@@ -2,7 +2,7 @@ Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

 Version: 1.2.1

-Date: 2015-12-18

+Date: 2015-12-19

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

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

 Description: This package provides a unified R/Bioconductor interface to the

@@ -47,6 +47,6 @@ clustalomega:

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

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

 	cd src; \

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

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

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

 	cp libClustalOmega.a ../../

@@ -8,6 +8,6 @@ clustalw:

 	./configure; \

 	cd src; \

 	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS)"; \

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

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

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

 	cp libClustalW.a ../../

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

 muscle:

 	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I../gc-7.2/include"

-	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 ../