10 files changed, 67 insertions, 212 deletions
diff --git a/sci-biology/muscle/ChangeLog b/sci-biology/muscle/ChangeLog
index b3fb62c74eb2..14c76a536da1 100644
--- a/sci-biology/muscle/ChangeLog
+++ b/sci-biology/muscle/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/muscle
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.20 2015/04/21 18:54:50 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.21 2015/04/22 06:48:54 jlec Exp $
+
+  22 Apr 2015; Justin Lecher <jlec@gentoo.org> -muscle-3.7-r1.ebuild:
+  Drop old
 
   21 Apr 2015; Pacho Ramos <pacho@gentoo.org> muscle-3.8.31.ebuild:
   ppc stable wrt bug #544956
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
index 557d99bc2027..160ba141e367 100644
--- a/sci-biology/muscle/Manifest
+++ b/sci-biology/muscle/Manifest
@@ -1,18 +1,28 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX 3.7-bufferoverflow.patch 595 SHA256 2acf33bcf8ebb6ee6c4171fd0dd4407a08a3c4577902c683a948a1b3231a243e SHA512 77b62486bbf59a29f12e7237da573b52ed5b72fc76eb07e5894ab32d5b955b82e0ca2678c6abae5065860faa049cdda84f194e8de2b809572ab9fa32b0bf41ec WHIRLPOOL 73a66c7e74ae767bd9159b30103694fab15c50ae19e1803fa8050b42b8895e66f1c5f70a80b1b266326ba07fcf6de64939395d3cc7a9428c73de64981a52142e
 AUX 3.8.31-make.patch 989 SHA256 f5352a5fc8a792d7af177d1e829a33e59bc39dedb81baf17c6424f8520ea6879 SHA512 e528b032d4e60d2ca22de1129da56125b8915ed288ee25965b2bc5b1d6118d1d589fa632dac9829011a405c3189b8b6b6c056eedde9dd30a9b6a6f572a5e2d2c WHIRLPOOL db552ae2482532c6034c86eb9be71eb99652e1d24e2031545eb5eff7ab558775ae0bcd0f467520df0a6b47ced18d8f163b7fbe83a1b6642118c86a53e8c7a298
-DIST muscle3.7_src.tar.gz 189907 SHA256 a028f545612f9d260e35909959e98ae7aec552b1eac8806c3ae59cf1b00f7235
 DIST muscle3.8.31_src.tar.gz 515267 SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce WHIRLPOOL daea88aaeaaacf5a2da68484010091ae46c69713659f92f45e5e2096af9e7d8c645d14e5b6c4c8e73e4df35a086dee823fcab6d442cd3881b773fb0113ce897d
-EBUILD muscle-3.7-r1.ebuild 930 SHA256 0379c05b8523067a9f4160278e1bb8e5803df0f0220f2bc0f79f9d276f8f4809 SHA512 52b8763cd3b7f9c948dbfb367725fb6240fec0eda72df38fb3f56369ac5188ac204422ae5ef77ade1c517f4e4c22dc4c990215d2f0ac4f36788874d64b9ac25f WHIRLPOOL 469fef67bbd7f167dc297c55becfb42283a594f86e07e491e73ff15cad3c5b28cf428d86efc1f035993b344465613c6dda003e25e441cabe6613c97db74c3277
 EBUILD muscle-3.8.31.ebuild 715 SHA256 0e432f8a7341ce631ef9d155b1d325dabf1ebf6e1ea389751957f39565722721 SHA512 b1e1b0b6df425ba6bb65a0d2df1437872e4d97d9d0bca221b9fa346ed8771179e2d0fe8537903c90bdb97bd8a008e4f3d1dcc1af568e59991fcbaf411f69d3c9 WHIRLPOOL 9ab9ea8fb3901fe7eee3582c37e2a919b037e44d1c650a4a7a3fc5c936df3b97491aa7148427c8e281fb97d93110bdd74bbed966c4488aca22ab9117f0455f2e
-MISC ChangeLog 2611 SHA256 fd187adfe299ddd144f1ccdd4a8b611ba4f9f1e88353c06c29793fee51425c01 SHA512 421eabf2063dd2f4edec7e1fa9655a887482a51ab8277b6dd2db1bd7822017fe71e59ccd4d7ea7f9e332befdd6cc4c3b093fd3adc2e072c1d9414d8202649c06 WHIRLPOOL fb622c6b25e8e7e365de19313da11ef59c4990aa08832e0e2cd119c989677df2b837ee096a3c982bdb8c7f9cddff675bf5c64db06a8bbf649586d24a6c96d82b
+MISC ChangeLog 2692 SHA256 fa708ddf75b2d3d4fb6b3167e43f157d99a5c9354d919baae3777fbeeee3c52f SHA512 76d9a7bb9b1ab7775c645be47dc5bb01a8482535b540d1983d5f8e15012514746892a67422ae56241e8ea40b521a28759c95c056df5c4b3a870af2e3d51cade9 WHIRLPOOL 86868989b062eac44e05a750955c207ca3577557b138934ab6842e98f34c4af84f9b97a569fe18b0a5cf61c8ebb62f8c10b5d3f4da5afe5a1fa9b836b2c9a0f5
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2
+Version: GnuPG v2.1
 
-iEYEAREIAAYFAlU2nPsACgkQCaWpQKGI+9SybwCfbjKFVV+eU7aXLONbCfqeE82y
-6MYAn0Qy/YyHAndYb49kkte9GpC24uCM
-=GUfH
+iQJ8BAEBCgBmBQJVN0RXXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w
+ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC
+OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirFaMP/iCoxPthKvWvEkl1/a5U3S4c
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+ukHfH0kFjLp40vFuy7iVJxaef8rtqGswEwiNVNwi2xurXFU1VAvpoHKYrL5Zvlv2
+VpczRh/yd4Jf1syiGNpCduPhRTPjk5+rU9DAM/WXwUoqbN6mFTNSfGmk5seVFOGF
+vD0PZYNtOdhqTfmNN2p/Q5wlNGyMEUQxrFXT8sNYQXkkfSlIPcsnBdMeW2Uss2QW
+pI6BOpoXaUnxczNUSUqFODtLYJCFT0dkdrSKrLWRTvpnWjCoKjGeKpFWdaRjYBCM
+KQWYXPbt53Bi+Gz9nge5Xyqgr1U0IdCmxlfkXRku1u0gz6dVcRWd2pclQtu/vAee
++tPEQyc4oUqwSsd1qBjJEMyqrBKChqTXFnYDuCoPKdgGflzN3j9P83iOUtojus4q
+ugZdM/7n/BDyBhWKSyLwjU7t2sjXQdJ94gQ4Q1Njkt5Ze4koaPYvTTJOdNC50Mpk
+NqYZli+Pb6yW85VbHqWEoduXkXxqJ/SczjVevRxOwlE2y6SH7evP1nrYW7EEzdTI
+PAgAfvkabmbw4uA6ve7P
+=HWsx
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/muscle/muscle-3.7-r1.ebuild b/sci-biology/muscle/muscle-3.7-r1.ebuild
deleted file mode 100644
index d334cb2ddb23..000000000000
--- a/sci-biology/muscle/muscle-3.7-r1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.7-r1.ebuild,v 1.5 2010/07/20 11:54:30 josejx Exp $
-
-EAPI="3"
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}${PV}_src"
-DESCRIPTION="Multiple sequence comparison by log-expectation"
-HOMEPAGE="http://www.drive5.com/muscle/"
-SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ppc x86"
-IUSE=""
-
-RDEPEND="!sci-libs/libmuscle"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	edos2unix progress.cpp globalslinux.cpp
-	epatch "${FILESDIR}"/${PV}-bufferoverflow.patch
-	sed -i \
-		"s:-static::g" \
-		"${S}/Makefile"
-	sed -i \
-		"/strip/d" \
-		"${S}/Makefile"
-}
-
-src_compile() {
-	emake \
-		GPP="$(tc-getCXX)" \
-		CFLAGS="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	dobin muscle || die
-}
diff --git a/sci-biology/phylip/ChangeLog b/sci-biology/phylip/ChangeLog
index d8a9003b2832..0679eac71f97 100644
--- a/sci-biology/phylip/ChangeLog
+++ b/sci-biology/phylip/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/phylip
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/ChangeLog,v 1.46 2015/04/21 19:08:18 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/ChangeLog,v 1.47 2015/04/22 06:51:38 jlec Exp $
+
+  22 Apr 2015; Justin Lecher <jlec@gentoo.org> -phylip-3.67.ebuild,
+  -phylip-3.69.ebuild:
+  Drop old
 
   21 Apr 2015; Pacho Ramos <pacho@gentoo.org> phylip-3.69-r1.ebuild:
   ppc stable wrt bug #544946
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
index 9384df71c4fd..af355857331b 100644
--- a/sci-biology/phylip/Manifest
+++ b/sci-biology/phylip/Manifest
@@ -1,20 +1,29 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX README.Gentoo 643 SHA256 d8a737f2ca6e0366fcebb96fbc9e12200b6402fea4c4f71696f4d9175980dfbd SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a WHIRLPOOL 671a6aa44cae7054d402ac111a572145b705052e6d084687a188fe451c8c6f30fd276f8abb89d40bf150be8d119616f696ccaa59fb3ed9177040eae8b3f8b80e
-DIST phylip-3.67.tar.gz 1467526 SHA256 089f31c0519b1af162628c02d4ff78570b42cd261f39b87c6406733f2f759b5d
 DIST phylip-3.69.tar.gz 1511935 SHA256 27947ce8dab4416e4823db38b3d1b0bf17bc545b6907cf09dcf6177df94c1a8f SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d WHIRLPOOL 25c45ac2a96278eaef9a62aecc367aa32a894df0cd5aff9b626abd013ecbe52f9d4bdaf7805ba5c5d8699f9a74d3d26cfe6e1c1b22960c03061171625d16415f
 DIST phylip-3.696.tar.gz 3955721 SHA256 cd0a452ca51922142ad06d585e2ef98565536a227cbd2bd47a2243af72c84a06 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be WHIRLPOOL 7d4d4bd703ecd84b7570c937484c15f52643221ca178fb494f81b18991149fc2f8d1c8c5b99b57e20ada0bef7e93dcb15c55410f8f1012b1656419fab19b3cab
-EBUILD phylip-3.67.ebuild 1432 SHA256 d943ae41c07d66149c41d44d5cb541d6ffbef6b249ea626c3c022873134f91c8 SHA512 61c3fa6d2ab8d87153cab17621e1ce6250be32a1b7909fc92b22d383863e56105b738fcd73c2b7740c82cc64a4568d85ef589ff6956a56e1945e1c18b416a83a WHIRLPOOL d7b69ba5b0a1e8772816873a22d731f68193b2a5b51ea920393c605e5b1d15753fe5c77edb9066d9640d230fb906bd25fca6ec59438adc954b074611cabe3161
 EBUILD phylip-3.69-r1.ebuild 1257 SHA256 74278fa4d72de3af695b6df45e8cfcdfb2054367408b3566d6b94a3fb6a26c9e SHA512 ab8ee640c20fd5e627d5cdfc2c95d65961cc93f90fe2fe9dc36153a857a56e054a5c815747786e27e0878a523c02b12f35acf1d34edc2097a2576fe21c042e8a WHIRLPOOL 6da0f19079ea2894e19a95d740aaa89240e680a729d0932048882cd93473a63f62bd8f1cb7e350d3a7317e782ca0699747cfd046219d182b27daf7445c4a3dbb
-EBUILD phylip-3.69.ebuild 1468 SHA256 83ec5bf8253997c088603b1b8de28eea11d63a1c0b81cf3fe12d52dc86d1132b SHA512 cd1acfb9d7f2cc7b96774981b10d2045d04fba033a852d78da85711359cdd347087fd3408d9f41a9a27a4076b7f58d6938fa600c6794d6628e856a19cda8248f WHIRLPOOL 5394a2b20a5c79a9cd3eb26e271bc2cc7a16deb3a6162b7b8f90d6448b6add6ec1f63b8a061a3a9159c44cbbea404f115f76d5ff384667075ec2cea94f7b0f72
 EBUILD phylip-3.696.ebuild 1207 SHA256 e724018e03d0834a1c09d5528265e3e8cc069dade85832fb924267f79d6f0a1e SHA512 7efe504111d20b4ca2acb738e441f36fafe4d587630bf499dc8b7e490846d29f00c27d92d3bb1844e92b74a770382aa9562acf3fcaea2a3231cad5e1cb2861f8 WHIRLPOOL c4cb026b41ebb44411a67b63a7b35718cfb4201c433a1673741bf4da124ba7950166399c35d89cf0f6e73518ac142e226657e0924748acc3579d27455a22212a
-MISC ChangeLog 6924 SHA256 0561aa6c9f0331e669ee4713f8a775babdfa48396471895cb3d36ebd403be7f7 SHA512 387087f958a824d296f5526f8a75a7bbd16afe6fd0a23772fc2a7249b77e7137d2bf2d01a16446dec252b9e45c6285b7218f90260c203ef6082de110739ed358 WHIRLPOOL 32357b9667bea2ff0b3f8834e1b923289e7769f37555dca1242637362ada420cdb6944436a96a1703beac262d4d7533b95a89b26f6175755cbc4b9f970fd6f20
+MISC ChangeLog 7026 SHA256 733a3765122ab15458e701cbf902f9408672e47696b84f971182f968e70129bd SHA512 fa87c1d1959303b6d8e402812c1600cd5868724c93e4e8a6bee14f9ec320f8e967da5f443622c39e476b17b6bbe90006e52a0cfcaab8504a23267af74d79c897 WHIRLPOOL 1fb268aea348f615a17c2bee08c81592ff1ea20934cb5ab0b634adb5f490179efecdd67e446308a84f4e562067971dcc5db5935a755bea995969db65d1e81b50
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2
+Version: GnuPG v2.1
 
-iEYEAREIAAYFAlU2oCMACgkQCaWpQKGI+9RvDQCeOE9OlMWXZuACJuZfKnLfIBZF
-7v0An0ghL7MPQkpIeUdGEZLumSE7MvEi
-=+AdR
+iQJ8BAEBCgBmBQJVN0T7XxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w
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+4F4W5V7WHD2/XtAlqQ6H
+=PfAy
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/phylip/phylip-3.67.ebuild b/sci-biology/phylip/phylip-3.67.ebuild
deleted file mode 100644
index 3d58114fed3d..000000000000
--- a/sci-biology/phylip/phylip-3.67.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.67.ebuild,v 1.7 2015/03/29 14:05:50 jlec Exp $
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-LICENSE="freedist"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 ppc x86"
-
-RDEPEND="x11-libs/libXaw"
-
-DEPEND="${RDEPEND}
-	x11-proto/xproto"
-
-S="${WORKDIR}/${P}/src"
-
-src_compile() {
-	sed -e "s/CFLAGS  = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \
-		-e "s/CC        = cc/CC        = $(tc-getCC)/" \
-		-e "s/DC        = cc/DC        = $(tc-getCC)/" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts
-	emake -j1 all put || die "Compilation failed."
-	mv ../exe/font* ../fonts || die "Font move failed."
-	mv ../exe/factor ../exe/factor-${PN} || die "Renaming factor failed."
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}"
-
-	dobin exe/* || die "Failed to install programs."
-
-	dodoc "${FILESDIR}"/README.Gentoo || die "Failed to install Gentoo notes."
-
-	dohtml phylip.html || die "Failed to install HTML documentation index."
-	insinto /usr/share/doc/${PF}/html/doc
-	doins doc/* || die "Failed to install HTML documentation."
-
-	insinto /usr/share/${PN}/fonts
-	doins fonts/* || die "Fonts installation failed."
-}
diff --git a/sci-biology/phylip/phylip-3.69.ebuild b/sci-biology/phylip/phylip-3.69.ebuild
deleted file mode 100644
index 1bd640e92f07..000000000000
--- a/sci-biology/phylip/phylip-3.69.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.69.ebuild,v 1.4 2015/03/29 14:05:50 jlec Exp $
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-LICENSE="freedist"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-RDEPEND="x11-libs/libXaw"
-
-DEPEND="${RDEPEND}
-	x11-proto/xproto"
-
-S="${WORKDIR}/${P}/src"
-
-src_compile() {
-	sed -e "s/CFLAGS  = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \
-		-e "s/CC        = cc/CC        = $(tc-getCC)/" \
-		-e "s/DC        = cc/DC        = $(tc-getCC)/" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts
-	emake -j1 all put || die "Compilation failed."
-	mv ../exe/font* ../fonts || die "Font move failed."
-	mv ../exe/factor ../exe/factor-${PN} || die "Renaming factor failed."
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}"
-
-	dobin exe/* || die "Failed to install programs."
-
-	dodoc "${FILESDIR}"/README.Gentoo || die "Failed to install Gentoo notes."
-
-	dohtml phylip.html || die "Failed to install HTML documentation index."
-	insinto /usr/share/doc/${PF}/html/doc
-	doins doc/* || die "Failed to install HTML documentation."
-
-	insinto /usr/share/${PN}/fonts
-	doins fonts/* || die "Fonts installation failed."
-}
diff --git a/sci-biology/primer3/ChangeLog b/sci-biology/primer3/ChangeLog
index d7cc94649d25..8026b370090d 100644
--- a/sci-biology/primer3/ChangeLog
+++ b/sci-biology/primer3/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/primer3
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.45 2015/04/21 19:22:54 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.46 2015/04/22 06:51:36 jlec Exp $
+
+  22 Apr 2015; Justin Lecher <jlec@gentoo.org> -primer3-2.3.1.ebuild:
+  Drop old
 
   21 Apr 2015; Pacho Ramos <pacho@gentoo.org> primer3-2.3.5.ebuild:
   ppc stable wrt bug #544908
diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
index 71704cf1b03c..6258ff5fc530 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -1,20 +1,30 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX primer3-1.1.4-ldflags.patch 882 SHA256 10ef0f1491df83c60f5919fcc461a0864e12a0303d8242f4e3ea1c2f8963c436 SHA512 8e9d48b8c504db96a3e632189527e4bab54765686d153560d415c2ef0d7bc5f8d0e6ba350fd571b6d1c3386ef745be108f866b52ceebab0f0412155bf079a306 WHIRLPOOL b6fb36622c44d078052e9a09f4389d6e6cdb63d1a7bd45dc6b016767b369954a8040c6ac01bb8131520034863edc9ac246b94fd64265118890224e7dc73227f6
 AUX primer3-2.3.4-buildsystem.patch 5460 SHA256 13fa4df0026faa97b574e3de3a99183e66ab18eec883db92e9f234acafe8b3b8 SHA512 52f539f52c92e5e21c3166da62813c6fa9f90fd9e0ca87d9ab67658496e13f4b5ce5c53770802cb1cdd21044244e21f09b0de2ce3c6d3db0182b3d9cbf64a037 WHIRLPOOL f09d952479f929d5e17abc3bb3a0313eae9d5811c3da14beb4d7111d17035f4077798b13f7b047ba7decd2b841c731373fb477f71a9b82f64906bbacf0118e2a
-DIST primer3-2.3.1.tar.gz 2539917 SHA256 34a27e5c442e41fca1202be4fbe90f97c791fa93e2235e28b625574ccf90c137 SHA512 ff035fc1bc96ff4ce1fa29d867f01fc2df62e3bcff23de62c753cef3a92a7209ef8fda27dc19cdf0173aa98c5b2fa36ad0b58cca9a7d225be26f3ebc970b08f8 WHIRLPOOL c2801ea96733729121a70ef77a710d1e0668ecdc5243ef70b4073930b421b708bf771805eec8d26d39af12f1d5b57dbbaf0384d565e887d26b916149dd5e23d2
 DIST primer3-2.3.5.tar.gz 1655871 SHA256 e0c06a36dc384f656835a8d5ecb4b5069493b7dd98775b38a233863ab591c54b SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec WHIRLPOOL 321069f568fad409b31f2fd4caa36f1128523383f5b294dffc68d57a67489ee2ac17d53bedd8e36df9b688c43c06c91f47bdaf81b4fda6597d916ea06643e666
 DIST primer3-src-2.3.6.tar.gz 1667573 SHA256 2ff54faf957f0d7e4c79d9536fa1027b028bc5e4c6005f142df42ef85562ecd4 SHA512 671b420f3bc9b6b9972e19a757925ada170e5f8c0e3e8a90630a48e6cde44abc0e1e09b9ea90129f94b58f835e30440f3d91c14fb4b796fd94eb478b2ca28ead WHIRLPOOL 61bbc676c38b1b96806c9ac54d130aae936a5406213759613a3be76016cdd4ebf76c5a54d1ceffc7bd2634829d9aef9d64f87cc85289793b40ab031e01a5917f
-EBUILD primer3-2.3.1.ebuild 1141 SHA256 2ac353686324059aeded1d82531c6a8c5326117457f0ce1c6712ec0961bd2a45 SHA512 53775cb6d4e11ebff12f29d4c4f46fc8872a270a1557f7a7d6ac0ef58ca18329dd77c0ea92ca504a47ef4997dce38ad9818a7840adc5f02fb0c4284be0c938c4 WHIRLPOOL ce1e8eacf50116a12440c8c458aaaf40ad02fbcbbdea6477e2c7f53023c342782aa59aa8929566b41345262919a59f33ed7712dd11cbef4b632228a8e66f65d3
 EBUILD primer3-2.3.5.ebuild 1143 SHA256 18411b87193a04d66405f1f92cbde3ff5cc71e293d2ca8ab071a7c44fa735b28 SHA512 3e46e924eaae11833a8701631b23d4a38c725ee4ab4d3e24ec0035b3b2274b6d3d6743fd61941df9edbe67650f8b9fcc360c0efc750cf949e3379ddb9f5d62e4 WHIRLPOOL a84e004777283d80847e3a804da5d33d991bcc8e7ecefbb648e34148f39e82616b9aa5ccfde143b26b89791f2e0345a849685b97c1539540899a5843a4690e13
 EBUILD primer3-2.3.6.ebuild 1156 SHA256 6057281bd575e8d0b746b61d6da06416efe85c81c56fcabb4f9803d7aeb0f936 SHA512 2f5780aa6830a67b3cd07e4fac2026bcd1f612d25940607af73c4ef652e521dbdb3417f84192511629fd322054432b86c0b1dc434964e1bd09529d61f1e66bce WHIRLPOOL 8b9d0689209391c0ec0b888f068f6eb3b3325c4ef40786f51b3f8e4bf62d1b83348516a869b5d70cac11f76fb60b43a0153e88ccb971efebdef1cf30f0abaffd
-MISC ChangeLog 6475 SHA256 30c4a20eda7ac1e508598ad19acf66a359c74597015c91f41a528ec0d16d6e5f SHA512 3979cd7fe839f88f83f48447c35ce1c55c8ba21b6aaf3ca4fb56c2f74feab310643d486c06ebf3dc21ed536229d6a050358b2593f9de8e04fbd5292c64368873 WHIRLPOOL cb26b852191e4c2db60feac1b3b4571ef2864cea0c9270aeea6f8143ec22fcdc7f0fb2f1bc22e4c558c559a0cff97e3821d8eb81c227a656486b79d1ba67983f
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 MISC metadata.xml 626 SHA256 7f92fdb9d901cce63f02bce075366ea0fcd34c54809c6cff6a5074671e528c97 SHA512 cd1df947da6ce9bfc424658af5149a431f9f049938d74b0ff83e5fe585829006dc4c4707833e7b4308242fed6e92b3c83263754aadadb2e22c76cf964c32fc25 WHIRLPOOL 5a8f088e9fb2a29b73cc6ad8da1808314f38f04e611b96a76de1054c290fbb662177b757c8a198885fa03c0f881376cebe95906606279193d2852f443176ef04
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+Version: GnuPG v2.1
 
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diff --git a/sci-biology/primer3/primer3-2.3.1.ebuild b/sci-biology/primer3/primer3-2.3.1.ebuild
deleted file mode 100644
index 8a1c48412963..000000000000
--- a/sci-biology/primer3/primer3-2.3.1.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.3.1.ebuild,v 1.5 2012/12/16 19:51:49 ago Exp $
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Primer Design for PCR reactions"
-HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-IUSE=""
-KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-
-DEPEND="dev-lang/perl"
-RDEPEND=""
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
-
-	if [[ ${CHOST} == *-darwin* ]]; then
-		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
-	fi
-
-	tc-export CC CXX AR RANLIB
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_test () {
-	emake -C test | tee "${T}"/test.log
-	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
-}
-
-src_install () {
-	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
-	dodoc src/release_notes.txt example
-	insinto /opt/primer3_config
-	doins -r src/primer3_config/* primer3*settings.txt
-	dohtml primer3_manual.htm
-}