From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/emboss/files/README.gentoo | 34 ++ .../files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch | 11 + .../files/emboss-6.6.0_fix-build-system.patch | 411 +++++++++++++++++++++ .../files/emboss-6.6.0_plplot-declarations.patch | 61 +++ .../emboss-6.6.0_qa-implicit-declarations.patch | 74 ++++ 5 files changed, 591 insertions(+) create mode 100644 sci-biology/emboss/files/README.gentoo create mode 100644 sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch create mode 100644 sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch create mode 100644 sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch create mode 100644 sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch (limited to 'sci-biology/emboss/files') diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo new file mode 100644 index 000000000000..d1879bd0811c --- /dev/null +++ b/sci-biology/emboss/files/README.gentoo @@ -0,0 +1,34 @@ +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 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 new file mode 100644 index 000000000000..7704873e9d26 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch @@ -0,0 +1,11 @@ +--- 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 new file mode 100644 index 000000000000..266bddd95a37 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch @@ -0,0 +1,411 @@ + 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 ++#include + + 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 new file mode 100644 index 000000000000..15f5f967a07d --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch @@ -0,0 +1,61 @@ +--- 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 + + + 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 + #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 new file mode 100644 index 000000000000..eff10b2e6700 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch @@ -0,0 +1,74 @@ +--- EMBOSS-6.6.0/ajax/core/ajfeatread.c ++++ EMBOSS-6.6.0/ajax/core/ajfeatread.c +@@ -45,6 +45,7 @@ + + #include + #include ++#include + #include + + #ifdef WIN32 +--- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c ++++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c +@@ -43,7 +43,7 @@ + + #include + #include +- ++#include + + 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 + #include +- ++#include + + + +--- 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 + + + +--- 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 + + + +--- EMBOSS-6.6.0/nucleus/embindex.c ++++ EMBOSS-6.6.0/nucleus/embindex.c +@@ -35,6 +35,7 @@ + #include "ajnam.h" + + #include ++#include + + #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 +- ++#include + + + -- cgit v1.2.3