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>
