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

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.5.4

-Date: 2016-07-20

+Version: 1.5.5

+Date: 2016-08-09

 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 +1,10 @@

 Change history of package msa:

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

+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

@@ -38,7 +38,7 @@ clustalomega:

 	cp windows/src/config.h src/; \

 	cp windows/src/clustal-omega-config.h src/; \

 	export PKG_LIBS="$(PKG_LIBS) -L"../../gc-7.2" -lgccpp72 -lgc72"; \

-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \

+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -std=c++98 -DWINMATHH -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \

 	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc"; \

 	cd src; \

 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o ClustalOmega.dll $(CPPNames) && \

@@ -36,8 +36,13 @@

 #include <string.h>     // strcmp, strstr

 #include <stdio.h>    // printf

 #include <stdlib.h>   // exit

-//#include <math.h>     // sqrt, pow

+

+#ifdef WINMATHH

+#include <math.h>     // sqrt, pow

+#else

 #include <cmath>     // sqrt, pow

+#endif

+

 #include <limits.h>   // INT_MIN

 #include <float.h>    // FLT_MIN

 #include <time.h>     // clock

@@ -834,6 +834,10 @@ bibliography below).

 \section{Change Log}

 \begin{description}

+\item[Version 1.5.5:] \mbox{ }  \begin{itemize}

+   \item fixes in ClustalOmega source code to ensure Windows compatibility of

+   GCC6 compatibility fix

+   \end{itemize}

 \item[Version 1.5.4:] \mbox{ }  \begin{itemize}

    \item bug fix in \verb+msaClustalW()+: unsupported parameter `\verb+tree+' deactivated

    \item fixes in ClustalOmega source code to ensure GCC 6 compatibility