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!
author: Justin Lecher <jlec@gentoo.org> 2015-03-28 17:33:53 +0000
committer: Justin Lecher <jlec@gentoo.org> 2015-03-28 17:33:53 +0000
commit: 6e1567e0ed5360a8ecf4e0489973138cedaabed2 (patch)
tree: f1449eb8fdd88b8c31cdd657fc59db19b5744eb4 /sci-biology
parent: keyword ~arm, bug 544684, thanks Vincent Hardy for reporting (diff)
download: historical-6e1567e0ed5360a8ecf4e0489973138cedaabed2.tar.gz
historical-6e1567e0ed5360a8ecf4e0489973138cedaabed2.tar.bz2
historical-6e1567e0ed5360a8ecf4e0489973138cedaabed2.zip
36 files changed, 1058 insertions, 160 deletions
diff --git a/sci-biology/embassy-clustalomega/ChangeLog b/sci-biology/embassy-clustalomega/ChangeLog
new file mode 100644
index 000000000000..4af2c2b9a646
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/embassy-clustalomega
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-clustalomega/ChangeLog,v 1.1 2015/03/28 17:33:53 jlec Exp $
+
+*embassy-clustalomega-1.1.0 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +embassy-clustalomega-1.1.0.ebuild,
+  +files/embassy-clustalomega-1.1.0_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-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest
new file mode 100644
index 000000000000..87bff755f767
--- /dev/null
+++ b/sci-biology/embassy-clustalomega/Manifest
@@ -0,0 +1,5 @@
+AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2383 SHA256 42b1e713f2e987226ec6a9ce4177755139e573a752d7b16ed8dddfe6732a7230 SHA512 e0b517d5e6a5969d7428b8dfb72f71e9dd871383827db36a0bc9149c3fc4aa90638e7e9b0752927b1a081eae3ac62d2d8d0feb9aaa5c5434a1d09dc42f4104ef WHIRLPOOL d62e8e6888e09fcc592a0d5fc7383a76611f6ca09113726d4e744452ffe66c5359e843a5b4009969d59cc543b9a3e9d9003f1b7a6fe8a67091570dd9c597f769
+DIST embassy-clustalomega-1.1.0.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54
+EBUILD embassy-clustalomega-1.1.0.ebuild 390 SHA256 74257039492f6d0010aa70d61770636a521b4789f34409be647900317a96c37a SHA512 56962c8e4d6e6e687711c078cf7101ce13f17a76839b93d6bde519ea1ea7d278bbca8ea35d9fd4290fe530f8b75c4d8fca47fd33eb843963656e88666b0fe219 WHIRLPOOL da84aae8accd3c79318ad8a519c7be7a3aba7605b72de51fcf43ee38a26d792967368310165c93402b92f1471922fa85cd30fb93a4ea3e560c5a223bf3286f6f
+MISC ChangeLog 432 SHA256 0c1bfc6bece0d5cdb7c2bd61ef43ae03727e3c3b108e2223f1ad97b8c4addc7f SHA512 089d3d73c734b54d7bd809fe6b3eb1f7524c8012375ef8919c411cdeea6b9246484cd50ae9c2994639108583aec32717e28ede200558b0cc78a26134dbf89bd1 WHIRLPOOL 197985f7959fdfe9b61376435e34802f2ed8a1d9ddfacb617ea6ca6e9a2cd79cecae4d11cea7540e18597e488e954e780db5ec546d47849b51f246e9e20f016b
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog
index 48d4eb4612e0..4ca9c278249c 100644
--- a/sci-biology/embassy-domainatrix/ChangeLog
+++ b/sci-biology/embassy-domainatrix/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/embassy-domainatrix
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.32 2011/10/20 08:57:09 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.33 2015/03/28 17:31:57 jlec Exp $
+
+*embassy-domainatrix-0.1.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +embassy-domainatrix-0.1.650.ebuild,
+  +files/embassy-domainatrix-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-domainatrix-0.1.0-r3.ebuild, embassy-domainatrix-0.1.0-r4.ebuild:
diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest
index 2bd827e444ef..b1cd5e10a753 100644
--- a/sci-biology/embassy-domainatrix/Manifest
+++ b/sci-biology/embassy-domainatrix/Manifest
@@ -1,28 +1,33 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+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-domainatrix-0.1.0.tar.gz 420983 RMD160 902b0a31c2bb64f04912aa70c23cca5390850686 SHA1 2f8148d8c0781a12a103286de65464603bf2bef0 SHA256 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1
-DIST embassy-6.1.0-domainatrix-0.1.0.tar.gz 399655 RMD160 6a719745621c29b41ba21cf354b7681c1bcb4850 SHA1 d8db155889c88ecbdf9c0f9ee032a47c24ee509f SHA256 54f4aa2bd8753a261722f16098e42f01a9083467162c027e2f1738a740f880d3
-EBUILD embassy-domainatrix-0.1.0-r3.ebuild 511 RMD160 423f8695d2ad4c53c329a4a67b1d3af7e5703385 SHA1 9b7aeea0e069bfb5ffed78e646d0adb85c8672d9 SHA256 4a0293c37b1f414f8699767c029b3cbcfa51bccd847288155c5da33d48f71250
-EBUILD embassy-domainatrix-0.1.0-r4.ebuild 535 RMD160 de1dce4331ae6cd476cfc84246933d19bbd12ea5 SHA1 1ff44c221087327527f28d6630abc04fe1308716 SHA256 af43b3014e915d3c71bccbe2142a63f005c04eea16db188ee3b6439acb4c6fd1
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-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2388 SHA256 8b66b6a1499bb3700c23958726cf1ca92ed8387c0112ec3a2f426cfaa4cec281 SHA512 d607b1153113b503279a14478871f13a594fe8894daa14e4f558d6051971dc70bc4bedbcdaad20c9be85841d409eab494ecdeb3f8f73631e6acaa1911dd645b3 WHIRLPOOL 889a02a76695558290e8b1595197f8ebe5d28332fc02d1ad75e4062800730fff996cef58101105134b63b6f23a97b10cb3ed96d86353977e9d6e87695f2d2406
+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-domainatrix-0.1.0.tar.gz 420983 SHA256 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1
+DIST embassy-6.1.0-domainatrix-0.1.0.tar.gz 399655 SHA256 54f4aa2bd8753a261722f16098e42f01a9083467162c027e2f1738a740f880d3
+DIST embassy-domainatrix-0.1.650.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0
+EBUILD embassy-domainatrix-0.1.0-r3.ebuild 511 SHA256 4a0293c37b1f414f8699767c029b3cbcfa51bccd847288155c5da33d48f71250 SHA512 f40d442c07a8049c1f9636c99f6a9e8580050b27f1d5c62b1e64f3648515e905cdf6c25b94e31b0607e5a0e2ba6df78f475874ef0a036ef1875c0194dde58e95 WHIRLPOOL 5db1ea0c39f2ec4e701f35c2f839ad73fe5a3f0aecabb53cad86f795512e1d795fb2525768286e3360efe519f954baaa575278e25554676458000b1fddede4e2
+EBUILD embassy-domainatrix-0.1.0-r4.ebuild 535 SHA256 af43b3014e915d3c71bccbe2142a63f005c04eea16db188ee3b6439acb4c6fd1 SHA512 92d23eceeb6dd88ae949df4f470a83439084d32faea38c196ca14d7114c6b6ae6dc8b5287083c6cf7bdfa46c05a47d13a0160fa2ebf05cb3118fbbeb18606a0f WHIRLPOOL 64bb5116ffdf8368d97e8710e13f96e3420a2f597720900a033deab5cc4db255c24ab283045cdd0eb204cf42fd09cb6339794c139143b6a327375fbb053aa0d4
+EBUILD embassy-domainatrix-0.1.650.ebuild 459 SHA256 ea47e42014cf7b3cd81b587f9e034a26f2587d4b2d6023354889f6727cfcfad5 SHA512 d2133bb4224daae332c1289e49b92351d69eb9c1eb4b324a5dffadaef3e161952c1d1bf66244c587c878de2ae94192af386a368c4b40e2f510855d4584db2eb5 WHIRLPOOL bfa5500cb637ee5a88c5f2e5c1ccbabdb5d972f439ce3d3ae7e8910d3de99fd0f05ae8619dd61554c5affecbab501144f9290977b32c1cb227577e9bfa8d20d5
+MISC ChangeLog 5508 SHA256 d923cc253a3103fdb9774e8c935aacbda574cedaa06848799b4e6541e194509f SHA512 1cbbd206595aae8b4799c02863f5e9405dfe56a2034afe016fb7ede063fef2a508498e581ea138af1f596f3ea1cac0f50b1f3bd1c0b62f4f3a6ec0391449e332 WHIRLPOOL 44472d22194f65641a0d1ac9c798bc6451baccbe68b015f52a6f67c76b8037ecc5d875a1279131dd85175a4bab32278c481735d4033130a52111f7f61cce7a80
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild
new file mode 100644
index 000000000000..0325abd696a0
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild,v 1.1 2015/03/28 17:31:57 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein domain analysis add-on package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..f76b0237c7de
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
@@ -0,0 +1,91 @@
+--- DOMAINATRIX-0.1.650/configure.ac
++++ DOMAINATRIX-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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- DOMAINATRIX-0.1.650/src/Makefile.am
++++ DOMAINATRIX-0.1.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -64,5 +62,5 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
+
diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-domainatrix/metadata.xml
+++ b/sci-biology/embassy-domainatrix/metadata.xml
@@ -1,5 +1,5 @@
 <?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>
diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog
index 414b8c4df291..56c0bc2ba631 100644
--- a/sci-biology/embassy-domsearch/ChangeLog
+++ b/sci-biology/embassy-domsearch/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/embassy-domsearch
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.22 2011/10/20 08:55:04 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.23 2015/03/28 17:26:58 jlec Exp $
+
+*embassy-domsearch-0.1.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +embassy-domsearch-0.1.650.ebuild,
+  +files/embassy-domsearch-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-domsearch-0.1.0-r4.ebuild, embassy-domsearch-0.1.0-r3.ebuild:
@@ -98,4 +106,3 @@
   07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
   +embassy-domsearch-0.1.0.ebuild:
   Initial import. Part of EMBASSY 3.0.0.
-
diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest
index 84abebd83ecf..8be543dbdd4d 100644
--- a/sci-biology/embassy-domsearch/Manifest
+++ b/sci-biology/embassy-domsearch/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-domsearch-0.1.0.tar.gz 470537 RMD160 37a087286717ce3aac2da1699f4eea9b10d06c4b SHA1 a3fc9198380bab4aa7465f22cafb8918d16b68ce SHA256 fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95
-DIST embassy-6.1.0-domsearch-0.1.0.tar.gz 443681 RMD160 33540897ccad19e8bb5909a8a1276881a1c3ffa7 SHA1 d97915b4bde1c79c172e3c7c2380c3cab3045bf4 SHA256 781461790a85d259a49130d5220a644213d5aaf352e9f72ab8fbb0dfaa331120
-EBUILD embassy-domsearch-0.1.0-r3.ebuild 505 RMD160 fb293ca3b962cd88fd8517aefd13fbd25f9d84e2 SHA1 c899bdf49952854b89036addcd40552c0fa34388 SHA256 28f64b95af38a4dc4b0f170fd83a9a6f3c025dd562b5b3c7ca750548aaaaa7b5
-EBUILD embassy-domsearch-0.1.0-r4.ebuild 529 RMD160 ac8cff80204ad5d0d2a309c9c9782043aeba771f SHA1 92973eb90495c65536054059a871c7a11298ca01 SHA256 1708bf7da0a9d9cc68b4a92e7668de3ec350979d1c21932054a340d2de8a9813
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-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-domsearch-0.1.650_fix-build-system.patch 2410 SHA256 c18d9208dcb000e12fe023863180ac1d3643c236a8bf4259e930526ead7f8257 SHA512 d6e0ef61a009b5df0c8e3d4a61a366a0a202c73e47fa86917a0eb9c476f3bf77b1dda399f1db7e6fd6d504247f31b84b022496b230fe570867239c70584fa68f WHIRLPOOL ecbdb32b6dec691de7808aea25bb7b46bdbe80b219aa36a006bd839de50011801134cdab66b770a81a7dcf62e349a2197e67d830dec1fa6e9c1a0ae7c56f7928
+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-domsearch-0.1.0.tar.gz 470537 SHA256 fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95
+DIST embassy-6.1.0-domsearch-0.1.0.tar.gz 443681 SHA256 781461790a85d259a49130d5220a644213d5aaf352e9f72ab8fbb0dfaa331120
+DIST embassy-domsearch-0.1.650.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 WHIRLPOOL 02afa5cdf4d82b127317537c088b91592f6c4624769b7b13f030fd59590b533fb8ec62189b165bbf885d967069883f5e08f562e7187294468700ce9571a47111
+EBUILD embassy-domsearch-0.1.0-r3.ebuild 505 SHA256 28f64b95af38a4dc4b0f170fd83a9a6f3c025dd562b5b3c7ca750548aaaaa7b5 SHA512 b910f18f86a1372dedc311ed6c1b853ac3cad9e9f02aa5b2659cdc42243654fee698d1fec1b0464eb35db5ccbab099e05fb3c5314e80ddfbb56d992b075e21f4 WHIRLPOOL 201a92a5f96a6f3e4e669b69ff52b641ff77c20d306f01b186514cb31a745a552c1c048971241a79cd01079e5001a1189411becad745b8780cf942a5721d5c36
+EBUILD embassy-domsearch-0.1.0-r4.ebuild 529 SHA256 1708bf7da0a9d9cc68b4a92e7668de3ec350979d1c21932054a340d2de8a9813 SHA512 0ebde667797193354c61beb67b2faa4d3e6bcffaab718f40295ae45619fd0a8c648856841a9c86ffd2ad4236a71921a1e53abb8551d57035dc9472cfc60747f6 WHIRLPOOL 21281d4abd67f430ca2434867d31122e39159003f95fab2c31b5331d6d6ab72b5605d390f28be4b9fdec59e738e789f6b4b880450abdbc3e3c0499c5b8fdaa27
+EBUILD embassy-domsearch-0.1.650.ebuild 453 SHA256 4905295ae5e148a63f59462604f26162c0dd0b1124f22bee9beef5cfa174db53 SHA512 5a8c8c0d4a2960d43d866831431a92b069cce1e2e2abf2e26c0c5a9de97413908a49e7e13cb2ab2491599aa94a49fe35bc912457bd7319cbe2973a5809291cbb WHIRLPOOL 1efcc663b92a6d857d6cab8fa451afeb05502c8791c7eb8f3b333897289f647da207dd6370a17bad45e15c3d3d0beeff85cba0c23dc3ddd0aa5377b07134b836
+MISC ChangeLog 3580 SHA256 f52b1ad3f1892bde888ccf0379e17ba5be0f3fd90cd057c0ed3ac3ede395cd2f SHA512 5cf9ccae2bfe5189151d61de356d9408f2f2a4aa5c4538080995e4f5cba0ec1c3e3e271452f05e88abbb9532a019ba773fcef012847c39c378d81f6ba5c4fe6b WHIRLPOOL 0f9403c1d3d085d572b022ae7bb8ba68a24803b51eabaf6b187e996183b14e579e36f00f9285939ed400c3bdebf864d77f7f5cd638b901ec519d394fe14f6ecf
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0
 
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diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild
new file mode 100644
index 000000000000..c1619bfd7f46
--- /dev/null
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild,v 1.1 2015/03/28 17:26:58 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein domain search add-on package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..f3f4b3950100
--- /dev/null
+++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
@@ -0,0 +1,91 @@
+--- DOMSEARCH-0.1.650/configure.ac
++++ DOMSEARCH-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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- DOMSEARCH-0.1.650/src/Makefile.am
++++ DOMSEARCH-0.1.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -62,5 +60,5 @@
+ 	../../../plplot/libeplplot.la $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
+
diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-domsearch/metadata.xml
+++ b/sci-biology/embassy-domsearch/metadata.xml
@@ -1,5 +1,5 @@
 <?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>
diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog
index c2462e926bc1..e4f8e1310b0c 100644
--- a/sci-biology/embassy-emnu/ChangeLog
+++ b/sci-biology/embassy-emnu/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/embassy-emnu
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.32 2011/10/20 08:54:43 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.33 2015/03/28 17:24:57 jlec Exp $
+
+*embassy-emnu-1.05.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-emnu-1.05.650.ebuild,
+  +files/embassy-emnu-1.05.650_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-emnu-1.05-r5.ebuild, embassy-emnu-1.05-r6.ebuild:
diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest
index b67930cc3c26..f21f17683ef2 100644
--- a/sci-biology/embassy-emnu/Manifest
+++ b/sci-biology/embassy-emnu/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-emnu-1.05.tar.gz 390229 RMD160 1d6bbb61cc22d72c130c90c33b4e6ecb14c89aab SHA1 06a57905af7fa7807825e000377b3d8626c99d2e SHA256 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333
-DIST embassy-6.1.0-emnu-1.05.tar.gz 364956 RMD160 9b84bf7590200e0b386d9440016203c5e8e7048e SHA1 1f4ff9e592ab42557a16815c2ee3851f5b3bdc68 SHA256 cf02a8a30b3d84330279cf553488cb3f2fef63bab31dc01b6b9e69a97d619b2c
-EBUILD embassy-emnu-1.05-r5.ebuild 585 RMD160 a968573cff64d56fe76ce79367d4212753500177 SHA1 fd0688d9c4a8b966f52bc78b1d4e6f5d77072ccc SHA256 107017fa4db5806261142fca90ab67f8b37ad27d844676ebc868f5ab648d0c2d
-EBUILD embassy-emnu-1.05-r6.ebuild 609 RMD160 08aa13b892ea36c48e019996fda3b0312f7ef1b4 SHA1 e51b427f0e171c3eb12a485de5c1a4762507353b SHA256 3efb2f1f2a0c2f7cf0700708a9278769931937ea3a51e416f6c48fa09a63addc
-MISC ChangeLog 4670 RMD160 0de35c8869c1b95dbf992d4174e75aaaddd598fa SHA1 c86473d02ae529de02c69cec394138cae266843c SHA256 bc6dd04bf24665e15d00e551a18aed5ca105ca3281786350bc9f3e4944d5b78f
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-emnu-1.05.650_fix-build-system.patch 3455 SHA256 6f165662eb1e8d57eed8f51fa6c836b949f6be83327732bb7a7fa1b93373c763 SHA512 fd0a51d12009d3ccd25a0a60b0fd2133b22988594667b2c68498c987b9a41ac0ac75421996940d7480864912a2316f0d7a0ca4bd2bb777f16706d0a4907d6896 WHIRLPOOL ef04417248b83999c8c83769c7576acb4da71387904a83d7876d0a2a8be59032140aaf624b22b1c8c85ffb4e2ec63eb2d9ea6bca079a541f330a8f37842f9e15
+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-emnu-1.05.tar.gz 390229 SHA256 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333
+DIST embassy-6.1.0-emnu-1.05.tar.gz 364956 SHA256 cf02a8a30b3d84330279cf553488cb3f2fef63bab31dc01b6b9e69a97d619b2c
+DIST embassy-emnu-1.05.650.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a
+EBUILD embassy-emnu-1.05-r5.ebuild 585 SHA256 107017fa4db5806261142fca90ab67f8b37ad27d844676ebc868f5ab648d0c2d SHA512 5007d4bb4f96210d0602ff489533d8a5deee8c6eed55fa6c745d85a9304a9b6f8dea18f4ba22519ab0f39c9d6c2d44c2bc30d30fa900255abe3ca36066c99153 WHIRLPOOL 4ff71bd1ba6025f335a4d1970ca0d5acfd0d2c545def98f8becc971deddb67e880ed379d3c6ec2a9250ccd3aa6b0e4ab3fcbff7ada7fd7bf890e51be0c04b4ed
+EBUILD embassy-emnu-1.05-r6.ebuild 609 SHA256 3efb2f1f2a0c2f7cf0700708a9278769931937ea3a51e416f6c48fa09a63addc SHA512 0682ac937318e4b8156d34df9a0b8fc254ec81cabea48b3ed6d1914bcc19a5d730299a48288f1fdeab66dd8382a49f43c41a8012b3d7947b8d2290b0865532bc WHIRLPOOL ec5648807dd813024fe03226e31075cbf580ddda15d033882612e7c87960992d505bbd1b91bf4cf912ef88d4986e0571e8052533b4da38af12f0b0f0347afcf2
+EBUILD embassy-emnu-1.05.650.ebuild 549 SHA256 23f388299bf4aec4355c2287a45c892f859a98d1ade2379174a764a77a3a25a9 SHA512 a47452aec70960e5ed562871980b6d84c6974ca01a6d48f5e3de2ff7f111e16ad1e0ea929b2be429e81524042d2de21ce473f30d397f5da91d7ed1d5e059f9e2 WHIRLPOOL ff4f4dbc5ddcc30c3e7d7871d8d5debaae2d78a93d7196bee076c52c7ff6bee754832b04cd04e3ca0d281650296120c57215693378856a72eda37a8174f0d925
+MISC ChangeLog 4946 SHA256 8e25e94071dd273334221c40a8a6a2e03dc46b8f6c198b37bd29b4c8df26f815 SHA512 3a8a0152cc9735204a9de8132657805dea68c4e77e18e25229d54509730d6f72d97dd2de71a14ffc132a5677c3f4931a30a72db748383c3c16c54fcc9fcf1faa WHIRLPOOL ac9691e09d5bbcdd8f36e1cb7818fd043161751a21bff593f377859dad08790daf501ef11277761b006ae997c1f4a35fef0644bda209cdf8ec1b8bc085c758bf
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0
 
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diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
new file mode 100644
index 000000000000..15daeda9d936
--- /dev/null
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild,v 1.1 2015/03/28 17:24:57 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Simple menu of EMBOSS applications"
+EBO_EXTRA_ECONF="$(use_enable ncurses curses)"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+IUSE+=" ncurses"
+
+RDEPEND+=" ncurses? ( sys-libs/ncurses )"
diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
new file mode 100644
index 000000000000..e73eb7b170ce
--- /dev/null
+++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
@@ -0,0 +1,127 @@
+--- EMNU-1.05.650/configure.ac
++++ EMNU-1.05.650/configure.ac
+@@ -635,33 +635,6 @@
+ 
+ 
+ 
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${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
+@@ -899,20 +862,16 @@
+ 
+ 
+ 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)])])
+-
+-AC_MSG_CHECKING([for curses])
+-
+-AS_IF([test "${with_curses}"],
+-[
+-  CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
+-  LDFLAGS="$LDFLAGS -L${with_curses}/lib"
++dnl Test if --enable-curses is given
++AC_ARG_ENABLE([curses],
++[AS_HELP_STRING([--enable-curses], [curses])])
++
++AS_IF([test "x$enable_curses" = "xyes"], [
++  PKG_CHECK_MODULES([NCURSES], [ncurses])
++  PKG_CHECK_MODULES([FORM], [form])
++  PKG_CHECK_MODULES([MENU], [menu])
+ ])
+ 
+-AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"])
+-
+ 
+ 
+ 
+--- EMNU-1.05.650/src/Makefile.am
++++ EMNU-1.05.650/src/Makefile.am
+@@ -17,9 +17,8 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \
++	$(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -57,5 +56,5 @@
+ 	../../../plplot/libeplplot.la -lmenu -lform $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB)
++        -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB)
+ endif
+--- EMNU-1.05.650/emboss_acd/Makefile.am
++++ EMNU-1.05.650/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-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-emnu/metadata.xml
+++ b/sci-biology/embassy-emnu/metadata.xml
@@ -1,5 +1,5 @@
 <?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>
diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog
index 549d86832d6f..c7243b02282c 100644
--- a/sci-biology/embassy-esim4/ChangeLog
+++ b/sci-biology/embassy-esim4/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/embassy-esim4
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.31 2011/10/20 08:54:22 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.32 2015/03/28 17:23:35 jlec Exp $
+
+*embassy-esim4-1.0.0.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-esim4-1.0.0.650.ebuild,
+  +files/embassy-esim4-1.0.0.650_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-esim4-1.0.0-r6.ebuild, embassy-esim4-1.0.0-r5.ebuild:
diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
index 466d29bb81a1..77980aa589b2 100644
--- a/sci-biology/embassy-esim4/Manifest
+++ b/sci-biology/embassy-esim4/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-esim4-1.0.0.tar.gz 431898 RMD160 228f886fa5804e2558884e035c90e8837a6939be SHA1 10710ade8f85c7adf5ded862b211726d2c1000d5 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577
-DIST embassy-6.1.0-esim4-1.0.0.tar.gz 405076 RMD160 7db28acb948de25501dd2428567e208376066e07 SHA1 853aaafb776270e607e5a4040fb6062280484a30 SHA256 ff4c01548a4a70f0e27b25df439588d25db417a6f80371590acc4254b3876b7c
-EBUILD embassy-esim4-1.0.0-r5.ebuild 519 RMD160 5dd0458d94ef6da81069e7a10410daef12c74575 SHA1 87de3028bcfc8d3821b68302f79853192b1b02c3 SHA256 f8b35c9e3fd4c0b2b44501628a7daacb31a9ada8c58f029fa3dccd850928bdab
-EBUILD embassy-esim4-1.0.0-r6.ebuild 543 RMD160 3c885a479d09f6f85e9ee317bf31b8327a0fd859 SHA1 a468266dd0ca9971e692341a3fc94192da700f13 SHA256 1d0c45a80b4a3ff5b53edb353ccacd2778e20d331ce7a31fc24214aecf0f6460
-MISC ChangeLog 4611 RMD160 3da98d80cb7b7e5d1506c728dc189e8db64ac44a SHA1 7fa545cee07344fcdfa974fe8dd9fa7809d28df7 SHA256 65363d052a21e0e3f79994eb19309834ffbc56babad2b9661c7fa80e4e9fb079
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-esim4-1.0.0.650_fix-build-system.patch 2568 SHA256 b19e115c5e2585349cea1a67e10d2928eb57ec65d2d55d305145d942cf7592b3 SHA512 2205c7b6ddcbbb17be6ae7242ddc54240c8087f04be5b7b9b245ce5d14c16ac196e227589b579d9c10ec433eaef7d69af9acb0ba16795130f630ef4b597997c2 WHIRLPOOL 8e52232753759142512035c86753214bf40b1e4433bf643b6866e8802aa53125ec61b5c3387a259aa81cadb3ddc1854eaaf7e8d15e3ec4d68d5fa6209bd3b49d
+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-esim4-1.0.0.tar.gz 431898 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577
+DIST embassy-6.1.0-esim4-1.0.0.tar.gz 405076 SHA256 ff4c01548a4a70f0e27b25df439588d25db417a6f80371590acc4254b3876b7c
+DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62
+EBUILD embassy-esim4-1.0.0-r5.ebuild 519 SHA256 f8b35c9e3fd4c0b2b44501628a7daacb31a9ada8c58f029fa3dccd850928bdab SHA512 23b41eea8b3c0dd1f41887305afa18596cc82e6853e83355399a81545932c95c661760df2d926b1fd295bb04554e471f3926669808c0a625813216dc3e3750c3 WHIRLPOOL 47d8e921988c76e15d5a77adafe5df01b655be2a9d60201a139a098b2b45252b81befc23f6e5b8813bf71a64c6c843f676c99f194a7b2cb9b5e5902fd1388771
+EBUILD embassy-esim4-1.0.0-r6.ebuild 543 SHA256 1d0c45a80b4a3ff5b53edb353ccacd2778e20d331ce7a31fc24214aecf0f6460 SHA512 13e8a52f313123b41ba178feb8e44aa7f8607cebb7c1a3a700b22e31a6f057980edf9aea09b55dc300d404b1731590c05f3f9e4dd5a52ee9cd8c5d65a138b5ac WHIRLPOOL 9736e56d99bee5dda554f73ce76e4960ff2917c09548d9e9e98fa11b1e1ef6007fde567d1c7253eb44c51648691da0cf68bfcff670df88055258b83109ddf586
+EBUILD embassy-esim4-1.0.0.650.ebuild 451 SHA256 cedd752525a6e510b5a3c7adc5424472778e0de87a22d1f67e9bb4532d4c3ea7 SHA512 b5e81d4bb0b139804487a7a30ddd3aa8ca8e5b3ca4041db97a2b4b109edbc7746406ae5db634f3290ac8c124a9b1c6c521b6303eca2e9f4c8d9b28017d3ecb53 WHIRLPOOL b20f58c1807c4c57e6ad176df9a6f7afb0dc9ddece6764bc740ab4bf41bc2b124df243e8e9163dee5cdcbd5822a20b2c91fe270596a60a77aab348d2594e84d9
+MISC ChangeLog 4893 SHA256 86a3df30fa37c786322043f00916fc8396a7b89e898f64ed97e73c2bcafd75dd SHA512 4fd7f941e6992c975775e22f68516f1b48bbcf5efcd4380a99157be88e1783f285c93440503c96d81f72567233972f32916beb22abb79f52bc7f989c2a7b1f53 WHIRLPOOL 6c59230e525cfe9fd07614430155feaef3bac01ff0539a3d691bd9e768e63767c7cf651f046bcdb020bf6d0be23f704138b60df6ace71e54c078b6b936dbb321
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild
new file mode 100644
index 000000000000..218b569b4a1c
--- /dev/null
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild,v 1.1 2015/03/28 17:23:35 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
new file mode 100644
index 000000000000..8279071806c6
--- /dev/null
+++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
@@ -0,0 +1,97 @@
+--- ESIM4-1.0.0.650/configure.ac
++++ ESIM4-1.0.0.650/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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- ESIM4-1.0.0.650/src/Makefile.am
++++ ESIM4-1.0.0.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -63,5 +61,5 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
+--- ESIM4-1.0.0.650/emboss_acd/Makefile.am
++++ ESIM4-1.0.0.650/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-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-esim4/metadata.xml
+++ b/sci-biology/embassy-esim4/metadata.xml
@@ -1,5 +1,5 @@
 <?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>
diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog
index 87fd3a15e63b..df2f6f77c52a 100644
--- a/sci-biology/embassy-hmmer/ChangeLog
+++ b/sci-biology/embassy-hmmer/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/embassy-hmmer
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.33 2011/10/20 08:54:01 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.34 2015/03/28 17:21:22 jlec Exp $
+
+*embassy-hmmer-2.3.2.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-hmmer-2.3.2.650.ebuild,
+  +files/embassy-hmmer-2.3.2.650_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-hmmer-2.3.2-r3.ebuild, embassy-hmmer-2.3.2-r2.ebuild:
diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest
index 6e3faba4e431..5edae00022f8 100644
--- a/sci-biology/embassy-hmmer/Manifest
+++ b/sci-biology/embassy-hmmer/Manifest
@@ -1,28 +1,33 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+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-hmmer-2.3.2.tar.gz 565686 RMD160 d2fdaf691f3064d44739fde42809a5222729f532 SHA1 642f6f7601cab5f18181157dde4496570a661541 SHA256 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258
-DIST embassy-6.1.0-hmmer-2.3.2.tar.gz 541801 RMD160 214c0155e2f14c8a0968cd4d8ee55642fdcf0b18 SHA1 c324164767d4503a0c567d113d280c5dd4e39bfd SHA256 725d1b1f7b79a29b6b2a0569ce82fbd773c1199cd041b1c2360f66e4be78aaab
-EBUILD embassy-hmmer-2.3.2-r2.ebuild 650 RMD160 49ac5c79f5c32a0add1b3065e57a3918b8e378a5 SHA1 072bc62ed25d7ab080926eb52b7797cd4862b93c SHA256 9d952f1c50419349979369829d3a1b64e3ac73778377c7f95862c8d7a7e728bb
-EBUILD embassy-hmmer-2.3.2-r3.ebuild 674 RMD160 49a102e296959761627c4cb79f5ca537629d9919 SHA1 40c97c984fc68bb61a9daf16d929d192ebb16dfe SHA256 961aed77fb30a8f24225c079bfa0a16c83d5c3ea612e0b658d5b9a926b516bef
-MISC ChangeLog 4887 RMD160 ceaada2bec36bbfaa8f4028b0c8aec58d7b8edfb SHA1 73c94882a6332df048f87145f62d729b079729f2 SHA256 d10b2e4cc052c1839530a58ba51c03ab1b629275110bca1610802558d5cc9a3d
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
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+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-hmmer-2.3.2.tar.gz 565686 SHA256 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258
+DIST embassy-6.1.0-hmmer-2.3.2.tar.gz 541801 SHA256 725d1b1f7b79a29b6b2a0569ce82fbd773c1199cd041b1c2360f66e4be78aaab
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+EBUILD embassy-hmmer-2.3.2-r2.ebuild 650 SHA256 9d952f1c50419349979369829d3a1b64e3ac73778377c7f95862c8d7a7e728bb SHA512 638d2581dfe55337b5658e23cdc523f7645f3754b7b1168c0ccf157bfce20cafd78167eec12a66fbfb727b5af2f1111dcef296c402aa20a746770a59b79a38b5 WHIRLPOOL b261ea3ec91f3d527e8b6adf6c68b3fc0f952424428a804bfcee320ce26015dd917799928578bb9540519212af996fa1b24735d92cf1785baa83a74129cac027
+EBUILD embassy-hmmer-2.3.2-r3.ebuild 674 SHA256 961aed77fb30a8f24225c079bfa0a16c83d5c3ea612e0b658d5b9a926b516bef SHA512 a4e7a2292ed8567a1c31379755bfd5c331a46d7b7636213402eddd78aa09db2cb478f23229b982a61ee85215f1e9bb39e0ca0df241422c1e5ed846aa5f8b9ee5 WHIRLPOOL 7da84b2526c3ed4e356376688bc55e382312f20d14325d309d44ff3d0e681d21333dd57465ca9ce71f59f0e502ee0183b8aa12e508d64bdec126632beee00b08
+EBUILD embassy-hmmer-2.3.2.650.ebuild 508 SHA256 648a72b19a6c179780ae9f9d7fcb52fe90a729316abae1456724a4e411240783 SHA512 09493fb5abfa727a068474901fb738171b544dc8fd4cc9c823d86db453ca7cf6e23e968dbc391d0dee7340717bd584c5f0abcb7bd68b3449523f96669c5759e2 WHIRLPOOL f2663f85325b13717890c00eca90016e457ba85387538715354eacc461950aeb65cb05429127506879c60c8485f69e941b67733b7f91b0c711b41baa3e2077db
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+oGO7HCdUt552F8mq8hGNK6D43lCER/g3q1AQw/zVx50K+eIQP4tGGbPs0KaWfV5K
++IIixYJiSlr2Ldm2iqaymK298pfjvA1rTVf9BYWo6mBinHruWYyy+FdYfYBPyGrV
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+5mugbl9Q0Ds6PmMfqAryl5xsnV/RaU0oCFWQx4g0w45JL6ZiMUq/PZZ9XAssFhHI
+DA8lFYkB5XNABHPlqDJEaCY7wlMgionNWPMRajIQnZ2btxf3hsmZAeH+JLbxUD8+
+5yAolxq/4y2cvf+rje4cfE4WcIpv7V776U2dvndsXABNdVoxSFjC4STac5ZqjhMd
+iuy9XVYToeUGW5iS/qhyZJvEPPX1GxJIWGf19q04CkkwWPS9fv+iqVh/ERkTdo5z
+u5Yu1AUf28HgELfbIw5k
+=WmKk
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
new file mode 100644
index 000000000000..9df99b843eb5
--- /dev/null
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild,v 1.1 2015/03/28 17:21:22 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile HMMs"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+
+RDEPEND+="sci-biology/hmmer"
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
new file mode 100644
index 000000000000..78d0c254f25d
--- /dev/null
+++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
@@ -0,0 +1,90 @@
+--- HMMER-2.3.2.650/configure.ac
++++ HMMER-2.3.2.650/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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- HMMER-2.3.2.650/src/Makefile.am
++++ HMMER-2.3.2.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -67,5 +65,5 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-hmmer/metadata.xml
+++ b/sci-biology/embassy-hmmer/metadata.xml
@@ -1,5 +1,5 @@
 <?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>
diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog
index d282ee0ce54f..d58acceadb12 100644
--- a/sci-biology/embassy-iprscan/ChangeLog
+++ b/sci-biology/embassy-iprscan/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/embassy-iprscan
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.7 2011/10/20 08:53:38 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.8 2015/03/28 17:20:18 jlec Exp $
+
+*embassy-iprscan-4.3.1.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +embassy-iprscan-4.3.1.650.ebuild,
+  +files/embassy-iprscan-4.3.1.650_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-iprscan-4.3.1-r1.ebuild, embassy-iprscan-4.3.1.ebuild:
@@ -32,4 +40,3 @@
   27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
   +embassy-iprscan-4.3.1.ebuild:
   Initial import for EMBASSY 6.0.1.
-
diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest
index c1907f316f0d..b246d609c6f0 100644
--- a/sci-biology/embassy-iprscan/Manifest
+++ b/sci-biology/embassy-iprscan/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-iprscan-4.3.1.tar.gz 339939 RMD160 bdedabd2b86cbf4cc33ebfb4e55650faadffa0aa SHA1 cf3de395e0642126e1a9e23fdad0288f80e0e7e0 SHA256 df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a
-DIST embassy-6.1.0-iprscan-4.3.1.tar.gz 343265 RMD160 6c7afbe8fbafc01eacf9634d44f0e38659e2b06c SHA1 8eaf9bf518ff770ae58bed6ba89985fa01bb2099 SHA256 a98c08136d98dcbaa45e61714c3598c1ce705fd3a1578a85c94674f41ff1b3ba
-EBUILD embassy-iprscan-4.3.1-r1.ebuild 545 RMD160 d8828e08dd0b2802091bd6272bd9b2251488541a SHA1 6003c53e5d5fb6124c7058d30bdb96f5e7382edd SHA256 c785cbed3440f0391eca0f5bfda4d382b2994cf50adfafde5e801dc27a4591e0
-EBUILD embassy-iprscan-4.3.1.ebuild 505 RMD160 e9b6d9f077e2ba156257e0029f7bce26d5a72d40 SHA1 36c205a0a1bab91a1b0ff9b581633b76c76094b4 SHA256 f64afda1a967a295c3468100fa61f6961695af1ff8c760356dc15c4ae137897d
-MISC ChangeLog 1204 RMD160 2700bd7fd4ee1edbac81617c5c4f024cedc6582c SHA1 6dcde1fa70747fb0657446a7b991bb638cdee14a SHA256 37bf46afd396e8714db21867dbdf553d8dc7aef1b162c802014aecaa37017c4b
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 2580 SHA256 8027ce9bd9b318fc6bce543770ab59fc8bd50237a68b959bc05274cdb3caa282 SHA512 de367b404d1f772276f4ca8f51c031ba148db6b80a480a4594f5e4151594eefae49ade820c145ae2b2feb5d7bd32bbb4196c82b3e809bc160ab88ce3a7b74913 WHIRLPOOL 71fb4928262df5669d828d945d47fa22f963c928e0dd0b24e1962191e63f803f354a15093c604caf7a1c8372a9b329c0183791c4577f456f634cdb5bdb6062bc
+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-iprscan-4.3.1.tar.gz 339939 SHA256 df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a
+DIST embassy-6.1.0-iprscan-4.3.1.tar.gz 343265 SHA256 a98c08136d98dcbaa45e61714c3598c1ce705fd3a1578a85c94674f41ff1b3ba
+DIST embassy-iprscan-4.3.1.650.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8
+EBUILD embassy-iprscan-4.3.1-r1.ebuild 545 SHA256 c785cbed3440f0391eca0f5bfda4d382b2994cf50adfafde5e801dc27a4591e0 SHA512 a845734ed8f1ca811c62149d811715d17189fc05f67e5c44d538ca3b69ce29b7e893b4afc1160036e56526cb72afea9b57ae2ddc3350a2adf2aedea17bdcc3da WHIRLPOOL 540f9237ba980962a99492183ca355e869d8d123a25948a4554e45453e7369edef49cfcd1d0b56bc9122bed210be8959ed78d4bbdc8c1256f2b958dfde98e22d
+EBUILD embassy-iprscan-4.3.1.650.ebuild 471 SHA256 3ec77ba7ebed4d0cc94a846f65c78b91d5d424b8403e4fac8384ff5b4f2d4dd3 SHA512 08b1345f41f7213e445d30b048285c7a303cf07d237295bd69b7ddc718b5986e4ef458d18b5a41466cc8e84025235865100846733e543c68c89fcf8e5393b810 WHIRLPOOL 8ec24e16e6858f4bcfd5407143a3bf96d0cea0428c00ee1cbcb805113cda6041fef73a5f87279a46e3ea1c0f14c4757549089805529edd33aadd5a5326ee5596
+EBUILD embassy-iprscan-4.3.1.ebuild 505 SHA256 f64afda1a967a295c3468100fa61f6961695af1ff8c760356dc15c4ae137897d SHA512 0d48b41756575422adfa44c1303b35f41a7b36953b47997f4b7748471c4e95e8d31c16be9c6b21af0eecce643eb2f65f8a5a6dd140ae698cc70e03bb5f0b0696 WHIRLPOOL a1a54ad6ea1f29ac6b1482fb7f9ecbe0db24db6d08eedc310c8fbaad046eb6e7f40fd6cbe06e7c11a53dbd33fdad4f0ee7a03fb4de4161f4a2bf598f68f62551
+MISC ChangeLog 1493 SHA256 e2d973289f80af17a9388df77e3e0b2cf81fff2baa638671b991fbda7da8e7e8 SHA512 cafa77c87dd604614953707704402595d36303261a299c1c335dd4e4552bfb6d6481e49ef248f11eea2a59fd0dfabe860ff1ffd3c9805d0492ed7e73517fa895 WHIRLPOOL 2d70f04ca2efe69059487851e6838375e2f667907fd6a9e78f7fd93a7f96845f1f7249f6c24efe7232a2ad9ed226f9a0c610bb536fbd022582e88c7d99bf05cd
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+Version: GnuPG v2.0
 
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diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
new file mode 100644
index 000000000000..48ee401e232b
--- /dev/null
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild,v 1.1 2015/03/28 17:20:18 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="InterProScan motif detection add-on package"
+
+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-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..955005d51211
--- /dev/null
+++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
@@ -0,0 +1,97 @@
+--- IPRSCAN-4.3.1.650/configure.ac
++++ IPRSCAN-4.3.1.650/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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- IPRSCAN-4.3.1.650/src/Makefile.am
++++ IPRSCAN-4.3.1.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -58,5 +56,5 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
+--- IPRSCAN-4.3.1.650/emboss_acd/Makefile.am
++++ IPRSCAN-4.3.1.650/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-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-iprscan/metadata.xml
+++ b/sci-biology/embassy-iprscan/metadata.xml
@@ -1,5 +1,5 @@
 <?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>
diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest
index 4c5f81081608..57f36b259185 100644
--- a/sci-biology/embassy-meme/Manifest
+++ b/sci-biology/embassy-meme/Manifest
@@ -1,5 +1,27 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 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
+EBUILD embassy-meme-4.7.650.ebuild 498 SHA256 f845efeccacb7fb0c019744bc9fc2a71f57eae89ab21d47f81b092f638a0fdf3 SHA512 2ed461c195470f77ce8e32769eba95a55b7847a5b5ae22c08f02c352ed98c31a8e3561bc646b7dc0743aaa7572f03404018ba71155bacbb27e590f0982bb4f40 WHIRLPOOL 7d681a603fcf475249e9b7251ab40fa8e5a886c60f7f43d788a9646f9ce6732d775041ace6e5fa3a475e43320eb56011f9204bd3de0f2a5fa078c05006e572dd
+MISC ChangeLog 499 SHA256 4b0c320f4689b6dc66602d002d26029240d86d9fb43b0cc06bed34945cdcebdb SHA512 83e5128209446931f0228691513989949464c36171acaf71140957237ec60293e4a22696f372280e2d9587e1d4296326e216422c7537295602bd2fa41368c8be WHIRLPOOL ae3bf8f8972676781047aa3ff3fd1df9c1b9e9968788478fed0533d54e57dc236edc2a68308aa2ff24e05ad3ca39c6d80eba95d82e30353af6c00e90d0eec241
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0
+
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+=pIb5
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
new file mode 100644
index 000000000000..26a4aa2042a2
--- /dev/null
+++ b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild,v 1.1 2015/03/28 17:17:41 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="wrappers for MEME - Multiple Em for Motif Elicitation"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND+=" sci-biology/meme"
diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
new file mode 100644
index 000000000000..03c42460455e
--- /dev/null
+++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
@@ -0,0 +1,90 @@
+--- MEME-4.7.650/configure.ac
++++ MEME-4.7.650/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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- MEME-4.7.650/src/Makefile.am
++++ MEME-4.7.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${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
diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-meme/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
author	Justin Lecher <jlec@gentoo.org>	2015-03-28 17:33:53 +0000
committer	Justin Lecher <jlec@gentoo.org>	2015-03-28 17:33:53 +0000
commit	6e1567e0ed5360a8ecf4e0489973138cedaabed2 (patch)
tree	f1449eb8fdd88b8c31cdd657fc59db19b5744eb4 /sci-biology
parent	keyword ~arm, bug 544684, thanks Vincent Hardy for reporting (diff)
download	historical-6e1567e0ed5360a8ecf4e0489973138cedaabed2.tar.gz historical-6e1567e0ed5360a8ecf4e0489973138cedaabed2.tar.bz2 historical-6e1567e0ed5360a8ecf4e0489973138cedaabed2.zip