[gentoo-commits] gentoo-x86 commit in sci-biology/emboss/files: emboss-6.6.0_plplot-declarations.patch README.gentoo emboss-6.6.0_fix-build-system.patch emboss-6.6.0_FORTIFY_SOURCE-fix.patch emboss-6.6.0_qa-implicit-declarations.patch

[Justin Lecher (jlec)]

jlec        15/03/28 17:03:16

  Added:                emboss-6.6.0_plplot-declarations.patch
                        README.gentoo emboss-6.6.0_fix-build-system.patch
                        emboss-6.6.0_FORTIFY_SOURCE-fix.patch
                        emboss-6.6.0_qa-implicit-declarations.patch
  Log:
  Import latest changes from science overlay, thanks Ted Tanberry for the work; fixes #504680
  
  (Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

Revision  Changes    Path
1.1                  sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch?rev=1.1&content-type=text/plain

Index: emboss-6.6.0_plplot-declarations.patch
===================================================================
--- EMBOSS-6.6.0/ajax/graphics/ajgraph.c
+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c
@@ -49,7 +49,7 @@
 
 #define GRAPH_DEBUG 1
 
-#include "plplotP.h"
+#include <plplotP.h>
 
 
 static void     GraphArray(ajuint numofpoints,
@@ -964,10 +964,10 @@
     if(!thys->ready)
     {
 #if GRAPH_DEBUG
-        ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
+        ajDebug("=g= plsfnam ('%S')\n", txt);
 #endif
 
-        plxsfnam(ajStrGetPtr(txt), ext);
+        plsfnam(ajStrGetPtr(txt));
         ajStrAssignS(&graphBasename, txt);
         ajStrAssignC(&graphExtension, ext);
         if(ajStrGetCharFirst(graphExtension) == '.')
@@ -1213,10 +1213,10 @@
 void ajGraphicsSetPenwidth(float penwidth)
 {
 #if GRAPH_DEBUG
-    ajDebug("=g= plwid(%.2f) [width]\n", penwidth);
+    ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth);
 #endif
 
-    plwid((PLINT)penwidth);
+    c_plwidth((PLINT)penwidth);
 
     return;
 }
@@ -1538,10 +1538,10 @@
 static void GraphSetPen(ajint colour)
 {
 #if GRAPH_DEBUG
-    ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
+    ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
 #endif
 
-    plcol((PLINT)colour);
+    plcol0((PLINT)colour);
 
     return;
 }
--- EMBOSS-6.6.0/ajax/graphics/ajgraph.h
+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h
@@ -32,7 +32,7 @@
 /* ========================================================================= */
 
 #include "ajdefine.h"
-#include "plplot.h"
+#include <plplot.h>
 #include "ajgraphstruct.h"
 #include "ajdefine.h"
 #include "ajstr.h"



1.1                  sci-biology/emboss/files/README.gentoo

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

Index: README.gentoo
===================================================================
Administrating EMBOSS on Gentoo systems
=======================================


Codon data files location
-------------------------

The codon data files that are distributed with EMBOSS are installed in the
``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
these codon files and those installed with the CUTG database. The names of
these files sometimes vary only by their case. Having both sets of files in
the same directory is also impossible on systems such as MacOSX, where the
root filesystem is case insensitive. If you do not have the CUTG database
installed and want to use the codon files distributed with EMBOSS, you can
symlink the ``CODONS.orig`` directory to ``CODONS``::

	# cd ${EPREFIX}/usr/share/EMBOSS/data
	# ln -s CODONS.orig CODONS


Restriction enzymes equivalence file location
---------------------------------------------

The restriction enzymes equivalence file distributed with EMBOSS is installed
as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
collision with the equivalence file provided by the Rebase database. If you do
not have the Rebase database installed and want to use the equivalence file
distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
``embossre.equ``::

	# cd ${EPREFIX}/usr/share/EMBOSS/data
	# ln -s embossre.equ.orig embossre.equ



1.1                  sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch?rev=1.1&content-type=text/plain

Index: emboss-6.6.0_fix-build-system.patch
===================================================================
--- EMBOSS-6.6.0/ajax/acd/Makefile.am
+++ EMBOSS-6.6.0/ajax/acd/Makefile.am
@@ -3,16 +3,20 @@
 lib_LTLIBRARIES = libacd.la
 
 libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
 
 libacd_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ajaxdb
+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 if !ESYSTEMLIBS
+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
 libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+libacd_la_CFLAGS   += $(PLPLOT_CFLAGS)
+endif
 libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
 libacd_la_LDFLAGS  = -version-info 6:5:0
--- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am
+++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am
@@ -3,14 +3,16 @@
 lib_LTLIBRARIES = libajaxdb.la
 
 libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
 
 libajaxdb_la_CPPFLAGS  = -I$(top_srcdir)/ajax/ensembl
-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
 libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
+endif
 libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
 libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
--- EMBOSS-6.6.0/ajax/core/ajreg.h
+++ EMBOSS-6.6.0/ajax/core/ajreg.h
@@ -39,9 +39,8 @@
 #include "ajdefine.h"
 #include "ajstr.h"
 
-#include "pcre_config.h"
-#include "pcre_internal.h"
-#include "pcreposix.h"
+#include <pcre.h>
+#include <pcreposix.h>
 
 AJ_BEGIN_DECLS
 
@@ -84,7 +83,7 @@
 
 typedef struct AjSRegexp
 {
-    real_pcre *pcre;
+    struct real_pcre *pcre;
     pcre_extra *extra;
     int *ovector;
     const char* orig;
--- EMBOSS-6.6.0/ajax/core/Makefile.am
+++ EMBOSS-6.6.0/ajax/core/Makefile.am
@@ -3,13 +3,15 @@
 lib_LTLIBRARIES = libajax.la
 
 libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS)
 
-libajax_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libajax_la_CPPFLAGS  =
 if !ESYSTEMLIBS
+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
 libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
+endif
 libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
 libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
--- EMBOSS-6.6.0/ajax/ensembl/Makefile.am
+++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am
@@ -3,13 +3,15 @@
 lib_LTLIBRARIES = libensembl.la
 
 libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libensembl_la_LIBADD = ../core/libajax.la
 
-libensembl_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libensembl_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
-endif
 libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
+endif
 libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
 libensembl_la_LDFLAGS  = -version-info 6:5:0
--- EMBOSS-6.6.0/ajax/graphics/Makefile.am
+++ EMBOSS-6.6.0/ajax/graphics/Makefile.am
@@ -3,12 +3,16 @@
 lib_LTLIBRARIES = libajaxg.la
 
 libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS)
 
-libajaxg_la_CPPFLAGS  = -I$(top_srcdir)/ajax/pcre
+libajaxg_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
-endif
 libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+libajaxg_la_CFLAGS   += $(PLPLOT_CFLAGS)
+endif
 libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
 
 libajaxg_la_LDFLAGS  = -version-info 6:5:0
--- EMBOSS-6.6.0/ajax/Makefile.am
+++ EMBOSS-6.6.0/ajax/Makefile.am
@@ -1,7 +1,7 @@
 ## Process this file with automake to produce Makefile.in
 
-SUBDIRS  = pcre
+SUBDIRS  =
 if !ESYSTEMLIBS
-SUBDIRS += expat zlib
+SUBDIRS += pcre expat zlib
 endif
 SUBDIRS += core graphics ensembl ajaxdb acd
--- EMBOSS-6.6.0/configure.ac
+++ EMBOSS-6.6.0/configure.ac
@@ -629,32 +629,6 @@
 
 
 
-
-dnl PCRE library definitions - see the MAJOR and MINOR values
-dnl to see which version's configure.in these lines come from
-
-dnl Provide the current PCRE version information. Do not use numbers
-dnl with leading zeros for the minor version, as they end up in a C
-dnl macro, and may be treated as octal constants. Stick to single
-dnl digits for minor numbers less than 10. There are unlikely to be
-dnl that many releases anyway.
-
-PCRE_MAJOR="7"
-PCRE_MINOR="9"
-PCRE_DATE="11-Apr-2009"
-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
-
-dnl Default values for miscellaneous macros
-
-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
-
-dnl Provide versioning information for libtool shared libraries that
-dnl are built by default on Unix systems.
-
-PCRE_LIB_VERSION="0:1:0"
-PCRE_POSIXLIB_VERSION="0:0:0"
-
-
 dnl Define where the EMBOSS package is located
 AC_SUBST([AJAX_FIXED_ROOT])
 AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
@@ -743,17 +717,7 @@
 
 
 
-dnl "Export" these variables for PCRE
 
-AC_SUBST([HAVE_MEMMOVE])
-AC_SUBST([HAVE_STRERROR])
-AC_SUBST([PCRE_MAJOR])
-AC_SUBST([PCRE_MINOR])
-AC_SUBST([PCRE_DATE])
-AC_SUBST([PCRE_VERSION])
-AC_SUBST([PCRE_LIB_VERSION])
-AC_SUBST([PCRE_POSIXLIB_VERSION])
-AC_SUBST([POSIX_MALLOC_THRESHOLD])
 
 
 
@@ -849,7 +813,51 @@
 
 AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
 
-
+AS_IF([test "x${enable_systemlibs}" = "xyes"],
+[
+dnl using system libraries
+  PKG_CHECK_MODULES([PCRE], [libpcre])
+  PKG_CHECK_MODULES([EXPAT], [expat])
+  PKG_CHECK_MODULES([ZLIB], [zlib])
+  PKG_CHECK_MODULES([PLPLOT], [plplotd])
+],
+[
+dnl using bundled libraries
+  dnl PCRE library definitions - see the MAJOR and MINOR values
+  dnl to see which version's configure.ac these lines come from
+
+  dnl Provide the current PCRE version information. Do not use numbers
+  dnl with leading zeros for the minor version, as they end up in a C
+  dnl macro, and may be treated as octal constants. Stick to single
+  dnl digits for minor numbers less than 10. There are unlikely to be
+  dnl that many releases anyway.
+
+  PCRE_MAJOR="7"
+  PCRE_MINOR="9"
+  PCRE_DATE="11-Apr-2009"
+  PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+
+  dnl Default values for miscellaneous macros
+
+  POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+
+  dnl Provide versioning information for libtool shared libraries that
+  dnl are built by default on Unix systems.
+
+  PCRE_LIB_VERSION="0:1:0"
+  PCRE_POSIXLIB_VERSION="0:0:0"
+
+  dnl "Export" these variables for PCRE
+  AC_SUBST([HAVE_MEMMOVE])
+  AC_SUBST([HAVE_STRERROR])
+  AC_SUBST([PCRE_MAJOR])
+  AC_SUBST([PCRE_MINOR])
+  AC_SUBST([PCRE_DATE])
+  AC_SUBST([PCRE_VERSION])
+  AC_SUBST([PCRE_LIB_VERSION])
+  AC_SUBST([PCRE_POSIXLIB_VERSION])
+  AC_SUBST([POSIX_MALLOC_THRESHOLD])
+])
 
 
 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
--- EMBOSS-6.6.0/emboss/Makefile.am
+++ EMBOSS-6.6.0/emboss/Makefile.am
@@ -28,15 +28,18 @@
 
 AM_CPPFLAGS  = -I$(top_srcdir)/ajax/acd
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
-AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 if !ESYSTEMLIBS
+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+AM_CPPFLAGS += -I$(top_srcdir)/plplot
+else
+AM_CFLAGS   += $(PLPLOT_CFLAGS)
 endif
 AM_CPPFLAGS += -I$(top_srcdir)/nucleus
-AM_CPPFLAGS += -I$(top_srcdir)/plplot
 AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
 AM_CPPFLAGS += $(JAVA_CPPFLAGS)
 
@@ -49,9 +52,11 @@
 if !ESYSTEMLIBS
 LDADD += ../ajax/zlib/libezlib.la
 LDADD += ../ajax/expat/libeexpat.la
-endif
 LDADD += ../ajax/pcre/libepcre.la
 LDADD += ../plplot/libeplplot.la
+else
+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS)
+endif
 LDADD += $(XLIB)
 
 #if PURIFY
--- EMBOSS-6.6.0/jemboss/lib/Makefile.am
+++ EMBOSS-6.6.0/jemboss/lib/Makefile.am
@@ -12,7 +12,7 @@
 jalviewApplet.jar \
 jemboss.jar
 
-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java
+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java
 if JAVA_BUILD
 	$(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes;
 endif
--- EMBOSS-6.6.0/m4/idxdbs.m4
+++ EMBOSS-6.6.0/m4/idxdbs.m4
@@ -1,17 +1,8 @@
 AC_DEFUN([CHECK_IDXDBS],
 [
-AC_MSG_CHECKING(for EMBOSS pre-indexed databases)
+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases)
 
-
-if test -f ./emboss/index/edam.xac; then
-AC_MSG_RESULT(yes)
-else
-AC_MSG_RESULT(no)
-echo ""
-echo "Pre-indexed edam, taxon + drcat databases not found."
-echo "Please download them from within this directory using:"
-echo "    rsync -av rsync://emboss.open-bio.org/EMBOSS/ ."
-echo "and then repeat the configure step."
-exit 1
-fi
+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac],
+	[],
+	[AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])])
 ])
--- EMBOSS-6.6.0/Makefile.am
+++ EMBOSS-6.6.0/Makefile.am
@@ -12,8 +12,11 @@
 ONEWS \
 PROBLEMS
 
-SUBDIRS = \
-plplot \
+SUBDIRS =
+if !ESYSTEMLIBS
+SUBDIRS += plplot
+endif
+SUBDIRS += \
 ajax \
 nucleus \
 emboss \
@@ -33,5 +36,3 @@
 	tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
 	tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf )
 
-install-exec-hook:
-	$(bindir)/embossupdate
--- EMBOSS-6.6.0/nucleus/Makefile.am
+++ EMBOSS-6.6.0/nucleus/Makefile.am
@@ -3,6 +3,7 @@
 lib_LTLIBRARIES = libnucleus.la
 
 libnucleus_la_CFLAGS  = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
+libnucleus_la_LIBADD  = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
 
 if ISSHARED
 if ISAIXIA64
@@ -10,11 +11,14 @@
 endif
 endif
 
-libnucleus_la_CPPFLAGS  = -I$(top_srcdir)/plplot
-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
+libnucleus_la_CPPFLAGS  = -I$(top_srcdir)/ajax/core
 if !ESYSTEMLIBS
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
+else
+libnucleus_la_CFLAGS   += $(PLPLOT_CFLAGS)
 endif
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
 libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl



1.1                  sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch?rev=1.1&content-type=text/plain

Index: emboss-6.6.0_FORTIFY_SOURCE-fix.patch
===================================================================
--- EMBOSS-6.6.0/emboss/embossversion.c
+++ EMBOSS-6.6.0/emboss/embossversion.c
@@ -415,7 +415,7 @@
 	ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING);
 #endif
 #ifdef _FORTIFY_SOURCE
-	ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE);
+	ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL);
 #endif
 	ajFmtPrintF(outfile, "\n");
 	ajFmtPrintF(outfile, "Sizes (bytes):\n");



1.1                  sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch?rev=1.1&content-type=text/plain

Index: emboss-6.6.0_qa-implicit-declarations.patch
===================================================================
--- EMBOSS-6.6.0/ajax/core/ajfeatread.c
+++ EMBOSS-6.6.0/ajax/core/ajfeatread.c
@@ -45,6 +45,7 @@
 
 #include <limits.h>
 #include <math.h>
+#include <string.h>
 #include <errno.h>
 
 #ifdef WIN32
--- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c
+++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c
@@ -43,7 +43,7 @@
 
 #include <limits.h>
 #include <math.h>
-
+#include <string.h>
 
 static AjPRegexp featoutRegUfoFmt = NULL;
 static AjPRegexp featoutRegUfoFile = NULL;
--- EMBOSS-6.6.0/ajax/core/ajpdbio.c
+++ EMBOSS-6.6.0/ajax/core/ajpdbio.c
@@ -37,7 +37,7 @@
 
 #include <limits.h>
 #include <math.h>
-
+#include <string.h>
 
 
 
--- EMBOSS-6.6.0/ajax/core/ajreg.c
+++ EMBOSS-6.6.0/ajax/core/ajreg.c
@@ -32,6 +32,7 @@
 #include "ajlib.h"
 
 #include "ajreg.h"
+#include <string.h>
 
 
 
--- EMBOSS-6.6.0/ajax/core/ajseqtype.c
+++ EMBOSS-6.6.0/ajax/core/ajseqtype.c
@@ -32,7 +32,7 @@
 #include "ajfeat.h"
 #include "ajfile.h"
 #include "ajreg.h"
-
+#include <string.h>
 
 
 
--- EMBOSS-6.6.0/nucleus/embindex.c
+++ EMBOSS-6.6.0/nucleus/embindex.c
@@ -35,6 +35,7 @@
 #include "ajnam.h"
 
 #include <errno.h>
+#include <string.h>
 
 #define BTENTRYFILE     ".ent"
 #define KWLIMIT 12
--- EMBOSS-6.6.0/nucleus/embword.c
+++ EMBOSS-6.6.0/nucleus/embword.c
@@ -36,7 +36,7 @@
 #include "ajutil.h"
 
 #include <math.h>
-
+#include <string.h>