@@ -28,7 +28,8 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R

         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R

         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R

         msaClustalOmega.R msaConvert.R msaCheckNames.R

-	msaConsensusSequence-methods.R msaConservationScore-methods.R

+        msaConsensusSequence-methods.R msaConservationScore-methods.R

 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,

         Sequencing

 NeedsCompilation: yes

+Packaged: 2021-10-15 08:56:43 UTC; ulrich

new file mode 100644

Binary files /dev/null and b/build/vignette.rds differ

@@ -6,46 +6,46 @@ rm -rf src/*.a

 rm -rf src/*.o

 rm -rf src/*.rds

-## gc-7.2

-rm -rf src/gc-7.2/.deps

-rm -rf src/gc-7.2/.libs

-rm -rf src/gc-7.2/*.o

-rm -rf src/gc-7.2/*.la

-rm -rf src/gc-7.2/*.lo

-rm -rf src/gc-7.2/Makefile

-rm -rf src/gc-7.2/bdw-gc.pc

-rm -rf src/gc-7.2/config.log

-rm -rf src/gc-7.2/config.status

-rm -rf src/gc-7.2/cord/.deps

-rm -rf src/gc-7.2/cord/.libs

-rm -rf src/gc-7.2/cord/*.o

-rm -rf src/gc-7.2/cord/*.lo

-rm -rf src/gc-7.2/cord/*.la

-rm -rf src/gc-7.2/include/private/config.h

-rm -rf src/gc-7.2/include/private/stamp-h1

-rm -rf src/gc-7.2/libatomic_ops/Makefile

-rm -rf src/gc-7.2/libatomic_ops/config.log

-rm -rf src/gc-7.2/libatomic_ops/config.status

-rm -rf src/gc-7.2/libatomic_ops/doc/Makefile

-rm -rf src/gc-7.2/libatomic_ops/pkgconfig/atomic_ops-uninstalled.pc

-rm -rf src/gc-7.2/libatomic_ops/pkgconfig/atomic_ops.pc

-rm -rf src/gc-7.2/libatomic_ops/src/.deps

-rm -rf src/gc-7.2/libatomic_ops/src/.libs

-rm -rf src/gc-7.2/libatomic_ops/src/*.o

-rm -rf src/gc-7.2/libatomic_ops/src/*.la

-rm -rf src/gc-7.2/libatomic_ops/src/*.lo

-rm -rf src/gc-7.2/libatomic_ops/src/.dirstamp

-rm -rf src/gc-7.2/libatomic_ops/src/Makefile

-rm -rf src/gc-7.2/libatomic_ops/src/atomic_ops/Makefile

-rm -rf src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/Makefile

-rm -rf src/gc-7.2/libatomic_ops/src/config.h

-rm -rf src/gc-7.2/libatomic_ops/src/stamp-h1

-rm -rf src/gc-7.2/libatomic_ops/tests/.deps

-rm -rf src/gc-7.2/libatomic_ops/tests/Makefile

-rm -rf src/gc-7.2/libtool

-rm -rf src/gc-7.2/tests/.deps

-rm -rf src/gc-7.2/cord/.dirstamp

-rm -rf src/gc-7.2/m4/lt~obsolete.m4

+## gc-7.6.12

+rm -rf src/gc-7.6.12/.deps

+rm -rf src/gc-7.6.12/.libs

+rm -rf src/gc-7.6.12/*.o

+rm -rf src/gc-7.6.12/*.la

+rm -rf src/gc-7.6.12/*.lo

+rm -rf src/gc-7.6.12/Makefile

+rm -rf src/gc-7.6.12/bdw-gc.pc

+rm -rf src/gc-7.6.12/config.log

+rm -rf src/gc-7.6.12/config.status

+rm -rf src/gc-7.6.12/cord/.deps

+rm -rf src/gc-7.6.12/cord/.libs

+rm -rf src/gc-7.6.12/cord/*.o

+rm -rf src/gc-7.6.12/cord/*.lo

+rm -rf src/gc-7.6.12/cord/*.la

+rm -rf src/gc-7.6.12/include/private/config.h

+rm -rf src/gc-7.6.12/include/private/stamp-h1

+rm -rf src/gc-7.6.12/libatomic_ops/Makefile

+rm -rf src/gc-7.6.12/libatomic_ops/config.log

+rm -rf src/gc-7.6.12/libatomic_ops/config.status

+rm -rf src/gc-7.6.12/libatomic_ops/doc/Makefile

+rm -rf src/gc-7.6.12/libatomic_ops/pkgconfig/atomic_ops-uninstalled.pc

+rm -rf src/gc-7.6.12/libatomic_ops/pkgconfig/atomic_ops.pc

+rm -rf src/gc-7.6.12/libatomic_ops/src/.deps

+rm -rf src/gc-7.6.12/libatomic_ops/src/.libs

+rm -rf src/gc-7.6.12/libatomic_ops/src/*.o

+rm -rf src/gc-7.6.12/libatomic_ops/src/*.la

+rm -rf src/gc-7.6.12/libatomic_ops/src/*.lo

+rm -rf src/gc-7.6.12/libatomic_ops/src/.dirstamp

+rm -rf src/gc-7.6.12/libatomic_ops/src/Makefile

+rm -rf src/gc-7.6.12/libatomic_ops/src/atomic_ops/Makefile

+rm -rf src/gc-7.6.12/libatomic_ops/src/atomic_ops/sysdeps/Makefile

+rm -rf src/gc-7.6.12/libatomic_ops/src/config.h

+rm -rf src/gc-7.6.12/libatomic_ops/src/stamp-h1

+rm -rf src/gc-7.6.12/libatomic_ops/tests/.deps

+rm -rf src/gc-7.6.12/libatomic_ops/tests/Makefile

+rm -rf src/gc-7.6.12/libtool

+rm -rf src/gc-7.6.12/tests/.deps

+rm -rf src/gc-7.6.12/cord/.dirstamp

+rm -rf src/gc-7.6.12/m4/lt~obsolete.m4

 ## -- Muscle

 rm -rf src/Muscle/muscle.make.std???.txt

@@ -6,9 +6,9 @@ rm -rf src/*.o

 rm -rf src/*.a

 ## -- gc

-rm -rf src/gc-7.2/*.dll

-rm -rf src/gc-7.2/*.o

-rm -rf src/gc-7.2/*.a

+rm -rf src/gc-7.6.12/*.dll

+rm -rf src/gc-7.6.12/*.o

+rm -rf src/gc-7.6.12/*.a

 ## -- Muscle

 rm -rf src/Muscle/muscle.make.std???.txt

@@ -47,8 +47,8 @@ all: clustalomega

 clustalomega:

 	./configure $(CONFIGURE_FLAGS); \

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

-	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"; \

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

+	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"; \

+	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"; \

 	cd src; \

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

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

@@ -37,9 +37,9 @@ all: clustalomega

 clustalomega:

 	cp windows/src/config.h src/; \

 	cp windows/src/clustal-omega-config.h src/; \

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

-	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"; \

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

+	export PKG_LIBS="$(PKG_LIBS) -L"../../gc-7.6.12" -lgccpp72 -lgc72"; \

+	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"; \

+	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include -lgccpp -lgc"; \

 	cd src; \

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

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

@@ -244,7 +244,7 @@

 /* The size of `fpos_t', as computed by sizeof. */

 #ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T

-#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 12

+#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16

 #endif

 /* The size of `unsigned int', as computed by sizeof. */

@@ -254,7 +254,7 @@

 /* The size of `unsigned long', as computed by sizeof. */

 #ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG

-#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 4

+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8

 #endif

 /* The size of `unsigned long long', as computed by sizeof. */

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

 clustalw:

 	./configure; \

 	cd src; \

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

+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) -Wno-deprecated -Wno-unused-result"; \

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

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

 	cp libClustalW.a ../../

@@ -11,7 +11,7 @@ clustalw:

 	cp windows/src/clustalw_version.h src/; \

 	cp windows/src/config.h src/; \

 	cd src; \

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

+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) -Wno-deprecated -Wno-unused-result"; \

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

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

 	cp libClustalW.a ../../

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

 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"

+PKG_CXXFLAGS=-I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"

 .PHONY: all mylibs

@@ -9,7 +9,7 @@ $(SHLIB): mylibs

 mylibs: build_gc build_muscle build_clustalw build_clustalomega

 build_gc:

-	make --file=msaMakefile --directory=gc-7.2

+	make --file=msaMakefile --directory=gc-7.6.12

 	@echo "----------------------------------------"

 	@echo "------------------ GC  -----------------"

 	@echo "----------------------------------------"

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

 .PHONY: all ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a

 PKG_LIBS=-Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive

-PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"

+PKG_CXXFLAGS=-I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -Wno-deprecated

 all: $(SHLIB)

 $(SHLIB): ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a

@@ -12,7 +12,7 @@ clean:

 	cd src

 ./libGC.a:

-	make --file=msaMakefile.win --directory=gc-7.2 AR="$(AR)"

+	make --file=msaMakefile.win --directory=gc-7.6.12 AR="$(AR)"

 	@echo "----------------------------------------"

 	@echo "------------------ GC  -----------------"

 	@echo "----------------------------------------"

@@ -5,7 +5,7 @@ OBJNames = aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o al

 all: muscle

 muscle:

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

+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I../gc-7.6.12/include"

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

 	ar rcs libMuscle.a $(OBJNames)

 	cp libMuscle.a ../

@@ -5,8 +5,8 @@ OBJNames=aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.

 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/"

+	export PKG_LIBS="$(PKG_LIBS) -L"../gc-7.6.12/" -lgc72 -lgccpp72"

+	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I../gc-7.6.12/include/"

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

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

 	cp libMuscle.a ../

@@ -3,7 +3,7 @@

 const char *SecsToStr(unsigned long Secs)

 	{

-	static char Str[16];

+	static char Str[100]; // [UB] waste some memory to prevent overflow warning

 	long hh, mm, ss;

 	hh = Secs/(60*60);