diff options
Diffstat (limited to 'sci-biology/vienna-rna/files')
14 files changed, 358 insertions, 0 deletions
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch new file mode 100644 index 000000000000..0a781667c70b --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch @@ -0,0 +1,22 @@ +diff -Naur ViennaRNA-1.6.5/Cluster/statgeom.c ViennaRNA-1.6.5.new/Cluster/statgeom.c +--- ViennaRNA-1.6.5/Cluster/statgeom.c 2001-04-05 04:36:41.000000000 -0400 ++++ ViennaRNA-1.6.5.new/Cluster/statgeom.c 2007-11-24 08:55:17.000000000 -0500 +@@ -5,6 +5,7 @@ + */ + + #include <stdio.h> ++#include <string.h> + #include <strings.h> + #include <ctype.h> + #include "utils.h" +diff -Naur ViennaRNA-1.6.5/Readseq/readseq.c ViennaRNA-1.6.5.new/Readseq/readseq.c +--- ViennaRNA-1.6.5/Readseq/readseq.c 1995-07-12 13:05:58.000000000 -0400 ++++ ViennaRNA-1.6.5.new/Readseq/readseq.c 2007-11-24 08:56:16.000000000 -0500 +@@ -173,6 +173,7 @@ + #include <stdio.h> + #include <string.h> + #include <ctype.h> ++#include <stdlib.h> + + #include "ureadseq.h" + diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch new file mode 100644 index 000000000000..37e2f8c6a880 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch @@ -0,0 +1,24 @@ +diff -Naur ViennaRNA-1.7.2/Perl/Makefile.am ViennaRNA-1.7.2.new/Perl/Makefile.am +--- ViennaRNA-1.7.2/Perl/Makefile.am 2007-12-19 05:33:14.000000000 -0500 ++++ ViennaRNA-1.7.2.new/Perl/Makefile.am 2008-10-06 14:20:54.000000000 -0400 +@@ -4,7 +4,7 @@ + RNA.i tmaps.i + + Makefile.perl: Makefile.PL Makefile +- @PerlCmd@ Makefile.PL ++ @PerlCmd@ Makefile.PL LDDLFLAGS="${LDFLAGS} -shared" + + # the perl command repairs some errors in the SWIG CVS version + RNA_wrap.c: RNA.i tmaps.i +diff -Naur ViennaRNA-1.7.2/Readseq/Makefile ViennaRNA-1.7.2.new/Readseq/Makefile +--- ViennaRNA-1.7.2/Readseq/Makefile 2008-01-23 05:32:00.000000000 -0500 ++++ ViennaRNA-1.7.2.new/Readseq/Makefile 2008-10-06 14:21:13.000000000 -0400 +@@ -40,7 +40,7 @@ + + build: $(SOURCES) + @echo "Compiling readseq..." +- $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c + + # if using NCBI, uncomment these lines in place of build: above + #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch new file mode 100644 index 000000000000..2c5ac3041297 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch @@ -0,0 +1,16 @@ +# unfortunately, vienna-rna's build system is a little broken and sometimes detects +# gd in RNAforested but then realizes in g2 that it can't actually build it +# resulting in unresolved symbols. + +diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in +--- ViennaRNA-1.8.3.orig/RNAforester/configure.in 2009-09-10 13:05:40.507932827 +0000 ++++ ViennaRNA-1.8.3/RNAforester/configure.in 2009-09-10 13:06:15.171952984 +0000 +@@ -47,7 +47,7 @@ + save_CPPFLAGS=$CPPFLAGS + CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"] + +-AC_CHECK_LIB(gd,main,,) ++dnl AC_CHECK_LIB(gd,main,,) + + dnl Checks for header files. + AC_HEADER_STDC diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch new file mode 100644 index 000000000000..025822f45c91 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch @@ -0,0 +1,76 @@ +diff -durr ViennaRNA-1.8.3.orig/Cluster/AS_main.c ViennaRNA-1.8.3/Cluster/AS_main.c +--- ViennaRNA-1.8.3.orig/Cluster/AS_main.c 2009-09-10 11:56:01.636674988 +0000 ++++ ViennaRNA-1.8.3/Cluster/AS_main.c 2009-09-10 11:58:32.915952366 +0000 +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <string.h> ++#include <stdlib.h> + #include "distance_matrix.h" + #include "statgeom.h" + #include "split.h" +diff -durr ViennaRNA-1.8.3.orig/Cluster/statgeom.c ViennaRNA-1.8.3/Cluster/statgeom.c +--- ViennaRNA-1.8.3.orig/Cluster/statgeom.c 2009-09-10 11:56:01.636674988 +0000 ++++ ViennaRNA-1.8.3/Cluster/statgeom.c 2009-09-10 11:58:53.192452141 +0000 +@@ -7,6 +7,7 @@ + #include <stdio.h> + #include <string.h> + #include <strings.h> ++#include <stdlib.h> + #include <ctype.h> + #include "utils.h" + #include "PS3D.h" +diff -durr ViennaRNA-1.8.3.orig/Cluster/treeplot.c ViennaRNA-1.8.3/Cluster/treeplot.c +--- ViennaRNA-1.8.3.orig/Cluster/treeplot.c 2009-09-10 11:56:01.636674988 +0000 ++++ ViennaRNA-1.8.3/Cluster/treeplot.c 2009-09-10 11:59:22.457509165 +0000 +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <string.h> ++#include <stdlib.h> + #include <math.h> + #include "distance_matrix.h" + #include "utils.h" +diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp ViennaRNA-1.8.3/RNAforester/src/main.cpp +--- ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp 2009-09-10 11:56:01.624743558 +0000 ++++ ViennaRNA-1.8.3/RNAforester/src/main.cpp 2009-09-10 12:00:37.693252890 +0000 +@@ -19,6 +19,8 @@ + #include <list> + #include <sstream> + #include <string> ++#include <cstring> ++#include <climits> + #include <map> + + //#include <sys/timeb.h> +diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h +--- ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h 2009-09-10 11:56:01.624743558 +0000 ++++ ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h 2009-09-10 12:01:41.631932654 +0000 +@@ -16,6 +16,7 @@ + + #include <algorithm> + #include <cassert> ++#include <cstring> + + #include "misc.h" + #include "types.h" +diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h +--- ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h 2009-09-10 11:56:01.620703294 +0000 ++++ ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h 2009-09-10 12:02:29.687952726 +0000 +@@ -4,6 +4,7 @@ + #include <assert.h> + #include <algorithm> + #include <climits> ++#include <cstring> + + #include "algebra.h" + #include "debug.h" +diff -durr ViennaRNA-1.8.3.orig/Readseq/ureadseq.c ViennaRNA-1.8.3/Readseq/ureadseq.c +--- ViennaRNA-1.8.3.orig/Readseq/ureadseq.c 2009-09-10 11:56:01.632743452 +0000 ++++ ViennaRNA-1.8.3/Readseq/ureadseq.c 2009-09-10 12:03:15.343952776 +0000 +@@ -20,6 +20,7 @@ + #include <stdio.h> + #include <ctype.h> + #include <string.h> ++#include <stdlib.h> + + #define UREADSEQ_G + #include "ureadseq.h" diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch new file mode 100644 index 000000000000..76a5a259a862 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch new file mode 100644 index 000000000000..c3f5b52141e8 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch @@ -0,0 +1,47 @@ +Fix implicit function declarations and attempt to free non-heap obj + +--- lib/subopt.c ++++ lib/subopt.c +@@ -80,12 +80,12 @@ + #include <string.h> + #include <math.h> + #include "fold.h" ++#include "cofold.h" + #include "utils.h" + #include "energy_par.h" + #include "fold_vars.h" + #include "pair_mat.h" + #include "list.h" +-#include "subopt.h" + #include "params.h" + + #define true 1 +--- Progs/RNAfold.c ++++ Progs/RNAfold.c +@@ -20,6 +20,7 @@ + #include "MEA.h" + extern void read_parameter_file(const char fname[]); + extern plist * stackProb(double cutoff); ++extern void init_pf_circ_fold(int length); + + /*@unused@*/ + static char UNUSED rcsid[] = "$Id$"; +--- Cluster/AS_main.c ++++ Cluster/AS_main.c +@@ -1,6 +1,7 @@ + #include <stdio.h> + #include <string.h> + #include <stdlib.h> ++#include <unistd.h> + #include "distance_matrix.h" + #include "statgeom.h" + #include "split.h" +@@ -226,7 +227,7 @@ + for(j=0;j<nn[i];j++) free(ss[i][j]); + free(ss[i]); + } +- free(ss); ++ // free(ss); // attempt to free a non-heap object ‘ss’ + } + else { + printf_taxa_list(); diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch new file mode 100644 index 000000000000..cfadc70bc6f6 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch @@ -0,0 +1,18 @@ +diff -ur ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in +--- ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in 2009-10-13 13:44:40.000000000 +0200 ++++ ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in 2010-03-27 21:39:21.000000000 +0100 +@@ -116,12 +116,12 @@ + + + clean: +- -(cd ./demo ; make clean) ++ -(cd ./demo ; $(MAKE) clean) + -rm -f $(OBJ) + -rm -f libg2.a config.cache config.log Makefile.bak config.status + -rm -f ./include/*.h + -$(FIND) . -name "*~" -exec rm -f {} \; +- -(cd ./g2_perl ; make clean) ++ -(cd ./g2_perl ; $(MAKE) clean) + -rm -f ./g2_perl/test.ps + -rm -f ./g2_perl/test.png + -rm -f ./g2_perl/test.jpg diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch new file mode 100644 index 000000000000..fcaa5f9a53b6 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch @@ -0,0 +1,26 @@ +Fix buffer overflows + +http://bugs.gentoo.org/show_bug.cgi?id=341089 + +--- Readseq/ureadseq.c ++++ Readseq/ureadseq.c +@@ -1579,7 +1579,7 @@ + + short linesout = 0, seqtype = kNucleic; + long i, j, l, l1, ibase; +- char idword[31], endstr[10]; ++ char idword[31], endstr[15]; + char seqnamestore[128], *seqname = seqnamestore; + char s[kMaxseqwidth], *cp; + char nameform[10], numform[10], nocountsymbols[10]; +--- lib/part_func_up.c ++++ lib/part_func_up.c +@@ -1438,7 +1438,7 @@ + PUBLIC int plot_free_pu_out(pu_out* res, interact *pint, char *ofile, char *head) { + int size,s,i,len; + double dG_u; +- char nan[4], *time, startl[2], dg[10];; ++ char nan[4], *time, startl[3], dg[10];; + FILE *wastl; + + wastl = fopen(ofile,"a"); diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py new file mode 100644 index 000000000000..0aeaf2a116d3 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py @@ -0,0 +1,27 @@ +from distutils.core import setup, Extension +import os +import sys + +old_filename = os.path.join("Perl", "RNA.py") +new_filename = os.path.join("Perl", "__init__.py") +if os.path.exists(old_filename): + os.rename(old_filename, new_filename) + +extra_link_args = [] + +extension = Extension("_RNA", + ["Perl/RNA_wrap.c"], + libraries=['RNA'], + library_dirs=['lib'], + extra_link_args=extra_link_args + ) + +setup(name="RNA", + version="1.8.5", + description="Vienna RNA", + author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", + url="http://www.tbi.univie.ac.at/RNA/", + package_dir = {'RNA':'Perl'}, + packages = ['RNA'], + ext_modules=[extension], + ) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch new file mode 100644 index 000000000000..6d35ecea9b0f --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch new file mode 100644 index 000000000000..de457f318e8e --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch @@ -0,0 +1,15 @@ + Readseq/readseq.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/Readseq/readseq.c b/Readseq/readseq.c +index 8af7b39..56a25ae 100644 +--- a/Readseq/readseq.c ++++ b/Readseq/readseq.c +@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' + #include <stdio.h> + #include <string.h> + #include <ctype.h> ++#include <stdlib.h> + + #include "ureadseq.h" + diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch new file mode 100644 index 000000000000..ee4aef5c3308 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch @@ -0,0 +1,30 @@ + Readseq/Makefile | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Readseq/Makefile b/Readseq/Makefile +index f073aaa..05f2edd 100644 +--- a/Readseq/Makefile ++++ b/Readseq/Makefile +@@ -6,11 +6,11 @@ + # + + # pick an ANSI C compiler (the default Sun CC is not ANSI) +-CC=gcc # Gnu C Compiler ++CC?=gcc # Gnu C Compiler + #CC=cc # SGI Irix + #CC=vcc # some DEC Ultrix + +-CFLAGS= ++CFLAGS?= + #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum + # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software + +@@ -40,7 +40,7 @@ all: build test + + build: $(SOURCES) + @echo "Compiling readseq..." +- $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c + + # if using NCBI, uncomment these lines in place of build: above + #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py new file mode 100644 index 000000000000..57f6b712ba3d --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py @@ -0,0 +1,27 @@ +from distutils.core import setup, Extension +import os +import sys + +old_filename = os.path.join("Perl", "RNA.py") +new_filename = os.path.join("Perl", "__init__.py") +if os.path.exists(old_filename): + os.rename(old_filename, new_filename) + +extra_link_args = [] + +extension = Extension("_RNA", + ["Perl/RNA_wrap.c"], + libraries=['RNA'], + library_dirs=['lib'], + extra_link_args=extra_link_args + ) + +setup(name="RNA", + version="2.1.1", + description="Vienna RNA", + author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", + url="http://www.tbi.univie.ac.at/RNA/", + package_dir = {'RNA':'Perl'}, + packages = ['RNA'], + ext_modules=[extension], + ) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch new file mode 100644 index 000000000000..e54dff95b485 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt ct2db + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl |