[gentoo-commits] gentoo-x86 commit in sci-biology/maq/files: maq-0.7.1-bfr-overfl.patch maq-0.7.1-flags.patch

[gentoo-commits] gentoo-x86 commit in sci-biology/maq/files: maq-0.7.1-bfr-overfl.patch maq-0.7.1-flags.patch

[Justin Lecher (jlec)]

jlec        11/04/14 07:46:28

  Added:                maq-0.7.1-bfr-overfl.patch maq-0.7.1-flags.patch
  Log:
  Fix for _FORTIFY_SOURCE indicates presence of overflow, #363537; Don't mix FLAGS
  
  (Portage version: 2.2.0_alpha30/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch?rev=1.1&content-type=text/plain

Index: maq-0.7.1-bfr-overfl.patch
===================================================================
 simulate.c |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/simulate.c b/simulate.c
index 788c440..67ba2ba 100644
--- a/simulate.c
+++ b/simulate.c
@@ -383,7 +383,7 @@ static void simustat_core(gzFile fp, int Q_thres)
 	memset(wc_single, 0, 40); memset(tot_single, 0, 40);
 	memset(wc_pair, 0, 40); memset(tot_pair, 0, 40);
 	memset(abpair, 0, 4 * 256 * 10);
-	memset(tc[2], 0, 4 * sizeof(int));
+	memset(tc, 0, 4 * sizeof(int));
 	while (maqmap_read1(fp, m1)) {
 		int is_correct;
 		bit32_t p1, p2;



1.1                  sci-biology/maq/files/maq-0.7.1-flags.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/maq/files/maq-0.7.1-flags.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/maq/files/maq-0.7.1-flags.patch?rev=1.1&content-type=text/plain

Index: maq-0.7.1-flags.patch
===================================================================
 configure.ac |    3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

diff --git a/configure.ac b/configure.ac
index ad2f1e6..4f9d7be 100644
--- a/configure.ac
+++ b/configure.ac
@@ -8,6 +8,7 @@ AC_PROG_CXX
 
 # set CFLAGS and CXXFLAGS
 user_CFLAGS=${CFLAGS}
+user_CXXFLAGS=${CXXFLAGS}
 generic_CFLAGS="-Wall"
 ext_CFLAGS=""
 case "${host_cpu}-${host_os}" in
@@ -37,7 +38,7 @@ AC_ARG_ENABLE(shortread,    [  --enable-shortreads     use shortread mode],
 AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
 			  [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
 CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS}"
-CXXFLAGS=$CFLAGS
+CXXFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CXXFLAGS}"
 
 AC_STDC_HEADERS
 AC_CHECK_HEADER(zlib.h)