--- /dev/null
+# 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 <jlec@gentoo.org> +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
--- /dev/null
+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 88f501bbfc8a98722f1f5a15872268a0e74b56017e36ea379cedfd2f649ff5e3 SHA512 05993f00077d92dcf10d0badcd76fb1eda89d4f96ec74026f3ecd7166275f629574cbd92bf235c92216ad16b824adce8e01636c719c6b969495efb4f85826796 WHIRLPOOL b6c00c95ca3580ffbeac20aeda36cb75c8f150ef177271476f95c452ab6ed32a6a83eaa16e44cf078f89b7ede6edf53a7ba56413a7ffdbffc24dfaf3012d1f4b
+MISC ChangeLog 404 SHA256 c8d9d0bc2705dbe3b957c8676d32ecf57a4e8c3919984410ec5d772f9dfeeaec SHA512 8cfd2c8b64d8fee714c095192806ee4adbadc512710553386de915535c56a057acee8a5e3ba5c229fb7bb1371b794f7fb7fe052c2dba45f393dc6f2e79ac4d27 WHIRLPOOL de87b1cdf3846b6885a3b3dfb72504720cc9da994afbc31110ba4d3167658097a7148e70589f58eadd57e9b11b99b0051b1275bdd87ae7ccef42bce3678e9841
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
# 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 <jlec@gentoo.org> +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 <xarthisius@gentoo.org>
embassy-mse-1.0.0-r6.ebuild, embassy-mse-1.0.0-r7.ebuild:
-----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
-DIST embassy-6.1.0-mse-1.0.0.tar.gz 424839 RMD160 e99e312312ff4ec90e9e5c469946e427e6f4631c SHA1 ca46dbb270ef9dbb0191de5df5f19641c28ae9e4 SHA256 916e6cc772c499cb0519e1fa19e1f64f8d6502a1971239c08a55b8f0e3cf2c6a
-EBUILD embassy-mse-1.0.0-r6.ebuild 598 RMD160 dd19dbea2ff3fae175e6c3a928c6a83ddf1bdb2d SHA1 52efa910153987377d6d0239aea2038601e40dd5 SHA256 40ae8e6cb04fd32fcaa7d93c4a9b247d555f76fff212fb5b0ce2228ec46e4465
-EBUILD embassy-mse-1.0.0-r7.ebuild 622 RMD160 d7822236dcfebf4c867923bc396fca2ecae3a3c5 SHA1 92e4610f3ca090c7a37a60154605eb948aac72d3 SHA256 ba96c25c4e91946fc509113af0d4acca7409a293bb8ea757b3f8a63705736587
-MISC ChangeLog 5535 RMD160 40e3f90e5fc3ec49dfcf9389d3a8912355d482a6 SHA1 fc3bfea81f2a05873374a331c4b5a869f3d10fd2 SHA256 bdcd429c35c95cb4836ca0484fc0ab7956ee77048c592258271b62a782ed0e9c
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-mse-3.0.0.650_fix-build-system.patch 3603 SHA256 929a1caf44f233ed5254e6df080370c2d876692508c523f0184373090024ac5b SHA512 a9448a5c0530abf9c596a5742e73e76d93a5aeca006b116b53b955f007983f0832fc7bf388e67a5c833c16fd9934dd9c17ba1870fe05f1062f0b9f2dc26191f3 WHIRLPOOL 63575045b844ebb8dadf9d772a9cdd46328e200f492ec0576fb275d2f5773784cd40544bdb05fe24b23f887ed35a6664d8c2bdfb5919c090bcb1cd96433da8ad
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-mse-1.0.0.tar.gz 445562 SHA256 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90
+DIST embassy-6.1.0-mse-1.0.0.tar.gz 424839 SHA256 916e6cc772c499cb0519e1fa19e1f64f8d6502a1971239c08a55b8f0e3cf2c6a
+DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b
+EBUILD embassy-mse-1.0.0-r6.ebuild 598 SHA256 40ae8e6cb04fd32fcaa7d93c4a9b247d555f76fff212fb5b0ce2228ec46e4465 SHA512 fc8c501160f9d93eee5e5f72b2a3421fc8a290b66da5802f973c12102334050c8afb9727fd1a1598a1d8cefc6a05db926c1cd63ea94c82f6108959fa552989eb WHIRLPOOL e8368ff3f0e0d5f768964d84cc3c4934ecf6f45060a52e161030a93c160c88b848b0fa659ef84d10e2767f15b35dda53c263524cb3169d6b94f3adcda1d6c304
+EBUILD embassy-mse-1.0.0-r7.ebuild 622 SHA256 ba96c25c4e91946fc509113af0d4acca7409a293bb8ea757b3f8a63705736587 SHA512 bd742fee143508a9011a9a792f324af2fce01ef5d9c7d09d6165c305926a77df8aa21316ed04d914439aa134cc196b33e857de585f99aef4349b97f3d131c67a WHIRLPOOL 59eb19b7b117a13184da27d4e88ca48140f4ba0d51df291e37ca7298f23d16be768b3041a1384af898ab6c231fc7d166871b91d0c07abf89f769c97cd0410382
+EBUILD embassy-mse-3.0.0.650.ebuild 639 SHA256 2f82a102d42816ce5289649417b199f68a581e7f48c9c566a7b52fc565768910 SHA512 c0f9f3f41707f8e876d008cc0b4deba21b196e77eb42b8b353d621f39354d45e33777bcc6181e32b0cec38c8a28328796fa43a488a2fc2dcec8d26d8feb6b957 WHIRLPOOL 7c016efd1a5212834d880cd6bb0d7ee6c235551e19aa4ef267b7ec40f276c7677a2dea2f0d7e36fac8bfee826f99f4ae9c2cb86124434235e4c11ef64506968e
+MISC ChangeLog 5811 SHA256 04157a2450461229591c1a147e44e320d96a1f1752fed0a9e375fa44a8ce2898 SHA512 e96573d65cc678d7e53fec5884fbfd0f3fd79a3c40cf911a50308d6f313238eee33f0688a62610ad9931e1ee25e61979963f998a4f83a32a8c77e50308635790 WHIRLPOOL 35058d003bb538d44dbfe42e36d235102eb13bedfe58a26621c41946bcd479fae2846cd22fd11b5c0d3c6a5c7b1cf4d127514d6b044b5e68a66c7c110c5aacd6
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+Version: GnuPG v2.0
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+iUMkjbcpE03CyDS7ofuV
+=KXLN
-----END PGP SIGNATURE-----
--- /dev/null
+# 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}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+IUSE+=" ncurses"
+
+RDEPEND+=" ncurses? ( sys-libs/ncurses )"
+
+src_install() {
+ emboss-r1_src_install
+ insinto /usr/include/emboss/mse
+ doins h/*.h
+}
--- /dev/null
+--- MSE-3.0.0.650/configure.ac
++++ MSE-3.0.0.650/configure.ac
+@@ -635,33 +635,6 @@
+
+
+
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${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
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
+ <herd>sci-biology</herd>
</pkgmetadata>
# 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 <jlec@gentoo.org>
+ +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 <xarthisius@gentoo.org>
embassy-phylipnew-3.68.ebuild, embassy-phylipnew-3.67.ebuild:
+embassy-phylipnew-3.6b.ebuild:
Initial import. This package will probably replace EMBASSY-PHYLIP in new
EMBASSY releases.
-
-----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
-DIST embassy-6.1.0-phylipnew-3.68.tar.gz 1626990 RMD160 4f31dbb9b7f78b9b2b3a56b12aff7bbfaae297ea SHA1 db8415fc49556a5635549523a585a5c9a9834d4d SHA256 b22ec1efdae59160073acdcb57c660b58e0bd04d57fa8a86d8b0f48ec77bce78
-EBUILD embassy-phylipnew-3.67.ebuild 542 RMD160 e84c4576928fa5e6db85c30e983dcad9b8159ae7 SHA1 fee6b1026fbc2ab669223375bf17417884ee0837 SHA256 caaf16c790c0df32de03bb4b520cb123e9f544622b4fe8e0a75aff98f7d7f763
-EBUILD embassy-phylipnew-3.68.ebuild 566 RMD160 e77e274ec6a376d42a6af9c4cf583b1f79f5b2df SHA1 d858379740db912765347a04c3462bbe0eefaa9a SHA256 9c922f05f8ab6810d898e78d53885356a37143f80116297382e0b077dec4dd98
-MISC ChangeLog 2227 RMD160 0dc1af861db6e3bc8235fb38f749f3323aa91fff SHA1 8807c60dd17e83ab0e97c5cf8ce656b0cb5bb33f SHA256 ccbf147d59faad8a8c31436e84709f48dc49d0bf1ca437e50864c9fe7a059fd6
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-phylipnew-3.69.650_fix-build-system.patch 2660 SHA256 7a8701647c510d04a710d6cb52042dcc516124a5209662dd362f7e49c3f50e2f SHA512 ca2211e53077954a07d1a8997cff015f7a08e569d4c6d032703a9113ccb25ac2b191e866d35046ed02c0374cd3c177d90f0aeb4d182ec04cf6a39d1beda5c04a WHIRLPOOL 271ad6d7663f6aaac5a38750b00f262ebe37bf4c51b81238114c2bfe87e71fc897849781c2c052d792d17b5076e147db8a74e14f54278a82082fa92e73b268d0
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-phylipnew-3.67.tar.gz 1624802 SHA256 efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945
+DIST embassy-6.1.0-phylipnew-3.68.tar.gz 1626990 SHA256 b22ec1efdae59160073acdcb57c660b58e0bd04d57fa8a86d8b0f48ec77bce78
+DIST embassy-phylipnew-3.69.650.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58
+EBUILD embassy-phylipnew-3.67.ebuild 542 SHA256 caaf16c790c0df32de03bb4b520cb123e9f544622b4fe8e0a75aff98f7d7f763 SHA512 b04ac52ba9068ae2ab2fe5e910ce6b3bb94e205a5c58bc8cba8a812992290299735bdb5138051287c3d98ee2db77f411e54a43da7259905e030b9dcfc4a8d400 WHIRLPOOL c7e7b02e801dfc48d692d6bd771684d4c66bed6dbdd7daa8761b359e5ea03a635ddd40d94c3b73af00e23bb928e668c123a7b5d148ec9741f17d57d9afa0955e
+EBUILD embassy-phylipnew-3.68.ebuild 566 SHA256 9c922f05f8ab6810d898e78d53885356a37143f80116297382e0b077dec4dd98 SHA512 14da1059b097f4dbaa855c895b45d5eece1c51713adc0d03d7a54dd632fb7ada8ca25f264a8a0fae72c7027c1f0198a256dad41ce8dc3b954e7036c1c0e971a0 WHIRLPOOL 0172881938e7e547007cd3390774d839d79976fb28760267ce74ade0f37335c9d2488807bfd3c4d6779f16be484c70bc80b06b8023ef186d54802e55baf28d5a
+EBUILD embassy-phylipnew-3.69.650.ebuild 471 SHA256 217856328224548bedc41ef0b3671ac2306f7978495c73b788ef9a697fdaaf19 SHA512 6b386311b42e1037336a39505da03a779f623a9c62773f634372b5adc0db1f7742ef2b1cb73022fb5f32a9637454bcc334c47a8d04b7bbd83788599e77d79358 WHIRLPOOL 8b7255fb17062701a71f16c255faf9b1adc24648afceb14cd8cc0766b352e6b9cc8107f7ae793ac26d8abd79f17d47e6da120a54d3f2e50bcf091a8ec1695fb1
+MISC ChangeLog 2519 SHA256 160b644c68a91d35df7d0671a1d3213a174a33f125d23a847313f6557f62669b SHA512 c573d76fbf9670488ffbbe175f6cec88e0746adbcf3d21fd31636587a8a07b075a2debb866162003a3240b8940716720403945343d5c462b877e890c720fc00b WHIRLPOOL 71cdb497e577b1e8aa590c0cbd829b2ecd03629ce4258fc6ab5f2fdf4667e8edefecc8710580e97c619d6428a43050a882c193c97d1386d8322bd5f625fc1935
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+Version: GnuPG v2.0
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+=BJxb
-----END PGP SIGNATURE-----
--- /dev/null
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild,v 1.1 2015/03/28 17:13:13 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="the Phylogeny Inference Package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+LICENSE+=" freedist"
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
--- /dev/null
+--- 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
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
+ <herd>sci-biology</herd>
</pkgmetadata>
# 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 <jlec@gentoo.org>
+ +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 <xarthisius@gentoo.org>
embassy-signature-0.1.0-r3.ebuild, embassy-signature-0.1.0-r4.ebuild:
07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+embassy-signature-0.1.0.ebuild:
New import. This package is part of the EMBASSY 3.0.0 distribution.
-
-----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-signature-0.1.0.tar.gz 574940 RMD160 1fc35811e61a0d1f14ee35ef81a346a0793ee934 SHA1 b94ac68c376eed6c2a987e186d01ca1ba8f00454 SHA256 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f
-DIST embassy-6.1.0-signature-0.1.0.tar.gz 554554 RMD160 ef2c0200175dcdb76286b561be294c4941bbbc07 SHA1 12b3491e91b87cd2067279c114f81f0e6c78fb96 SHA256 2b2716f8cdea52153fbc5cc11fda12d1d30c4240d4314755b1ea51042f154837
-EBUILD embassy-signature-0.1.0-r3.ebuild 501 RMD160 16f12c625b8b66a8767678242ab5c9616cd21baa SHA1 b6c5dd779e8ea6dc0e0804ca0c9b4a6f921040e1 SHA256 31eb32c8b40c3c84d0c3c8f072560c309e714d6dcbd9bb4982816f3bda6ba97b
-EBUILD embassy-signature-0.1.0-r4.ebuild 525 RMD160 ad2776748483fba7e9c4aa2a062866171c0845c4 SHA1 f4fb0e50ada84f066f2986b1b024cc6e931f9893 SHA256 5a441dc2954d400fd4e8053b9a983c7ff1ca4b7143d46259df6dc62f9f4f530a
-MISC ChangeLog 3320 RMD160 ab48b8deabfd90ed61efebab6b4dd737570f27c0 SHA1 02e2e2a047837f82ae3d99a13d25eec58d236801 SHA256 3a53149c1aa9794e113b3475753ff871b034a760615a39ea50e680de0d67a9c6
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-signature-0.1.650_fix-build-system.patch 2379 SHA256 1ab4c73668ea4c3dc9c4cc8b0e3a1c02f083073aad1df82a03389f54d5903722 SHA512 ffe62fad569f71b6851e3aa3ae0435722261f484cdd4636e87f59c21f645c4aa9c714a0b9a1d2144b399a9db34bbfe7488e84b0e5e5f7b240b7ab1dc779f1db3 WHIRLPOOL 4ea315e7de17b4741178f79c7322c243b71f55beebd6a8d0727a4399046b548426a876e2f8556eee0318dd1c284555d043421db3a472503baedd6fdae05557d8
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-signature-0.1.0.tar.gz 574940 SHA256 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f
+DIST embassy-6.1.0-signature-0.1.0.tar.gz 554554 SHA256 2b2716f8cdea52153fbc5cc11fda12d1d30c4240d4314755b1ea51042f154837
+DIST embassy-signature-0.1.650.tar.gz 622294 SHA256 2ab34cc76caaaefe7914e9b00dd12ee81a32d7a7ccca20ba901d67f1e2c2f27e SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 WHIRLPOOL 1a943266ee9092f13fb3ad0779cdfe70e3cb5c1ed7d31164a93da90aaea2df95150970e0ef22df89c3cc97dfe7564092f2cab8aad7fb720e2f456cb363666de3
+EBUILD embassy-signature-0.1.0-r3.ebuild 501 SHA256 31eb32c8b40c3c84d0c3c8f072560c309e714d6dcbd9bb4982816f3bda6ba97b SHA512 b4b71971a32b8f90b933feb83e6e7a9d65f4119179ce4981a94a54fd15c137e784335779642d70c7d53fafa715332b40f354533ed0cf9b79a28cca18f64c1d92 WHIRLPOOL f3871dc066609327acc6597c9c2287949f6205b93f52407317c62bd7729a8b75ae6aaecd0786492cace9a2a899714857837acba3f46da84a6c6b2e3b84a03fb1
+EBUILD embassy-signature-0.1.0-r4.ebuild 525 SHA256 5a441dc2954d400fd4e8053b9a983c7ff1ca4b7143d46259df6dc62f9f4f530a SHA512 6eec1464fafc3c18cb5206ac0fee3998b05e07dde82c4bdfce7eeb7dcb8e31359469a0e5b8c6a4fd9b29c4f29c5094ec7f721a0c44682e6908e4e17bb9556759 WHIRLPOOL 44ee86a47b03887f38597ea368895fa73b234be6bb6db22e32e7e950b07a74fa8444b17d07a1b34e731373651a6b2e71b72ed529dc2e1fd840dc2e4758e4fc9f
+EBUILD embassy-signature-0.1.650.ebuild 449 SHA256 807bd99b7b6e241d102b041dd5faac7aa5b90201623d420908839fe5316c9528 SHA512 b0a0a2de39934b3124eba2ab0ebd1eab5a1a3e95a9b3b67dc26353b1114698ebdbff1bf19f2adce25b4d92529eebf29b528ed35a2725ebb18fb20c7d1b8d8c5e WHIRLPOOL 504c4d0de25c37634e8616697a6da7087e0127a2698dbbb73aeae7ca5205eba0bf78527417884f655676f3c81ac47b17a66c3de0cb2f9e0a56430d76254093a6
+MISC ChangeLog 3609 SHA256 38602ba53160029e3a14fde5c8f89de2a557c1975af1df80ec5eee4e53d49bb7 SHA512 1f0dacfde58e82da5662df27cc90d41889062082628a4a64d6e926f7c39284fd38fe74fd1a3d57b469257806b1254c53817051cbfd35c6b7b4d3c743f9705593 WHIRLPOOL e0ca9491928d1c7066422ffb970d9a072f8c430575d68e9b5f63ffdddbbbb12dff8d6548f722c3abb0b403f50ed726d92123315c300baa029918dd064d58c25e
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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--- /dev/null
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild,v 1.1 2015/03/28 17:11:24 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein signature add-on package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
--- /dev/null
+--- 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
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
+ <herd>sci-biology</herd>
</pkgmetadata>
# 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 <jlec@gentoo.org>
+ +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 <xarthisius@gentoo.org>
embassy-structure-0.1.0-r4.ebuild, embassy-structure-0.1.0-r3.ebuild:
07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+embassy-structure-0.1.0.ebuild:
New import. This package is part of the EMBASSY 3.0.0 distribution.
-
-----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 embassy-6.1.0-structure-0.1.0.tar.gz 519780 RMD160 c07cf29a81115adb2d8ae61ec4d52f726d2ce65a SHA1 f04c1ac60e3742d1b044a31c5efb4a3d99b630d6 SHA256 014ac2d07fdd79a3e4ffbfc70aa808fdd039214021972f87165eaa18aeb58e3f
-EBUILD embassy-structure-0.1.0-r3.ebuild 501 RMD160 24209ecd53f1c4c34dffcf104029f2e9cc142c26 SHA1 198595fd0cd695ec3344cc6205341f9f11a15bd4 SHA256 0b292a276467ae04180ca9c25c5a75c72ef5938848322f1f08cff49aa0d72d30
-EBUILD embassy-structure-0.1.0-r4.ebuild 525 RMD160 9e7837d82537e9bf15026211f825d8442bfcbe18 SHA1 1fa2914873cb057f8067b098ce28c93f68fb40d8 SHA256 15cbef4eaece14ffdfbf12b556c6551316903f1a9bfa33cac0807af821ebc743
-MISC ChangeLog 3320 RMD160 f547d72ba5b3e295264943d29e9d8ca9ad5c2706 SHA1 cf9b1b1235c2b0aae6c2d30c73219487fd3a735a SHA256 f216de4a1e95be9e4ed1250952d9d49da28627d3701d50716e9924d6553a6a4e
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-structure-0.1.650_fix-build-system.patch 2379 SHA256 167ed0cef4f275351dbdc52c7f0fb587527e62049edc987497e79c9d5c486ff0 SHA512 2ae3080fe28cd6ad03dfe02112e16a302ac2d2d65efd70b98676a137221d9897662930a6beb4eeae87cdbf66d29cacca4b4647314eedfe2aefdcb000c762af69 WHIRLPOOL 49d523d564afcb72db32eb475e4738706b7d60e2505bb309642cdb5b9b121d29370dcdf7571e9a02c9e699f79439b04a494cc22274aee7173ae73d03da03fcfe
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-structure-0.1.0.tar.gz 532035 SHA256 cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23
+DIST embassy-6.1.0-structure-0.1.0.tar.gz 519780 SHA256 014ac2d07fdd79a3e4ffbfc70aa808fdd039214021972f87165eaa18aeb58e3f
+DIST embassy-structure-0.1.650.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03
+EBUILD embassy-structure-0.1.0-r3.ebuild 501 SHA256 0b292a276467ae04180ca9c25c5a75c72ef5938848322f1f08cff49aa0d72d30 SHA512 ac9e82e81e88a2d9a065366ac7ff1327e43e00e9a06591475f7faf30b87a16b194b921bf40a5e1a469a889998cd93cd19cde9e2ddda5c8b247c19c76193ce6ff WHIRLPOOL 3b998631a045721c65b84f9dd442251920618b90acbcb2c535cf4d22f6b3a7a51ea3db01fee272aa23dd90af81a85ae77edb904a31a485510e673bf8eabca852
+EBUILD embassy-structure-0.1.0-r4.ebuild 525 SHA256 15cbef4eaece14ffdfbf12b556c6551316903f1a9bfa33cac0807af821ebc743 SHA512 45379690cf87d9ab1b3fc5c8b2096a5b8cd426ce391de82f0e159887a60f8f34a1e3ab089691ac3a0b3aad4af5a4b5eaea480a17e2658ad0ef9c0502d33c6a2d WHIRLPOOL d406b35dfeea6332d3c76ff7c454d3049acd2d1b58b6ea6fbe18ec0c40b10844ffabcf55ad0c1034f6efd0a5bd1b49ba2b7a3102b41d6d9edfd46b5996ea46c3
+EBUILD embassy-structure-0.1.650.ebuild 449 SHA256 a0e9104bb4f4f71d1d044884eb2f3772658ca35d73a2420deb353c61ea28945f SHA512 b787446f8145e033c44e9ab3d7d3846987c5561b5cda7b8f091d762becf4a3c8cd110f08627413699694bb6ae8613afa4efc3378a72cb118c93adaa407b1c04a WHIRLPOOL b370f7dae93ad9bcafafecc84c538d5eaaa5a537af3b5d5740f9c98dd744c75c7bc1c7cafb34551b6324754da3455c42e4ec67a1c8c6951106bae2f9ec6bcb5a
+MISC ChangeLog 3609 SHA256 53833bf6547f2c3e37f0cdf377a92e2039224ab8f56c1ac78b48a814821a57cc SHA512 8b606257424ee222ba234aa914b37eccf56f0f7908a9051c0ba8a6f35442354ed679c0294156934a7e84d0b33e9b9951debb850b9e3a86c2d2bf1dc0f69887fe WHIRLPOOL 71f840ee350a1284ecc32664280b9de009c7553497e3bbdc3539a033a384db24b9c50b2e9030619841e02ede733527521a3593fc6b5dd0ab733dd54e1ff56a0a
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+=2JCj
-----END PGP SIGNATURE-----
--- /dev/null
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild,v 1.1 2015/03/28 17:10:08 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein structure add-on package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
--- /dev/null
+--- 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
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
+ <herd>sci-biology</herd>
</pkgmetadata>
# 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 <jlec@gentoo.org> +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 <xarthisius@gentoo.org>
embassy-topo-1.0.0-r5.ebuild, embassy-topo-1.0.0-r6.ebuild:
-----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-topo-1.0.0.tar.gz 379929 RMD160 331cf5a872875f5d33490ae100f790312619940e SHA1 ecd8ae4ff87fb5f753eb1a1a5b292fffeccce152 SHA256 a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16
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+AUX embassy-topo-2.0.650_fix-build-system.patch 2550 SHA256 9ae3b09bd98c5d19e692bd5fdeeb6629b2ab74b5727a3d8e310d8db3c505a8ed SHA512 4ee1edb48108cdcf664038662a7da3f1708cb44a0986914f707756dba86c7882740e103d47e683d4df489c3e16e46ecc393bd1d394081fb24f025400aba64ffa WHIRLPOOL 81019a812bb2d693598c3732a1b77fba91a4509d5bf93b2493663c697cdebd849b1737bf6ff16f8a6296b62fc2f8a163dc325e37444058605c1843df950b9cf1
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-topo-1.0.0.tar.gz 379929 SHA256 a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16
+DIST embassy-6.1.0-topo-1.0.0.tar.gz 378850 SHA256 9a3cde11f36de512ce0d33b37a306dc157922f6121c8963296d29eb793b99af3
+DIST embassy-topo-2.0.650.tar.gz 443510 SHA256 a8b8b7c1e04be44b5d6982614a9af44b84d0282bb917ed29e23a0a710241ad6f SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 WHIRLPOOL fbe0edadeafe14b4b24be6fd65ed51dc9572f89e12e6f038017e9dd208a867138219350ccde6ca3eeab94ccedf34e5ec672a65cbf30c3819387407e778caeb55
+EBUILD embassy-topo-1.0.0-r5.ebuild 513 SHA256 d8afb0a82783055fff4e55759dca0fa32ecf17d612731d4102b19828cc98a448 SHA512 39ef1c5e28cfe0b36c7e6298f3e8b4aa70e40a70338f1aa6d2ae60d9071ddde07ac4516e89871fad571cc8e8ee5f5a5597f2ef78b23f93d25fb8e978674f48e0 WHIRLPOOL 32553faaaf32ce7bd08a07c6441dd9d7dda153e8cb94d12bb12643e046cb20ccbf93552a01e7516cb1d4b37bd0146721922b710606a0a12663b98d53c6490d61
+EBUILD embassy-topo-1.0.0-r6.ebuild 537 SHA256 410f8b56cbcbad842ee95fa02aacfe2dae709d8a92a853a40f21e1eed7b4e98d SHA512 4e4ae611ac4321fe5ccd32da4e0130f4478a83adb0172232a4013af6700b9b102b0e5446870edaf14c2f1980ba5af79d21b7cf8f375b717821441cee8228f347 WHIRLPOOL 6de5f176e9ed96f15e4c6c1a42d3c8b6793146efb6febb288a7bf92766708a4e7b8de26c0ce982695733ba2ead03799f295a7906aa23a4f19fb8bb56264f9de3
+EBUILD embassy-topo-2.0.650.ebuild 449 SHA256 db101d8b0e7f71c5b0429c462a76504047d8c768f5874f007937067b023afe04 SHA512 8a6790ce6e3c8202555479d01d00684f7f5ecf38c7824ff131def134cdcdc28ec3363451791719220ccda789b210d1e5694a624293bbd29429d72ff6aa368fb5 WHIRLPOOL d6ae65a8832d65a100b233d11ae8e3677483f0797709804ae08eb102a00bf81305321da49664ce620e2edefed16805019108862ce310b1d833fb2197d10ce3e6
+MISC ChangeLog 4938 SHA256 5c5aef1b098fd1300b087bdfc6b877428a899a6c186ba81dc39027309f788f3f SHA512 51a0fa8fe6453c29557ad8913d8cbf134dd2c3276c9eefa2b3a0143b2fffe8d5749aa600277cb2abecdc1f9f3b46f6e6a970bb51a2e2f1a964aea74973ed0c4f WHIRLPOOL 890edd2cef31c6dfcfdd66f97c29cbcee2bf7fad49fc8499ed196ab22e38c7066d3320b75daa55b6396a4c58f4a133ff6d33338c9bbf4a635ee0a0d4af846107
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+Version: GnuPG v2.0
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--- /dev/null
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild,v 1.1 2015/03/28 17:08:46 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Transmembrane protein display"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
--- /dev/null
+--- 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
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
+ <herd>sci-biology</herd>
</pkgmetadata>
# 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 <jlec@gentoo.org> +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 <xarthisius@gentoo.org>
embassy-vienna-1.7.2.ebuild, embassy-vienna-1.7.2-r1.ebuild:
18 Jul 2007; Olivier Fisette <ribosome@gentoo.org>
+embassy-vienna-1.6.ebuild:
Initial import.
-
-----BEGIN PGP SIGNED MESSAGE-----
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+Hash: SHA512
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-DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
-DIST embassy-6.0.1-vienna-1.7.2.tar.gz 682200 RMD160 2b4611af2d09a86d4bb842cab07aba2e937ab333 SHA1 5f04ffbe7c413e71483837ef9a49ed7cb839dfbb SHA256 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db
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-EBUILD embassy-vienna-1.7.2.ebuild 514 RMD160 e28db27aac8ec8fc269e92773eac5390ba6ab4d8 SHA1 835dfa8813c6ba78ac797888971b2c8d3ec9c302 SHA256 e09942caa6fe430a484e16e6573b627564e1b94c914ad2a86c249d8a82124e17
-MISC ChangeLog 1566 RMD160 58f59c50643ede112c3deacbfca5bd47d12bb104 SHA1 efef510a2bb3621018db0d069c7bca4d9a6301d9 SHA256 67906c99fe91aebdeeb782cd6526b1279ebf9671d99e1a7aa42fa290b7c6011d
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-vienna-1.7.2.650_fix-build-system.patch 2607 SHA256 4710a3477526134952cbaac58e373537ce5bed852052ee9d67ab8dffce9c86d2 SHA512 fcd14f06b2eebed9426a0ef8e47a7cf286529d5ae12a2cc145e8d755bf132ee0d157bedff9c81373c19f637449681de8977c9dce3725611fdbc27909dd437a10 WHIRLPOOL 1a7189d68244b7f3a436be3a12ba26fe855eacd3bfa67b54733e4bc92e8cfa18fa3d66f84dfef39f02d17bcd923d42dd18120b10faa1c322a63c9eff8cb63798
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-vienna-1.7.2.tar.gz 682200 SHA256 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db
+DIST embassy-6.1.0-vienna-1.7.2.tar.gz 634985 SHA256 c2be4279d7e666eac99a10b333a813fbcef4148140a6c9745f518c2d8667e727
+DIST embassy-vienna-1.7.2.650.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2
+EBUILD embassy-vienna-1.7.2-r1.ebuild 554 SHA256 10b2501f1e2f90c4fcbba97bfd259ad1e1bb5a6ee703e3e685cb33bc8b4dc1b3 SHA512 28618b05485f7dc947e330d0d1581632f61d81aa0db1166c023889cc379bb683fd78e9a985fb268dbddba1968c0263ce2e9b454f7a828fb85d9a5a02a88ea465 WHIRLPOOL 5a388e9a57e00c53d73329e25bf770d1ecce21797ae28124ec59b00cb2b2a941e543475a20162c5b99609a6cdc7034ea5a812e0e44f9a85c6193160bb9fed313
+EBUILD embassy-vienna-1.7.2.650.ebuild 458 SHA256 e773c5573c4be3f92c3eb5b999fef52413ed9e33c790a1a1737a53b177739cf6 SHA512 c0f2ae43400d3cdd99c507a2d071e840d183f9e1f7ab1379b468f6c1cb3cf717483e1bc9b3ff7fd3e542ee3ba04b876ab0f58f812a771f7549c9d50cbc8a9151 WHIRLPOOL eecdf324ee43173c6e5255ff1f8e01550357813d38963742e5523b5f23118c36e53deaeb885b9756ea3acdb928007bb2dd594d3fd87bcdb4b6bdcf4303057d54
+EBUILD embassy-vienna-1.7.2.ebuild 514 SHA256 e09942caa6fe430a484e16e6573b627564e1b94c914ad2a86c249d8a82124e17 SHA512 38408183679edfd551ce2a3c8604138775ff1ff7dbc91d531861e807bc2863a91837640f3405a756f96f998807fb04b17b14f286405382689d7405c2753f563f WHIRLPOOL 759b9816ea2ed28a8018302ad42907c7fbe15a13abc716e97e5e86beaf8197b8efb8f74f28c071be7144eed069b63b9f3cb432cc04d657a6a0400ddbf385ad7a
+MISC ChangeLog 1850 SHA256 02984bff12112758ada107449cf3d19a4f9850044045f83a6baff40ff4989619 SHA512 6f72529203fa14048afd52f819ee3d341b18396d773e3e662804a91e2190aa5bc8fdeab0d073ee0be9e5d788e3e34603ae608b7e3cfdc5769dc58e63df0f85c2 WHIRLPOOL e36808934c3be589a8bd267e4bcb92a132a5c03ec68d2d6508287397535265e12845a10c0b95d4e61c16cf895abe9f4e70c259b970ede8be717fc32a57f583ec
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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--- /dev/null
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild,v 1.1 2015/03/28 17:07:04 jlec Exp $
+
+EAPI=5
+
+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"
--- /dev/null
+--- 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
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
+ <herd>sci-biology</herd>
</pkgmetadata>
projects / gentoo.git / commitdiff