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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2011-05-18 18:10:34 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2011-05-18 18:10:34 +0200 |
| commit | 71511493b0866f094c9b7a11490facd09df27c86 (patch) | |
| tree | cf7536e3ae6c3997260f4269842746b32ce5b60a /sci-biology/mira/files | |
| parent | sci-biology/consed-20-r1: improve message on die() (diff) | |
| download | sci-71511493b0866f094c9b7a11490facd09df27c86.tar.gz sci-71511493b0866f094c9b7a11490facd09df27c86.tar.bz2 sci-71511493b0866f094c9b7a11490facd09df27c86.zip | |
sci-biology/mira-3.2.1-r1: added an extra patch for traceinfo off-by-one error
(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)
Diffstat (limited to 'sci-biology/mira/files')
| -rw-r--r-- | sci-biology/mira/files/mira-3.0.0-asneeded.patch | 56 | ||||
| -rw-r--r-- | sci-biology/mira/files/mira_left_clip.readpool.C.patch | 36 |
2 files changed, 92 insertions, 0 deletions
diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch new file mode 100644 index 000000000..9bbd267cf --- /dev/null +++ b/sci-biology/mira/files/mira-3.0.0-asneeded.patch @@ -0,0 +1,56 @@ +http://bugs.gentoo.org/show_bug.cgi?id=305547 + +--- config/m4/ax_lib_expat.m4 ++++ config/m4/ax_lib_expat.m4 +@@ -96,6 +99,7 @@ + + EXPAT_CFLAGS="" + EXPAT_LDFLAGS="" ++ EXPAT_LIBS="" + EXPAT_VERSION="" + + dnl +@@ -105,7 +109,8 @@ + + if test -n "$expat_prefix"; then + expat_include_dir="$expat_prefix/include" +- expat_lib_flags="-L$expat_prefix/lib -lexpat" ++ expat_lib_flags="-L$expat_prefix/lib" ++ expat_libs="-lexpat" + run_expat_test="yes" + elif test "$expat_requested" = "yes"; then + if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then +@@ -126,6 +131,8 @@ + saved_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS $expat_lib_flags" + ++ saved_LIBS="$LIBS" ++ LIBS="$LIBS $expat_libs" + dnl + dnl Check Expat headers + dnl +@@ -171,7 +178,8 @@ + ]] + )], + [ + EXPAT_LDFLAGS="$expat_lib_flags" ++ EXPAT_LIBS="$expat_libs" + expat_lib_found="yes" + AC_MSG_RESULT([found]) + ], +@@ -185,6 +193,7 @@ + + CPPFLAGS="$saved_CPPFLAGS" + LDFLAGS="$saved_LDFLAGS" ++ LIBS="$saved_LIBS" + fi + + AC_MSG_CHECKING([for Expat XML Parser]) +@@ -194,6 +203,7 @@ + + AC_SUBST([EXPAT_CFLAGS]) + AC_SUBST([EXPAT_LDFLAGS]) ++ AC_SUBST([EXPAT_LIBS]) + + HAVE_EXPAT="yes" + else diff --git a/sci-biology/mira/files/mira_left_clip.readpool.C.patch b/sci-biology/mira/files/mira_left_clip.readpool.C.patch new file mode 100644 index 000000000..12977dd7c --- /dev/null +++ b/sci-biology/mira/files/mira_left_clip.readpool.C.patch @@ -0,0 +1,36 @@ +*** src/mira/readpool.C.ori 2010-11-21 11:42:29.000000000 -0600 +--- src/mira/readpool.C 2011-01-13 10:20:38.000000000 -0600 +*************** +*** 1751,1757 **** + break; + } + case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT : { +! REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str())); + break; + } + case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT : { +--- 1751,1757 ---- + break; + } + case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT : { +! REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str())-1); + break; + } + case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT : { +*************** +*** 1759,1765 **** + break; + } + case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT : { +! REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str())); + break; + } + case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT : { +--- 1759,1765 ---- + break; + } + case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT : { +! REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str())-1); + break; + } + case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT : { |