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Fix for lowercase sequences; version number bumped to 1.29.3

UBod authored on 28/09/2022 11:24:00
Showing4 changed files

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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.29.2
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-Date: 2022-06-24
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+Version: 1.29.3
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+Date: 2022-09-28
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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@@ -53,7 +53,7 @@ transformInputSeq <- function(inputSeq) {
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         }
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     }
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-    return(inputSeq)
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+    return(toupper(inputSeq))
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 }
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 ###############################################################################
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 Change history of package msa:
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 ==============================
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+Version 1.29.3:
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+- fix for possibly malformed inputs: all sequences are forced to
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+  uppercase characters (previously, ClustalW and ClustalOmega produced
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+  wrong results when called with lowercase sequences)
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+
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 Version 1.29.2:
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 - fix in texshade.sty as suggested on TeXshade homepage at CTAN
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@@ -27,7 +32,7 @@ Version 1.27.1:
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 Version 1.27.0:
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 - new branch for Bioconductor 3.15 devel
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-Version 1.26.0:
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+Version 1.26.0: 
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 - release as part of Bioconductor 3.14
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 Version 1.25.3:
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new file mode 100755
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+## Variant 1: deactivate OpenMP on Mac Platforms
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+CONFIGURE_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
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+## Variant 2: deactivate OpenMP generally
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+#CONFIGURE_FLAGS=--without-openmp 
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+## Variant 3: let the configure script determine whether OpenMP is available
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+#CONFIGURE_FLAGS=
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+
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+## Additional flag for compatibility on Mac OS
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+MAC_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"`
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+
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+CPPNames=\
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+exceptions4c/e4c_lite.c \
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+argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c \
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+argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c \
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+kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp \
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+clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c \
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+clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c \
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+clustal/tree.c clustal/util.c clustal/weights.c \
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+squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c \
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+squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c \
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+squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c \
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+squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c \
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+squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c \
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+squid/types.c squid/vectorops.c squid/weight.c \
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+hhalign/hhalign.cpp \
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+RClustalOmega.cpp mymain.c clustal-omega.c
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+
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+OBJNames=\
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+exceptions4c/e4c_lite.o \
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+argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o \
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+argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o \
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+kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o \
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+clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o \
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+clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o \
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+clustal/tree.o clustal/util.o clustal/weights.o \
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+squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o \
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+squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o \
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+squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o \
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+squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o \
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+squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o \
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+squid/types.o squid/vectorops.o squid/weight.o \
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+hhalign/hhalign.o \
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+RClustalOmega.o mymain.o clustal-omega.o
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+
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+all: clustalomega
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+
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+removeopts=-pedantic -Wall -Wextra -Wpedantic -Weverything
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+
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+clustalomega:
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+	./configure $(CONFIGURE_FLAGS); \
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+	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
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+	export PKG_CXXFLAGS="$(filter-out $(removeopts),$(PKG_CXXFLAGS)) $(SHLIB_OPENMP_CXXFLAGS) $(MAC_FLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include -Wno-array-bounds -Wno-stringop-truncation"; \
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+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.6.12/include -Wno-array-bounds -Wno-stringop-truncation"; \
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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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+	cp libClustalOmega.a ../../