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

update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17; version number bumped to 1.31.6

UBod authored on 23/03/2023 15:22:56
Showing 1 changed files
src/ClustalW/msaMakefile
History View file @ 47114e9
... ... 
@@ -7,7 +7,7 @@ all: clustalw
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 clustalw:
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 	./configure; \
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 	cd src; \
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-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) -Wno-deprecated -Wno-unused-result"; \
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+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -D_HAS_AUTO_PTR_ETC=1 -I. $(PKG_CXXFLAGS) -Wno-deprecated -Wno-unused-result"; \
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 	${R_HOME}/bin/R CMD SHLIB -o libClustalW.so $(CPPNames) && \
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 	ar rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.a ../../
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/ClustalW/msaMakefile
History View file @ d236535
... ... 
@@ -7,7 +7,7 @@ all: clustalw
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 clustalw:
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 	./configure; \
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 	cd src; \
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-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS)"; \
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+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) -Wno-deprecated -Wno-unused-result"; \
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 	${R_HOME}/bin/R CMD SHLIB -o libClustalW.so $(CPPNames) && \
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 	ar rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.a ../../
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/ClustalW/msaMakefile
History View file @ fd1f660
... ... 
@@ -7,7 +7,7 @@ all: clustalw
7 7 
 clustalw:
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 	./configure; \
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 	cd src; \
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-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
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-	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalW.so $(CPPNames) && \
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+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS)"; \
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+	${R_HOME}/bin/R CMD SHLIB -o libClustalW.so $(CPPNames) && \
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 	ar rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.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/ClustalW/msaMakefile
History View file @ 8d8e4c6
... ... 
@@ -7,7 +7,7 @@ all: clustalw
7 7 
 clustalw:
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 	./configure; \
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 	cd src; \
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-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `Rscript -e "Rcpp:::CxxFlags()"`"; \
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-	R CMD SHLIB -o libClustalW.so $(CPPNames) && \
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+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
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+	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalW.so $(CPPNames) && \
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 	ar rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.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/ClustalW/msaMakefile
History View file @ b5f31f0
... ... 
@@ -7,7 +7,6 @@ all: clustalw
7 7 
 clustalw:
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 	./configure; \
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 	cd src; \
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-	export PKG_LIBS="$(PKG_LIBS) `Rscript -e "Rcpp:::LdFlags()"`"; \
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 	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `Rscript -e "Rcpp:::CxxFlags()"`"; \
12 11 
 	R CMD SHLIB -o libClustalW.so $(CPPNames) && \
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 	ar rcs libClustalW.a $(OBJNames) && \
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/ClustalW/msaMakefile
History View file @ 3fda9f7
... ... 
@@ -9,6 +9,6 @@ clustalw:
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 	cd src; \
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 	export PKG_LIBS="$(PKG_LIBS) `Rscript -e "Rcpp:::LdFlags()"`"; \
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 	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `Rscript -e "Rcpp:::CxxFlags()"`"; \
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-	R CMD SHLIB -o libClustalW.so $(CPPNames); \
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-	ar rcs libClustalW.a $(OBJNames); \
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+	R CMD SHLIB -o libClustalW.so $(CPPNames) && \
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+	ar rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.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/ClustalW/msaMakefile
History View file @ dafeef0
1 1 
new file mode 100755
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@@ -0,0 +1,14 @@
1 
+CPPNames=pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp
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+
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+OBJNames=pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o
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+
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+all: clustalw
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+
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+clustalw:
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+	./configure; \
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+	cd src; \
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+	export PKG_LIBS="$(PKG_LIBS) `Rscript -e "Rcpp:::LdFlags()"`"; \
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+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `Rscript -e "Rcpp:::CxxFlags()"`"; \
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+	R CMD SHLIB -o libClustalW.so $(CPPNames); \
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+	ar rcs libClustalW.a $(OBJNames); \
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+	cp libClustalW.a ../../