sci-biology/emboss: Fix C99 `bool` clash

* Also fix `-Wimplicit-function-declaration`

Closes: https://bugs.gentoo.org/695380
Signed-off-by: David Seifert <soap@gentoo.org>

6 files changed, 10 insertions, 562 deletions

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index e4650c04fb9a..f97d826f09b6 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1 +1,2 @@
 DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a
+DIST emboss-6.6.0-patches.tar.xz 5408 BLAKE2B ec1c55c90a64b1c27645804411b44e413ae881b1637ad2b8dfcff172e15b841cc3d2807039761f8307b0b5a29ab5b1a2c840e189f326091aa9ce25317ec9cda6 SHA512 942681df428f6254c1711902f667c6e8c71babf3e9b0c73b8b7d2fbfa5e8856ce5817560280948e588f6037011ad7055a3af5b88a58fc2b14349869927c889eb
diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
index 1c74ded5e22f..766dd6a61b0c 100644
--- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild
+++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
@@ -8,7 +8,9 @@ EBO_EAUTORECONF=1
 inherit emboss-r2 readme.gentoo-r1
 
 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz"
+SRC_URI="
+	ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz
+	https://dev.gentoo.org/~soap/distfiles/${P}-patches.tar.xz"
 S="${WORKDIR}/${P^^}"
 
 LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
@@ -29,10 +31,12 @@ PDEPEND="
 	)"
 
 PATCHES=(
-	"${FILESDIR}"/${P}_fix-build-system.patch
-	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
-	"${FILESDIR}"/${P}_plplot-declarations.patch
-	"${FILESDIR}"/${P}_qa-implicit-declarations.patch
+	"${WORKDIR}"/patches/${P}-fix-build-system.patch
+	"${WORKDIR}"/patches/${P}-FORTIFY_SOURCE-fix.patch
+	"${WORKDIR}"/patches/${P}-plplot-declarations.patch
+	"${WORKDIR}"/patches/${P}-qa-implicit-declarations.patch
+	"${WORKDIR}"/patches/${P}-C99-bool.patch
+	"${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch
 )
 
 src_install() {
diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch
deleted file mode 100644
index 7704873e9d26..000000000000
--- a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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");
diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
deleted file mode 100644
index 266bddd95a37..000000000000
--- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch
+++ /dev/null
@@ -1,411 +0,0 @@
- Makefile.am               |  9 +++---
- ajax/Makefile.am          |  4 +--
- ajax/acd/Makefile.am      |  8 +++--
- ajax/ajaxdb/Makefile.am   |  6 ++--
- ajax/core/Makefile.am     |  6 ++--
- ajax/core/ajreg.h         |  7 ++--
- ajax/ensembl/Makefile.am  |  6 ++--
- ajax/graphics/Makefile.am |  8 +++--
- configure.ac              | 82 ++++++++++++++++++++++++++---------------------
- emboss/Makefile.am        | 13 +++++---
- jemboss/lib/Makefile.am   |  2 +-
- m4/idxdbs.m4              | 17 +++-------
- nucleus/Makefile.am       |  8 +++--
- 13 files changed, 100 insertions(+), 76 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 177dec5..18dd99a 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -12,8 +12,11 @@ LICENSE \
- ONEWS \
- PROBLEMS
- 
--SUBDIRS = \
--plplot \
-+SUBDIRS =
-+if !ESYSTEMLIBS
-+SUBDIRS += plplot
-+endif
-+SUBDIRS += \
- ajax \
- nucleus \
- emboss \
-@@ -33,5 +36,3 @@ dist-hook:
- 	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
-diff --git a/ajax/Makefile.am b/ajax/Makefile.am
-index f27472c..de34e17 100644
---- a/ajax/Makefile.am
-+++ b/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
-diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
-index 9f0f700..3295a1d 100644
---- a/ajax/acd/Makefile.am
-+++ b/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
-diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
-index c2b0c00..9de14fe 100644
---- a/ajax/ajaxdb/Makefile.am
-+++ b/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)
- 
-diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
-index 2906837..3189c34 100644
---- a/ajax/core/Makefile.am
-+++ b/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)
-diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
-index 1623c82..5d928cf 100644
---- a/ajax/core/ajreg.h
-+++ b/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 @@ AJ_BEGIN_DECLS
- 
- typedef struct AjSRegexp
- {
--    real_pcre *pcre;
-+    struct real_pcre *pcre;
-     pcre_extra *extra;
-     int *ovector;
-     const char* orig;
-diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
-index 0d1250b..5484c02 100644
---- a/ajax/ensembl/Makefile.am
-+++ b/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
-diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
-index a4f202b..1114c2c 100644
---- a/ajax/graphics/Makefile.am
-+++ b/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 += $(JAVA_CPPFLAGS)
- 
- libajaxg_la_LDFLAGS  = -version-info 6:5:0
-diff --git a/configure.ac b/configure.ac
-index a7bd9c6..9ba3121 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -629,32 +629,6 @@ AS_CASE([${host_os}],
- 
- 
- 
--
--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 @@ AX_LIB_POSTGRESQL
- 
- 
- 
--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 +813,53 @@ AC_ARG_ENABLE([systemlibs],
- 
- 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],
-+    [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+    )
-+],
-+[
-+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
-diff --git a/emboss/Makefile.am b/emboss/Makefile.am
-index 89ada78..f987d40 100644
---- a/emboss/Makefile.am
-+++ b/emboss/Makefile.am
-@@ -28,15 +28,18 @@ endif
- 
- 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$(top_srcdir)/ajax/graphics
-+if !ESYSTEMLIBS
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
--if !ESYSTEMLIBS
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
--endif
--AM_CPPFLAGS += -I$(top_srcdir)/nucleus
- AM_CPPFLAGS += -I$(top_srcdir)/plplot
-+else
-+AM_CFLAGS   += $(PLPLOT_CFLAGS)
-+endif
-+AM_CPPFLAGS += -I$(top_srcdir)/nucleus
- AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
- AM_CPPFLAGS += $(JAVA_CPPFLAGS)
- 
-@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la
- 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 += $(XLIB)
- 
- #if PURIFY
-diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am
-index 5f7e21e..8b45ce2 100644
---- a/jemboss/lib/Makefile.am
-+++ b/jemboss/lib/Makefile.am
-@@ -12,7 +12,7 @@ mail.jar \
- jalviewApplet.jar \
- jemboss.jar
- 
--jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java
-+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java
- if JAVA_BUILD
- 	$(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes;
- endif
-diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4
-index 0ca7ea9..9b54f2a 100644
---- a/m4/idxdbs.m4
-+++ b/m4/idxdbs.m4
-@@ -1,17 +1,8 @@
- AC_DEFUN([CHECK_IDXDBS],
- [
--AC_MSG_CHECKING(for EMBOSS pre-indexed databases)
-+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases)
- 
--
--if test -f ./emboss/index/edam.xac; then
--AC_MSG_RESULT(yes)
--else
--AC_MSG_RESULT(no)
--echo ""
--echo "Pre-indexed edam, taxon + drcat databases not found."
--echo "Please download them from within this directory using:"
--echo "    rsync -av rsync://emboss.open-bio.org/EMBOSS/ ."
--echo "and then repeat the configure step."
--exit 1
--fi
-+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac],
-+	[],
-+	[AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])])
- ])
-diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
-index 37b8543..5819c89 100644
---- a/nucleus/Makefile.am
-+++ b/nucleus/Makefile.am
-@@ -3,6 +3,7 @@
- lib_LTLIBRARIES = libnucleus.la
- 
- libnucleus_la_CFLAGS  = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
-+libnucleus_la_LIBADD  = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
- 
- if ISSHARED
- if ISAIXIA64
-@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm
- endif
- endif
- 
--libnucleus_la_CPPFLAGS  = -I$(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
diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch
deleted file mode 100644
index 15f5f967a07d..000000000000
--- a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- 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"
diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch
deleted file mode 100644
index eff10b2e6700..000000000000
--- a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch
+++ /dev/null
@@ -1,74 +0,0 @@
---- 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>
- 
- 
-