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fixes in ClustalOmega source code to ensure Windows compatibility of GCC6 compatibility fix; version number bumped to 1.5.5

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@119986 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 09/08/2016 14:50:55
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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: 1.5.4
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-Date: 2016-07-20
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+Version: 1.5.5
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+Date: 2016-08-09
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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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@@ -1,6 +1,10 @@
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 Change history of package msa:
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 ==============================
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+Version 1.5.5:
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+- fixes in ClustalOmega source code to ensure Windows compatibility of
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+  GCC6 compatibility fix
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+
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 Version 1.5.4:
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 - bug fix in msaClustalW(): unsupported parameter 'tree' deactivated
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 - fixes in ClustalOmega source code to ensure GCC6 compatibility
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@@ -38,7 +38,7 @@ clustalomega:
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 	cp windows/src/config.h src/; \
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 	cp windows/src/clustal-omega-config.h src/; \
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 	export PKG_LIBS="$(PKG_LIBS) -L"../../gc-7.2" -lgccpp72 -lgc72"; \
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -std=c++98 -DWINMATHH -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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 	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc"; \
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 	cd src; \
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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o ClustalOmega.dll $(CPPNames) && \
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@@ -36,8 +36,13 @@
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 #include <string.h>     // strcmp, strstr
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 #include <stdio.h>    // printf
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 #include <stdlib.h>   // exit
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-//#include <math.h>     // sqrt, pow
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+
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+#ifdef WINMATHH
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+#include <math.h>     // sqrt, pow
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+#else
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 #include <cmath>     // sqrt, pow
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+#endif
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+
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 #include <limits.h>   // INT_MIN
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 #include <float.h>    // FLT_MIN
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 #include <time.h>     // clock
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@@ -834,6 +834,10 @@ bibliography below).
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 \section{Change Log}
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 \begin{description}
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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