOfFile, name);

@@ -1693,7 +1693,7 @@ void SubMatrix::printInFormat(vector<short>& temp, char* name)

  * @param temp 

  * @param name 

  */

-void SubMatrix::printVectorToFile(vector<short>& temp, char* name)

+void SubMatrix::printVectorToFile(vector<short>& temp, const char* name)

 {

     char nameOfFile[30];

     strcpy(nameOfFile, name);

@@ -103,8 +103,8 @@ class SubMatrix

         // The functions below are purely for testing purposes.

         void printGetMatrixResults(int mat[NUMRES][NUMRES]); 

         void compareMatrices(int mat1[NUMRES][NUMRES], int mat2[NUMRES][NUMRES]); 

-        void printInFormat(vector<short>& temp, char* name = "tempfile.out");

-        void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");

+        void printInFormat(vector<short>& temp, const char* name = "tempfile.out");

+        void printVectorToFile(vector<short>& temp, const char* name = "tempfile.out");

         Matrix* getUserMatAddress(int alignResidueType, int alignType);

         Xref* getUserXrefAddress(int alignResidueType, int alignType);

         void checkResidueAndAlignType(int alignResidueType, int alignType);