sci-biology/consed: Fix building under GCC 7+

consed (and MOTIF programs in general) is very sensitive
to link order:
* http://users.polytech.unice.fr/~buffa/cours/X11_Motif/motif-faq/part9/faq-doc-10.html
* https://bugzilla.redhat.com/show_bug.cgi?id=870712

Closes: https://bugs.gentoo.org/681920
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: David Seifert <soap@gentoo.org>

diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch
index 27c9c552fe3f3f5027c777783d8a3df61d16645b..30819f93ac80bcd21ce238d2f649422d605a32b0 100644 (file)
--- a/sci-biology/consed/files/consed-29-fix-build-system.patch
+++ b/sci-biology/consed/files/consed-29-fix-build-system.patch
@@ -45,7 +45,7 @@ Make build system semi-sane:
 -/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \
 -/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a
 +
-+MOTIF_LIBS ?= -lXt -lXm
++MOTIF_LIBS ?= -lXm -lXt
 +ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS)
  
  

diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch
index 5bdf0264d25bb6471dd91e0812770190ab59b967..90e180da017485099cc5bd5bff82e2d425e1d886 100644 (file)
--- a/sci-biology/consed/files/consed-29-fix-qa.patch
+++ b/sci-biology/consed/files/consed-29-fix-qa.patch
@@ -127,6 +127,25 @@ Fix various QA violations, due to
     printf( "x = %d\n", pEvent->x );
     printf( "y = %d\n", pEvent->y );
     printf( "x_root = %d\n", pEvent->x_root );
+--- a/parseAceFile.cpp
++++ b/parseAceFile.cpp
+@@ -45,6 +45,7 @@
+ using namespace std;
+ #include    "basesegment.h"
+ #include    <stdio.h>
++#include    <stddef.h>
+ #include    <string.h>
+ #include    <sstream>
+ #include    "mbt_errors.h"
+@@ -292,7 +293,7 @@
+    char* szPossibleComp = szReadName + nLength - nCOMP;
+ 
+    if (memcmp( szPossibleComp, szCOMP, nCOMP ) == 0 ) {
+-      szPossibleComp = '\0';
++      szPossibleComp = NULL;
+       return( true );
+    }
+    else
 --- a/phaster2PhdBall.cpp
 +++ b/phaster2PhdBall.cpp
 @@ -547,7 +547,7 @@