Browse code

Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 10:54:55
Showing14 changed files

... ...
@@ -28,7 +28,8 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
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         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
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         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
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         msaClustalOmega.R msaConvert.R msaCheckNames.R
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-	msaConsensusSequence-methods.R msaConservationScore-methods.R
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+        msaConsensusSequence-methods.R msaConservationScore-methods.R
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 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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         Sequencing
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 NeedsCompilation: yes
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+Packaged: 2021-10-15 08:56:43 UTC; ulrich
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new file mode 100644
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Binary files /dev/null and b/build/vignette.rds differ
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@@ -6,46 +6,46 @@ rm -rf src/*.a
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 rm -rf src/*.o
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 rm -rf src/*.rds
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-## gc-7.2
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-rm -rf src/gc-7.2/.deps
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-rm -rf src/gc-7.2/.libs
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-rm -rf src/gc-7.2/*.o
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-rm -rf src/gc-7.2/*.la
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-rm -rf src/gc-7.2/*.lo
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-rm -rf src/gc-7.2/Makefile
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-rm -rf src/gc-7.2/bdw-gc.pc
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-rm -rf src/gc-7.2/config.log
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-rm -rf src/gc-7.2/config.status
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-rm -rf src/gc-7.2/cord/.deps
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-rm -rf src/gc-7.2/cord/.libs
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-rm -rf src/gc-7.2/cord/*.o
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-rm -rf src/gc-7.2/cord/*.lo
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-rm -rf src/gc-7.2/cord/*.la
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-rm -rf src/gc-7.2/include/private/config.h
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-rm -rf src/gc-7.2/include/private/stamp-h1
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-rm -rf src/gc-7.2/libatomic_ops/Makefile
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-rm -rf src/gc-7.2/libatomic_ops/config.log
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-rm -rf src/gc-7.2/libatomic_ops/config.status
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-rm -rf src/gc-7.2/libatomic_ops/doc/Makefile
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-rm -rf src/gc-7.2/libatomic_ops/pkgconfig/atomic_ops-uninstalled.pc
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-rm -rf src/gc-7.2/libatomic_ops/pkgconfig/atomic_ops.pc
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-rm -rf src/gc-7.2/libatomic_ops/src/.deps
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-rm -rf src/gc-7.2/libatomic_ops/src/.libs
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-rm -rf src/gc-7.2/libatomic_ops/src/*.o
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-rm -rf src/gc-7.2/libatomic_ops/src/*.la
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-rm -rf src/gc-7.2/libatomic_ops/src/*.lo
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-rm -rf src/gc-7.2/libatomic_ops/src/.dirstamp
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-rm -rf src/gc-7.2/libatomic_ops/src/Makefile
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-rm -rf src/gc-7.2/libatomic_ops/src/atomic_ops/Makefile
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-rm -rf src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/Makefile
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-rm -rf src/gc-7.2/libatomic_ops/src/config.h
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-rm -rf src/gc-7.2/libatomic_ops/src/stamp-h1
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-rm -rf src/gc-7.2/libatomic_ops/tests/.deps
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-rm -rf src/gc-7.2/libatomic_ops/tests/Makefile
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-rm -rf src/gc-7.2/libtool
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-rm -rf src/gc-7.2/tests/.deps
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-rm -rf src/gc-7.2/cord/.dirstamp
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-rm -rf src/gc-7.2/m4/lt~obsolete.m4
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+## gc-7.6.12
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+rm -rf src/gc-7.6.12/.deps
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+rm -rf src/gc-7.6.12/.libs
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+rm -rf src/gc-7.6.12/*.o
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+rm -rf src/gc-7.6.12/*.la
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+rm -rf src/gc-7.6.12/*.lo
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+rm -rf src/gc-7.6.12/Makefile
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+rm -rf src/gc-7.6.12/bdw-gc.pc
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+rm -rf src/gc-7.6.12/config.log
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+rm -rf src/gc-7.6.12/config.status
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+rm -rf src/gc-7.6.12/cord/.deps
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+rm -rf src/gc-7.6.12/cord/.libs
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+rm -rf src/gc-7.6.12/cord/*.o
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+rm -rf src/gc-7.6.12/cord/*.lo
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+rm -rf src/gc-7.6.12/cord/*.la
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+rm -rf src/gc-7.6.12/include/private/config.h
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+rm -rf src/gc-7.6.12/include/private/stamp-h1
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+rm -rf src/gc-7.6.12/libatomic_ops/Makefile
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+rm -rf src/gc-7.6.12/libatomic_ops/config.log
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+rm -rf src/gc-7.6.12/libatomic_ops/config.status
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+rm -rf src/gc-7.6.12/libatomic_ops/doc/Makefile
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+rm -rf src/gc-7.6.12/libatomic_ops/pkgconfig/atomic_ops-uninstalled.pc
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+rm -rf src/gc-7.6.12/libatomic_ops/pkgconfig/atomic_ops.pc
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+rm -rf src/gc-7.6.12/libatomic_ops/src/.deps
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+rm -rf src/gc-7.6.12/libatomic_ops/src/.libs
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+rm -rf src/gc-7.6.12/libatomic_ops/src/*.o
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+rm -rf src/gc-7.6.12/libatomic_ops/src/*.la
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+rm -rf src/gc-7.6.12/libatomic_ops/src/*.lo
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+rm -rf src/gc-7.6.12/libatomic_ops/src/.dirstamp
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+rm -rf src/gc-7.6.12/libatomic_ops/src/Makefile
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+rm -rf src/gc-7.6.12/libatomic_ops/src/atomic_ops/Makefile
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+rm -rf src/gc-7.6.12/libatomic_ops/src/atomic_ops/sysdeps/Makefile
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+rm -rf src/gc-7.6.12/libatomic_ops/src/config.h
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+rm -rf src/gc-7.6.12/libatomic_ops/src/stamp-h1
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+rm -rf src/gc-7.6.12/libatomic_ops/tests/.deps
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+rm -rf src/gc-7.6.12/libatomic_ops/tests/Makefile
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+rm -rf src/gc-7.6.12/libtool
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+rm -rf src/gc-7.6.12/tests/.deps
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+rm -rf src/gc-7.6.12/cord/.dirstamp
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+rm -rf src/gc-7.6.12/m4/lt~obsolete.m4
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 ## -- Muscle
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 rm -rf src/Muscle/muscle.make.std???.txt
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@@ -6,9 +6,9 @@ rm -rf src/*.o
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 rm -rf src/*.a
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 ## -- gc
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-rm -rf src/gc-7.2/*.dll
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-rm -rf src/gc-7.2/*.o
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-rm -rf src/gc-7.2/*.a
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+rm -rf src/gc-7.6.12/*.dll
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+rm -rf src/gc-7.6.12/*.o
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+rm -rf src/gc-7.6.12/*.a
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 ## -- Muscle
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 rm -rf src/Muscle/muscle.make.std???.txt
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@@ -47,8 +47,8 @@ all: clustalomega
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 clustalomega:
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 	./configure $(CONFIGURE_FLAGS); \
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 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include"; \
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+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include"; \
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 	cd src; \
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 	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
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 	ar rcs libClustalOmega.a $(OBJNames) && \
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@@ -37,9 +37,9 @@ all: clustalomega
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 clustalomega:
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 	cp windows/src/config.h src/; \
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 	cp windows/src/clustal-omega-config.h src/; \
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-	export PKG_LIBS="$(PKG_LIBS) -L"../../gc-7.2" -lgccpp72 -lgc72"; \
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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-	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc"; \
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+	export PKG_LIBS="$(PKG_LIBS) -L"../../gc-7.6.12" -lgccpp72 -lgc72"; \
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include"; \
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+	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/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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 	$(AR) rcs libClustalOmega.a $(OBJNames) && \
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@@ -244,7 +244,7 @@
244 244
 
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 /* The size of `fpos_t', as computed by sizeof. */
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 #ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T
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-#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 12
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+#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16
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 #endif
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 /* The size of `unsigned int', as computed by sizeof. */
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@@ -254,7 +254,7 @@
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 /* The size of `unsigned long', as computed by sizeof. */
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 #ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG
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-#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 4
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+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8
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 #endif
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 /* The size of `unsigned long long', as computed by sizeof. */
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@@ -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 ../../
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@@ -11,7 +11,7 @@ clustalw:
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 	cp windows/src/clustalw_version.h src/; \
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 	cp windows/src/config.h src/; \
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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_ARCH_BIN}/R.exe CMD SHLIB -o ClustalW.dll $(CPPNames) &&\
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 	$(AR) rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.a ../../
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@@ -1,5 +1,5 @@
1 1
 PKG_LIBS=`${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')"`
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-PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"
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+PKG_CXXFLAGS=-I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"
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 .PHONY: all mylibs
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@@ -9,7 +9,7 @@ $(SHLIB): mylibs
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 mylibs: build_gc build_muscle build_clustalw build_clustalomega
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 build_gc:
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-	make --file=msaMakefile --directory=gc-7.2
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+	make --file=msaMakefile --directory=gc-7.6.12
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 	@echo "----------------------------------------"
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 	@echo "------------------ GC  -----------------"
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 	@echo "----------------------------------------"
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@@ -1,7 +1,7 @@
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 .PHONY: all ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a
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 PKG_LIBS=-Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive
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-PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"
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+PKG_CXXFLAGS=-I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -Wno-deprecated
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 all: $(SHLIB)
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 $(SHLIB): ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a
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@@ -12,7 +12,7 @@ clean:
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 	cd src
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 ./libGC.a:
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-	make --file=msaMakefile.win --directory=gc-7.2 AR="$(AR)"
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+	make --file=msaMakefile.win --directory=gc-7.6.12 AR="$(AR)"
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 	@echo "----------------------------------------"
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 	@echo "------------------ GC  -----------------"
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 	@echo "----------------------------------------"
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@@ -5,7 +5,7 @@ OBJNames = aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o al
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 all: muscle
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 muscle:
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I../gc-7.2/include"
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I../gc-7.6.12/include"
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 	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libMuscle.so $(CPPNames)
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 	ar rcs libMuscle.a $(OBJNames)
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 	cp libMuscle.a ../
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@@ -5,8 +5,8 @@ OBJNames=aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.
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 all: muscle
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 muscle:
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-	export PKG_LIBS="$(PKG_LIBS) -L"../gc-7.2/" -lgc72 -lgccpp72"
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-	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I../gc-7.2/include/"
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+	export PKG_LIBS="$(PKG_LIBS) -L"../gc-7.6.12/" -lgc72 -lgccpp72"
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+	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I../gc-7.6.12/include/"
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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o Muscle.dll $(CPPNames)
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 	$(AR) rcs libMuscle.a $(OBJNames)
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 	cp libMuscle.a ../
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@@ -3,7 +3,7 @@
3 3
 
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 const char *SecsToStr(unsigned long Secs)
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 	{
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-	static char Str[16];
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+	static char Str[100]; // [UB] waste some memory to prevent overflow warning
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 	long hh, mm, ss;
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 	hh = Secs/(60*60);