1. msa
  2. src
  3. ClustalOmega
  4. msaMakefile
Browse code

update of gc; version number bumped to 1.31.1

UBod authored on 02/12/2022 11:06:59
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ 79494b5
... ... 
@@ -47,8 +47,8 @@ all: clustalomega
47 47 
 clustalomega:
48 48 
 	./configure $(CONFIGURE_FLAGS); \
49 49 
 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
50 
-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include"; \
51 
-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include"; \
50 
+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \
51 
+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \
52 52 
 	cd src; \
53 53 
 	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
54 54 
 	ar rcs libClustalOmega.a $(OBJNames) && \
Browse code

Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 10:54:55
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ d236535
... ... 
@@ -47,8 +47,8 @@ all: clustalomega
47 47 
 clustalomega:
48 48 
 	./configure $(CONFIGURE_FLAGS); \
49 49 
 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
50 
-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
51 
-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
50 
+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include"; \
51 
+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include"; \
52 52 
 	cd src; \
53 53 
 	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
54 54 
 	ar rcs libClustalOmega.a $(OBJNames) && \
Browse code

Attempt to fix clang error on Mac OS ElCapitan; version number not bumped (not yet)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@128017 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 04/04/2017 07:43:41
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ 7599588
... ... 
@@ -5,6 +5,9 @@ CONFIGURE_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'
5 5 
 ## Variant 3: let the configure script determine whether OpenMP is available
6 6 
 #CONFIGURE_FLAGS=
7 7
8 
+## Additional flag for compatibility on Mac OS
9 
+MAC_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"`
10 
+
8 11 
 CPPNames=\
9 12 
 exceptions4c/e4c_lite.c \
10 13 
 argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c \
... ... 
@@ -44,7 +47,7 @@ all: clustalomega
44 47 
 clustalomega:
45 48 
 	./configure $(CONFIGURE_FLAGS); \
46 49 
 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
47 
-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
50 
+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
48 51 
 	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
49 52 
 	cd src; \
50 53 
 	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
Browse code

minor fixes (see inst/NEWS); version number bumped to 1.5.4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@119484 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 20/07/2016 13:18:53
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ b9525fd
... ... 
@@ -44,7 +44,7 @@ all: clustalomega
44 44 
 clustalomega:
45 45 
 	./configure $(CONFIGURE_FLAGS); \
46 46 
 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
47 
-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
47 
+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
48 48 
 	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
49 49 
 	cd src; \
50 50 
 	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
Browse code

further fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@111693 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 21/12/2015 10:29:13
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ fd1f660
... ... 
@@ -1,5 +1,5 @@
1 1 
 ## Variant 1: deactivate OpenMP on Mac Platforms
2 
-CONFIGURE_FLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
2 
+CONFIGURE_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
3 3 
 ## Variant 2: deactivate OpenMP generally
4 4 
 #CONFIGURE_FLAGS=--without-openmp
5 5 
 ## Variant 3: let the configure script determine whether OpenMP is available
... ... 
@@ -44,9 +44,9 @@ all: clustalomega
44 44 
 clustalomega:
45 45 
 	./configure $(CONFIGURE_FLAGS); \
46 46 
 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
47 
-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
48 
-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
47 
+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
48 
+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
49 49 
 	cd src; \
50 
-	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
50 
+	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
51 51 
 	ar rcs libClustalOmega.a $(OBJNames) && \
52 52 
 	cp libClustalOmega.a ../../
Browse code

Don't depend on R's presence on search path during install

- use "${R_HOME}/bin${R_ARCH_BIN}/R" & friends in Makevars files


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@111425 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 11/12/2015 22:59:15
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ 8d8e4c6
... ... 
@@ -1,5 +1,5 @@
1 1 
 ## Variant 1: deactivate OpenMP on Mac Platforms
2 
-CONFIGURE_FLAGS=`Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
2 
+CONFIGURE_FLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
3 3 
 ## Variant 2: deactivate OpenMP generally
4 4 
 #CONFIGURE_FLAGS=--without-openmp
5 5 
 ## Variant 3: let the configure script determine whether OpenMP is available
... ... 
@@ -44,9 +44,9 @@ all: clustalomega
44 44 
 clustalomega:
45 45 
 	./configure $(CONFIGURE_FLAGS); \
46 46 
 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
47 
-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
48 
-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
47 
+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
48 
+	export PKG_CFLAGS="$(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()"`"; \
49 49 
 	cd src; \
50 
-	R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
50 
+	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
51 51 
 	ar rcs libClustalOmega.a $(OBJNames) && \
52 52 
 	cp libClustalOmega.a ../../
Browse code

Multiple fixes; final comit before release; version number bumped to 0.99.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102514 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 15/04/2015 13:20:09
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ b5f31f0
... ... 
@@ -1,9 +1,9 @@
1 
-OS := $(shell uname)
2 
-ifeq ($(OS), Darwin)
3 
-	CONFIGURE_FLAGS='--without-openmp'
4 
-else
5 
-	CONFIGURE_FLAGS=''
6 
-endif
1 
+## Variant 1: deactivate OpenMP on Mac Platforms
2 
+CONFIGURE_FLAGS=`Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
3 
+## Variant 2: deactivate OpenMP generally
4 
+#CONFIGURE_FLAGS=--without-openmp
5 
+## Variant 3: let the configure script determine whether OpenMP is available
6 
+#CONFIGURE_FLAGS=
7 7
8 8 
 CPPNames=\
9 9 
 exceptions4c/e4c_lite.c \
... ... 
@@ -43,7 +43,7 @@ all: clustalomega
43 43
44 44 
 clustalomega:
45 45 
 	./configure $(CONFIGURE_FLAGS); \
46 
-	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS) `Rscript -e "Rcpp:::LdFlags()"`"; \
46 
+	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
47 47 
 	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
48 48 
 	export PKG_CFLAGS="$(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()"`"; \
49 49 
 	cd src; \
Browse code

Further fixes for Mac platform; version number bumped to 0.99.5

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102357 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 12/04/2015 19:59:20
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ 3fda9f7
... ... 
@@ -1,3 +1,10 @@
1 
+OS := $(shell uname)
2 
+ifeq ($(OS), Darwin)
3 
+	CONFIGURE_FLAGS='--without-openmp'
4 
+else
5 
+	CONFIGURE_FLAGS=''
6 
+endif
7 
+
1 8 
 CPPNames=\
2 9 
 exceptions4c/e4c_lite.c \
3 10 
 argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c \
... ... 
@@ -35,11 +42,11 @@ RClustalOmega.o mymain.o clustal-omega.o
35 42 
 all: clustalomega
36 43
37 44 
 clustalomega:
38 
-	./configure; \
45 
+	./configure $(CONFIGURE_FLAGS); \
39 46 
 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS) `Rscript -e "Rcpp:::LdFlags()"`"; \
40 47 
 	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
41 48 
 	export PKG_CFLAGS="$(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()"`"; \
42 49 
 	cd src; \
43 
-	R CMD SHLIB -o libClustalOmega.so $(CPPNames); \
44 
-	ar rcs libClustalOmega.a $(OBJNames); \
50 
+	R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
51 
+	ar rcs libClustalOmega.a $(OBJNames) && \
45 52 
 	cp libClustalOmega.a ../../
Browse code

add package to the repository

msa


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 10/04/2015 00:12:33
Showing 1 changed files
src/ClustalOmega/msaMakefile
History View file @ dafeef0
1 1 
new file mode 100755
... ... 
@@ -0,0 +1,45 @@
1 
+CPPNames=\
2 
+exceptions4c/e4c_lite.c \
3 
+argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c \
4 
+argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c \
5 
+kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp \
6 
+clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c \
7 
+clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c \
8 
+clustal/tree.c clustal/util.c clustal/weights.c \
9 
+squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c \
10 
+squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c \
11 
+squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c \
12 
+squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c \
13 
+squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c \
14 
+squid/types.c squid/vectorops.c squid/weight.c \
15 
+hhalign/hhalign.cpp \
16 
+RClustalOmega.cpp mymain.c clustal-omega.c
17 
+
18 
+OBJNames=\
19 
+exceptions4c/e4c_lite.o \
20 
+argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o \
21 
+argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o \
22 
+kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o \
23 
+clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o \
24 
+clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o \
25 
+clustal/tree.o clustal/util.o clustal/weights.o \
26 
+squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o \
27 
+squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o \
28 
+squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o \
29 
+squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o \
30 
+squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o \
31 
+squid/types.o squid/vectorops.o squid/weight.o \
32 
+hhalign/hhalign.o \
33 
+RClustalOmega.o mymain.o clustal-omega.o
34 
+
35 
+all: clustalomega
36 
+
37 
+clustalomega:
38 
+	./configure; \
39 
+	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS) `Rscript -e "Rcpp:::LdFlags()"`"; \
40 
+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
41 
+	export PKG_CFLAGS="$(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()"`"; \
42 
+	cd src; \
43 
+	R CMD SHLIB -o libClustalOmega.so $(CPPNames); \
44 
+	ar rcs libClustalOmega.a $(OBJNames); \
45 
+	cp libClustalOmega.a ../../