@@ -1,8 +1,8 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.29.2

-Date: 2022-06-24

+Version: 1.29.3

+Date: 2022-09-28

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

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

 Description: The 'msa' package provides a unified R/Bioconductor interface to

@@ -53,7 +53,7 @@ transformInputSeq <- function(inputSeq) {

         }

     }

-    return(inputSeq)

+    return(toupper(inputSeq))

 }

 ###############################################################################

@@ -1,6 +1,11 @@

 Change history of package msa:

 ==============================

+Version 1.29.3:

+- fix for possibly malformed inputs: all sequences are forced to

+  uppercase characters (previously, ClustalW and ClustalOmega produced

+  wrong results when called with lowercase sequences)

+

 Version 1.29.2:

 - fix in texshade.sty as suggested on TeXshade homepage at CTAN

@@ -27,7 +32,7 @@ Version 1.27.1:

 Version 1.27.0:

 - new branch for Bioconductor 3.15 devel

-Version 1.26.0:

+Version 1.26.0: 

 - release as part of Bioconductor 3.14

 Version 1.25.3:

new file mode 100755

@@ -0,0 +1,57 @@

+## Variant 1: deactivate OpenMP on Mac Platforms

+CONFIGURE_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`

+## Variant 2: deactivate OpenMP generally

+#CONFIGURE_FLAGS=--without-openmp 

+## Variant 3: let the configure script determine whether OpenMP is available

+#CONFIGURE_FLAGS=

+

+## Additional flag for compatibility on Mac OS

+MAC_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"`

+

+CPPNames=\

+exceptions4c/e4c_lite.c \

+argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c \

+argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c \

+kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp \

+clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c \

+clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c \

+clustal/tree.c clustal/util.c clustal/weights.c \

+squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c \

+squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c \

+squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c \

+squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c \

+squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c \

+squid/types.c squid/vectorops.c squid/weight.c \

+hhalign/hhalign.cpp \

+RClustalOmega.cpp mymain.c clustal-omega.c

+

+OBJNames=\

+exceptions4c/e4c_lite.o \

+argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o \

+argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o \

+kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o \

+clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o \

+clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o \

+clustal/tree.o clustal/util.o clustal/weights.o \

+squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o \

+squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o \

+squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o \

+squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o \

+squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o \

+squid/types.o squid/vectorops.o squid/weight.o \

+hhalign/hhalign.o \

+RClustalOmega.o mymain.o clustal-omega.o

+

+all: clustalomega

+

+removeopts=-pedantic -Wall -Wextra -Wpedantic -Weverything

+

+clustalomega:

+	./configure $(CONFIGURE_FLAGS); \

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

+	export PKG_CXXFLAGS="$(filter-out $(removeopts),$(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 -Wno-array-bounds -Wno-stringop-truncation"; \

+	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 -Wno-array-bounds -Wno-stringop-truncation"; \

+	cd src; \

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

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

+	cp libClustalOmega.a ../../