@@ -1,7 +1,7 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.3.0

+Version: 1.3.1

 Date: 2015-10-13

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

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

@@ -1,5 +1,5 @@

 ## Variant 1: deactivate OpenMP on Mac Platforms

-CONFIGURE_FLAGS=`Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`

+CONFIGURE_FLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`

 ## Variant 2: deactivate OpenMP generally

 #CONFIGURE_FLAGS=--without-openmp 

 ## Variant 3: let the configure script determine whether OpenMP is available

@@ -44,9 +44,9 @@ all: clustalomega

 clustalomega:

 	./configure $(CONFIGURE_FLAGS); \

 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \

-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \

-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \

+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \

+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \

 	cd src; \

-	R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \

+	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalOmega.so $(CPPNames) && \

 	ar rcs libClustalOmega.a $(OBJNames) && \

 	cp libClustalOmega.a ../../

@@ -7,7 +7,7 @@ all: clustalw

 clustalw:

 	./configure; \

 	cd src; \

-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `Rscript -e "Rcpp:::CxxFlags()"`"; \

-	R CMD SHLIB -o libClustalW.so $(CPPNames) && \

+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \

+	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalW.so $(CPPNames) && \

 	ar rcs libClustalW.a $(OBJNames) && \

 	cp libClustalW.a ../../

@@ -1,5 +1,5 @@

-PKG_LIBS=`Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a') else cat('-Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,--no-whole-archive')"`

-PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `Rscript -e "Rcpp:::CxxFlags()"`

+PKG_LIBS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('-Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a') else cat('-Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,--no-whole-archive')"`

+PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`

 .PHONY: all mylibs

@@ -6,6 +6,6 @@ all: muscle

 muscle:

 	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I"../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"

-	R CMD SHLIB -o libMuscle.so $(CPPNames)

+	"${R_HOME}/bin/R" CMD SHLIB -o libMuscle.so $(CPPNames)

 	ar rcs libMuscle.a $(OBJNames)

 	cp libMuscle.a ../

@@ -6,7 +6,7 @@ all: muscle

 muscle:

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

-	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I"../gc-7.2/include/" `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"

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

+	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I"../gc-7.2/include/" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::CxxFlags()"`"

+	"${R_HOME}/bin${R_ARCH_BIN}/R.exe" CMD SHLIB -o Muscle.dll $(CPPNames)

 	$(AR) rcs libMuscle.a $(OBJNames)

 	cp libMuscle.a ../