From 95a931bb4747f70c54b30bf1a8d3161fd0464614 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sat, 28 Mar 2015 17:17:41 +0000 Subject: [PATCH] Import latest changes from science overlay, thanks Ted Tanberry for the work; fixes #335603 Package-Manager: portage-2.2.18/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- sci-biology/embassy-meme/ChangeLog | 10 ++ sci-biology/embassy-meme/Manifest | 5 + sci-biology/embassy-mse/ChangeLog | 11 +- sci-biology/embassy-mse/Manifest | 51 ++++--- .../embassy-mse/embassy-mse-3.0.0.650.ebuild | 23 +++ ...bassy-mse-3.0.0.650_fix-build-system.patch | 133 ++++++++++++++++++ sci-biology/embassy-mse/metadata.xml | 2 +- sci-biology/embassy-phylipnew/ChangeLog | 13 +- sci-biology/embassy-phylipnew/Manifest | 51 ++++--- .../embassy-phylipnew-3.69.650.ebuild | 15 ++ ...-phylipnew-3.69.650_fix-build-system.patch | 98 +++++++++++++ sci-biology/embassy-phylipnew/metadata.xml | 2 +- sci-biology/embassy-signature/ChangeLog | 13 +- sci-biology/embassy-signature/Manifest | 51 ++++--- .../embassy-signature-0.1.650.ebuild | 13 ++ ...y-signature-0.1.650_fix-build-system.patch | 90 ++++++++++++ sci-biology/embassy-signature/metadata.xml | 2 +- sci-biology/embassy-structure/ChangeLog | 13 +- sci-biology/embassy-structure/Manifest | 51 ++++--- .../embassy-structure-0.1.650.ebuild | 13 ++ ...y-structure-0.1.650_fix-build-system.patch | 90 ++++++++++++ sci-biology/embassy-structure/metadata.xml | 2 +- sci-biology/embassy-topo/ChangeLog | 11 +- sci-biology/embassy-topo/Manifest | 51 ++++--- .../embassy-topo/embassy-topo-2.0.650.ebuild | 13 ++ ...mbassy-topo-2.0.650_fix-build-system.patch | 97 +++++++++++++ sci-biology/embassy-topo/metadata.xml | 2 +- sci-biology/embassy-vienna/ChangeLog | 12 +- sci-biology/embassy-vienna/Manifest | 51 ++++--- .../embassy-vienna-1.7.2.650.ebuild | 13 ++ ...sy-vienna-1.7.2.650_fix-build-system.patch | 98 +++++++++++++ sci-biology/embassy-vienna/metadata.xml | 2 +- 32 files changed, 942 insertions(+), 160 deletions(-) create mode 100644 sci-biology/embassy-meme/ChangeLog create mode 100644 sci-biology/embassy-meme/Manifest create mode 100644 sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild create mode 100644 sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch create mode 100644 sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild create mode 100644 sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch create mode 100644 sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild create mode 100644 sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch create mode 100644 sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild create mode 100644 sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch create mode 100644 sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild create mode 100644 sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch create mode 100644 sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild create mode 100644 sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch diff --git a/sci-biology/embassy-meme/ChangeLog b/sci-biology/embassy-meme/ChangeLog new file mode 100644 index 000000000000..d4133ff2be74 --- /dev/null +++ b/sci-biology/embassy-meme/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/embassy-meme +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/ChangeLog,v 1.22 2015/03/28 17:17:41 jlec Exp $ + +*embassy-meme-4.7.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher +embassy-meme-4.7.650.ebuild, + +files/embassy-meme-4.7.650_fix-build-system.patch, +metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest new file mode 100644 index 000000000000..4c5f81081608 --- /dev/null +++ b/sci-biology/embassy-meme/Manifest @@ -0,0 +1,5 @@ +AUX embassy-meme-4.7.650_fix-build-system.patch 2359 SHA256 d28fa6f227a8131d0f582c61c75679410712d696c81735903bae4f49e78ca897 SHA512 3669c1d9a19d531d63f45f0ca5ab81e50a714158d62304ef115bb3c3a19032856049eb16857f07ccec72150c5d6a50efdf8beafceb29b99fc96c2e3c554b7125 WHIRLPOOL b1f18556c06f4eede7ab731e34607b50348512153ac931626891fa02e4d8023d289817556491e33c36a333c446fbabfd8066dd670c13ad182f84e256cef0d5f7 +DIST embassy-meme-4.7.650.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51 +EBUILD embassy-meme-4.7.650.ebuild 386 SHA256 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211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog index cd6f7078ef0a..08248221ea75 100644 --- a/sci-biology/embassy-mse/ChangeLog +++ b/sci-biology/embassy-mse/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/embassy-mse -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.38 2011/10/20 08:52:56 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.39 2015/03/28 17:14:17 jlec Exp $ + +*embassy-mse-3.0.0.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher +embassy-mse-3.0.0.650.ebuild, + +files/embassy-mse-3.0.0.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 20 Oct 2011; Kacper Kowalik embassy-mse-1.0.0-r6.ebuild, embassy-mse-1.0.0-r7.ebuild: diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest index 3c6ac13dcb64..00bd96e6004f 100644 --- a/sci-biology/embassy-mse/Manifest +++ b/sci-biology/embassy-mse/Manifest @@ -1,28 +1,33 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 -DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 -DIST embassy-6.0.1-mse-1.0.0.tar.gz 445562 RMD160 c982e2107842521ec0c84198ee1f1dc7193b53d8 SHA1 85ab910a49252cbef6811296597cca226ccf9002 SHA256 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90 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+ovPQjPik0OPpHftmGWO6Gbw+4zyS5OCfsaV5zVivrHx3oyI2os5cLKn/Q6HiKe2s +iUMkjbcpE03CyDS7ofuV +=KXLN -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild new file mode 100644 index 000000000000..6b5725be73c3 --- /dev/null +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild,v 1.1 2015/03/28 17:14:17 jlec Exp $ + +EAPI=5 + +EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" +EBO_EXTRA_ECONF="$(use_enable ncurses curses)" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) +AUTOTOOLS_AUTORECONF=1 +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +IUSE+=" ncurses" + +RDEPEND+=" ncurses? ( sys-libs/ncurses )" + +src_install() { + emboss-r1_src_install + insinto /usr/include/emboss/mse + doins h/*.h +} diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..8b2f0574e3b0 --- /dev/null +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -0,0 +1,133 @@ +--- MSE-3.0.0.650/configure.ac ++++ MSE-3.0.0.650/configure.ac +@@ -635,33 +635,6 @@ + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ + + + +-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]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,11 @@ + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -1000,17 +963,13 @@ + + + +-dnl emnu and mse only: uses curses +-dnl Test if --with-curses is given +-AC_ARG_WITH([curses], +- [AS_HELP_STRING([--with-curses], +- [curses (or ncurses)])]) +-if test "${with_curses}" ; then +-AC_MSG_CHECKING([for curses]) +-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" +-LDFLAGS="$LDFLAGS -L${with_curses}/lib" +-fi +-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) ++ ++AS_IF([test "x$enable_curses" = "xyes"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++]) + + + +--- MSE-3.0.0.650/src/Makefile.am ++++ MSE-3.0.0.650/src/Makefile.am +@@ -18,9 +18,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../h -I${embprefix}/include \ +- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ +- $(NLINCLUDES) ++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ + $(XLIB) + else + LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) + endif +--- MSE-3.0.0.650/ckit/Makefile.am ++++ MSE-3.0.0.650/ckit/Makefile.am +@@ -2,7 +2,7 @@ + + lib_LTLIBRARIES = libckit.la + +-AM_CPPFLAGS = -I../h ++AM_CPPFLAGS = -I$(top_srcdir)/h + + CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ + seqspec.c ttyinterface.c nextseqentry.c \ +--- MSE-3.0.0.650/emboss_acd/Makefile.am ++++ MSE-3.0.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-mse/metadata.xml +++ b/sci-biology/embassy-mse/metadata.xml @@ -1,5 +1,5 @@ - sci-biology + sci-biology diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog index d50f17925693..90c7fbada465 100644 --- a/sci-biology/embassy-phylipnew/ChangeLog +++ b/sci-biology/embassy-phylipnew/ChangeLog @@ -1,6 +1,14 @@ # ChangeLog for sci-biology/embassy-phylipnew -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.15 2011/10/20 08:50:46 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.16 2015/03/28 17:13:13 jlec Exp $ + +*embassy-phylipnew-3.69.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher + +embassy-phylipnew-3.69.650.ebuild, + +files/embassy-phylipnew-3.69.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 20 Oct 2011; Kacper Kowalik embassy-phylipnew-3.68.ebuild, embassy-phylipnew-3.67.ebuild: @@ -65,4 +73,3 @@ +embassy-phylipnew-3.6b.ebuild: Initial import. This package will probably replace EMBASSY-PHYLIP in new EMBASSY releases. - diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest index 0f54fcd90510..1b69d0ba825a 100644 --- a/sci-biology/embassy-phylipnew/Manifest +++ b/sci-biology/embassy-phylipnew/Manifest @@ -1,28 +1,33 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 -DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 -DIST embassy-6.0.1-phylipnew-3.67.tar.gz 1624802 RMD160 4852b06ad1f288a750799017fea865c0390e5833 SHA1 d86515196b5a8ed0523ed5412acd613dbe2797b2 SHA256 efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945 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a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch new file mode 100644 index 000000000000..e0efb74bd79e --- /dev/null +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -0,0 +1,98 @@ +--- PHYLIPNEW-3.69.650/configure.ac ++++ PHYLIPNEW-3.69.650/configure.ac +@@ -635,33 +635,6 @@ + + + +-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 FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -781,21 +754,6 @@ + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -918,6 +876,11 @@ + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- PHYLIPNEW-3.69.650/src/Makefile.am ++++ PHYLIPNEW-3.69.650/src/Makefile.am +@@ -16,10 +16,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${embprefix}/include \ +- -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -120,5 +117,5 @@ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif +--- PHYLIPNEW-3.69.650/emboss_acd/Makefile.am ++++ PHYLIPNEW-3.69.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-phylipnew/metadata.xml +++ b/sci-biology/embassy-phylipnew/metadata.xml @@ -1,5 +1,5 @@ - sci-biology + sci-biology diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog index d296e07d1e4e..b0f87897f2c5 100644 --- a/sci-biology/embassy-signature/ChangeLog +++ b/sci-biology/embassy-signature/ChangeLog @@ -1,6 +1,14 @@ # ChangeLog for sci-biology/embassy-signature -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.22 2011/10/20 08:50:16 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.23 2015/03/28 17:11:24 jlec Exp $ + +*embassy-signature-0.1.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher + +embassy-signature-0.1.650.ebuild, + +files/embassy-signature-0.1.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 20 Oct 2011; Kacper Kowalik embassy-signature-0.1.0-r3.ebuild, embassy-signature-0.1.0-r4.ebuild: @@ -98,4 +106,3 @@ 07 Aug 2005; Olivier Fisette +metadata.xml, +embassy-signature-0.1.0.ebuild: New import. 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b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..5197c6422f5a --- /dev/null +++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch @@ -0,0 +1,90 @@ +--- SIGNATURE-0.1.650/configure.ac ++++ SIGNATURE-0.1.650/configure.ac +@@ -635,33 +635,6 @@ + + + +-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 FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,11 @@ + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- SIGNATURE-0.1.650/src/Makefile.am ++++ SIGNATURE-0.1.650/src/Makefile.am +@@ -17,9 +17,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -68,5 +66,5 @@ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-signature/metadata.xml +++ b/sci-biology/embassy-signature/metadata.xml @@ -1,5 +1,5 @@ - sci-biology + sci-biology diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog index fa7454dba1a8..3478211e0740 100644 --- a/sci-biology/embassy-structure/ChangeLog +++ b/sci-biology/embassy-structure/ChangeLog @@ -1,6 +1,14 @@ # ChangeLog for sci-biology/embassy-structure -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.22 2011/10/20 08:49:50 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.23 2015/03/28 17:10:08 jlec Exp $ + +*embassy-structure-0.1.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher + +embassy-structure-0.1.650.ebuild, + +files/embassy-structure-0.1.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 20 Oct 2011; Kacper Kowalik embassy-structure-0.1.0-r4.ebuild, embassy-structure-0.1.0-r3.ebuild: @@ -98,4 +106,3 @@ 07 Aug 2005; Olivier Fisette +metadata.xml, +embassy-structure-0.1.0.ebuild: New import. This package is part of the EMBASSY 3.0.0 distribution. - diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest index 3dac1030665d..f67fbf39a116 100644 --- a/sci-biology/embassy-structure/Manifest +++ b/sci-biology/embassy-structure/Manifest @@ -1,28 +1,33 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 -DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 -DIST embassy-6.0.1-structure-0.1.0.tar.gz 532035 RMD160 c02b486a2a8928c05386b020601ba89e0a6fed56 SHA1 b47a06f72add3a3d037ba608c4aeac06bbb8c4b5 SHA256 cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23 -DIST 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b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..c87eefde11ce --- /dev/null +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch @@ -0,0 +1,90 @@ +--- STRUCTURE-0.1.650/configure.ac ++++ STRUCTURE-0.1.650/configure.ac +@@ -635,33 +635,6 @@ + + + +-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 FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,11 @@ + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- STRUCTURE-0.1.650/src/Makefile.am ++++ STRUCTURE-0.1.650/src/Makefile.am +@@ -17,9 +17,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -66,5 +64,5 @@ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-structure/metadata.xml +++ b/sci-biology/embassy-structure/metadata.xml @@ -1,5 +1,5 @@ - sci-biology + sci-biology diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog index c62024a9dab2..d7d450d14047 100644 --- a/sci-biology/embassy-topo/ChangeLog +++ b/sci-biology/embassy-topo/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/embassy-topo -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.32 2011/10/20 08:49:25 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.33 2015/03/28 17:08:46 jlec Exp $ + +*embassy-topo-2.0.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher +embassy-topo-2.0.650.ebuild, + +files/embassy-topo-2.0.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 20 Oct 2011; Kacper Kowalik embassy-topo-1.0.0-r5.ebuild, embassy-topo-1.0.0-r6.ebuild: diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest index 488d51b896ea..0f53cf5ac2e9 100644 --- a/sci-biology/embassy-topo/Manifest +++ b/sci-biology/embassy-topo/Manifest @@ -1,28 +1,33 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 -DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 -DIST 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+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch new file mode 100644 index 000000000000..7ddda05cb62d --- /dev/null +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -0,0 +1,97 @@ +--- TOPO-2.0.650/configure.ac ++++ TOPO-2.0.650/configure.ac +@@ -635,33 +635,6 @@ + + + +-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 FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,11 @@ + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- TOPO-2.0.650/src/Makefile.am ++++ TOPO-2.0.650/src/Makefile.am +@@ -17,9 +17,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif +--- TOPO-2.0.650/emboss_acd/Makefile.am ++++ TOPO-2.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-topo/metadata.xml +++ b/sci-biology/embassy-topo/metadata.xml @@ -1,5 +1,5 @@ - sci-biology + sci-biology diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog index 23c45baf17b9..487329567511 100644 --- a/sci-biology/embassy-vienna/ChangeLog +++ b/sci-biology/embassy-vienna/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/embassy-vienna -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.10 2011/10/20 08:49:03 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.11 2015/03/28 17:07:04 jlec Exp $ + +*embassy-vienna-1.7.2.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher +embassy-vienna-1.7.2.650.ebuild, + +files/embassy-vienna-1.7.2.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 20 Oct 2011; Kacper Kowalik embassy-vienna-1.7.2.ebuild, embassy-vienna-1.7.2-r1.ebuild: @@ -46,4 +53,3 @@ 18 Jul 2007; Olivier Fisette +embassy-vienna-1.6.ebuild: Initial import. - diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest index 94533df03cd5..cea1e6b6c0d2 100644 --- a/sci-biology/embassy-vienna/Manifest +++ b/sci-biology/embassy-vienna/Manifest @@ -1,28 +1,33 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 -DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 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+EBO_DESCRIPTION="Vienna RNA package - RNA folding" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) +AUTOTOOLS_AUTORECONF=1 +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch new file mode 100644 index 000000000000..c9ece691229c --- /dev/null +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -0,0 +1,98 @@ +--- VIENNA-1.7.2.650/configure.ac ++++ VIENNA-1.7.2.650/configure.ac +@@ -649,33 +649,6 @@ + + + +-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 FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -751,21 +724,6 @@ + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -888,6 +846,11 @@ + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- VIENNA-1.7.2.650/src/Makefile.am ++++ VIENNA-1.7.2.650/src/Makefile.am +@@ -32,9 +32,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -87,6 +85,7 @@ + endif + + liboviennarna_la_LDFLAGS = $(LINKFLAGS) ++liboviennarna_la_LIBADD = -lajax + + ovrnaalifold_SOURCES = vrnaalifold.c + ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c +@@ -119,5 +118,5 @@ + $(XLIB) + else + LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-vienna/metadata.xml +++ b/sci-biology/embassy-vienna/metadata.xml @@ -1,5 +1,5 @@ - sci-biology + sci-biology -- 2.26.2