sci-biology/readseq: Drop old; Resolve file collision sci-biology/meme, #455010

Package-Manager: portage-2.2.0_alpha161/cvs/Linux x86_64
RepoMan-Options: --force
Manifest-Sign-Key: 0x70EB7916

6 files changed, 29 insertions, 84 deletions

diff --git a/sci-biology/readseq/ChangeLog b/sci-biology/readseq/ChangeLog
index 5489094e21cf..748097ff38db 100644
--- a/sci-biology/readseq/ChangeLog
+++ b/sci-biology/readseq/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/readseq
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/ChangeLog,v 1.9 2010/11/28 08:56:48 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/ChangeLog,v 1.10 2013/02/01 14:55:17 jlec Exp $
+
+  01 Feb 2013; Justin Lecher <jlec@gentoo.org> -readseq-19930201.ebuild,
+  -readseq-19930201-r1.ebuild, readseq-20080420.ebuild, metadata.xml:
+  Drop old; Resolve file collision sci-biology/meme, #455010
 
 *readseq-19930201-r1 (28 Nov 2010)
 
diff --git a/sci-biology/readseq/Manifest b/sci-biology/readseq/Manifest
index e51487ab7052..c7a8a8af50e5 100644
--- a/sci-biology/readseq/Manifest
+++ b/sci-biology/readseq/Manifest
@@ -1,21 +1,18 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
-AUX 19930201-buffer.patch 466 RMD160 f6da8828e1f0264a87ae903915fceac73106f4db SHA1 cda57f64825c8b6cabae691cce59f2e65268c856 SHA256 6718b321adbc3dfab471506b01acd7d0f6d4f0df77a258974333063cc2fbec18
-AUX 19930201-getline.patch 7833 RMD160 035e913771aca386868162ed809d97e544d9e75e SHA1 aef69225768b6f4ea08249fe06352f85cf3c9195 SHA256 bc68cd66bf6ff41d00007600b07e6cafddc826db24cd31b896fad2ac17882d76
-AUX 19930201-impl-dec.patch 511 RMD160 6c0d2d0cfacc62abf0feeaa4c915927b7853b06e SHA1 f74667ec4e1178a5dab49feb560dc764bb5060b9 SHA256 c7d14b22de4c905b382d897777a2615518c8d386d78636a9151b88e8e49e3f89
-AUX 19930201-ldflags.patch 377 RMD160 af148b3061679ff3bd86d35d52fd739f8381d7c1 SHA1 7b53fb8142947fc984702272313ef5d933229ff3 SHA256 ac36fb1c7771f0bfb790cfe6f835b790d2c318c8459d8989734ec218bfcb1e6f
-DIST readseq-source-20080420.zip 627341 RMD160 7931de08b53548908de3caee835e5a2e3398fe3b SHA1 89e250de9270f2d89f2064b08a23a165f5edec05 SHA256 d91ccadcbf5fde29525c639ece6ae132e0db863a7e63f96f69647e591617e8dd
-DIST readseq_1.orig.tar.gz 54557 RMD160 eb9f08df46f4cb439a22657c1ddb724f9b4a5e3d SHA1 474839186eec28f650ac89a33829673fa40c3bbb SHA256 b704d7a12c5d834390f3ed4233f1409c5f1ed53b0b9accf5ab632a513de1183c
-EBUILD readseq-19930201-r1.ebuild 892 RMD160 16d75b210a81269cc14ad37bfe1165f13b85c4df SHA1 9647228b38b5dea94e68b9718746c4286c731e1a SHA256 f66bab9363a1429f8d3c08da1c1dd5655cd55cfb754f2ddb8663de2b737e982e
-EBUILD readseq-19930201.ebuild 638 RMD160 cac475202534c8c8616043ba8da31e19321812b4 SHA1 3e947d605d38e97ea080bfbcc733150e4d5e4299 SHA256 367ad4fb3a0e0cb362304b4bb76177c3404a889f406c544018dcd06406560889
-EBUILD readseq-20080420.ebuild 1277 RMD160 bf50fc7068b0b100d7db8f2ac57793fefdabb4b6 SHA1 bf36fc9f3acc8fd60eb024120d0ca8ae81bebfdd SHA256 6e728f03248b8bd1d5005e5acd3d9283be5f4016ccefb2f17a5bdca0d606e958
-MISC ChangeLog 2062 RMD160 8913bad5cbec666eb04a2c9259ee5b2914ee5246 SHA1 08b9047c3245f391468c0eecb78888d52be945c4 SHA256 2de6be07a686136eecf4f0f7c0f963df2c54a0461d457dc6d082e715035546f7
-MISC metadata.xml 311 RMD160 ca3cec6e7b54692719d494eba780fe3684214f80 SHA1 cdc99cda84616c5cd1dcabb52b02caf706eb1600 SHA256 d6083238a62c4053d7a86fa23a7bb537dd34e0c5f43d05f258b0e5ff92fa6137
+AUX 19930201-buffer.patch 466 SHA256 6718b321adbc3dfab471506b01acd7d0f6d4f0df77a258974333063cc2fbec18 SHA512 182b7db71e272976417d0394a0eefde9dd944bb0ee629dc5da30fba6f4d2a09f4cb54f6316c9caf5b560a7b951df4dfadff42f7f1b518a36db11bd8da7aececb WHIRLPOOL e232c19b9bf8d801fc8421ac380ef1aedfeea812b88cb7bfe5cc506ec3f422eca4b1fed5b1f42005057db7e206802ec0d2f36d80018e130b50be959b8af08b60
+AUX 19930201-getline.patch 7833 SHA256 bc68cd66bf6ff41d00007600b07e6cafddc826db24cd31b896fad2ac17882d76 SHA512 e2a3cdc17b7a78069a5e40b7305cfc52df2ae3c1fc621be8ef525ddfdb32a405b54c481663597e945a2306277f90928b9dfce66f6ec2e777bf04f91a1b4c9b90 WHIRLPOOL e3f2521978bb59cec8635975145c2c49ff387cbbb825918d06fc8db1da01b8e8795bf3555b2ff7847e17acafdfc7cbdbd8cb21f0cae3695595cce0dba26ee5b8
+AUX 19930201-impl-dec.patch 511 SHA256 c7d14b22de4c905b382d897777a2615518c8d386d78636a9151b88e8e49e3f89 SHA512 1f7394f79edc2b357a1b2fceb2bd65631701e9d1d5832de3d6e79dc5d09e865c254466834ca522e4e5696716482e35ef546c026b9f35a4be5c96edcb5515e1f9 WHIRLPOOL 33066b3f1cfe15346068df13fa15568207d174f8f625c4983a5fd6904d019f1c5ec2355f81e4e017e8ab957f5c3336fdcd876c07025a9d63e4755fe944502bb4
+AUX 19930201-ldflags.patch 377 SHA256 ac36fb1c7771f0bfb790cfe6f835b790d2c318c8459d8989734ec218bfcb1e6f SHA512 63735fe67d9392a0f25d6656ce38f34c2cdbaece341bb9fdf76bc74c2b022ed71a5419348f41248fa2037379a051dd9b92ee39c6ea980979548113960a6ba0a5 WHIRLPOOL 6bc2d0e04b796a2d145b468ef226dddd58a7e881182b83ad6bef6f2474cbe4fac729d54c987ce0f79a8a4c0b364374f1e5f17c1de9f76738b0fdb86b35d32742
+DIST readseq-source-20080420.zip 627341 SHA256 d91ccadcbf5fde29525c639ece6ae132e0db863a7e63f96f69647e591617e8dd
+EBUILD readseq-20080420.ebuild 1304 SHA256 c52d54b4cf275ddfba42c7a4434374d8cfe0ac09b946f8432d2d04464e4b2360 SHA512 2ad6e6954737cd7949f95dab372f27868ba6651d0cf0cb1e1889c6bad0f8526a97b9cebe14e1535a1738c6c4af22f3d7693c7464ca83ba7f895361b0d935f0ec WHIRLPOOL 722c92cb8d20ab2d209b3d737bd0512a30684d61258d173b77cfda807ab42a025401bbb18e88f0fbe1d8b0941df9c1f7e6a6d834864c7afa6350be99b69a6676
+MISC ChangeLog 2268 SHA256 f9c1fef20cd37646055bacae2adaa725cff90a22f371a3526c1db7fb948f5162 SHA512 f248b550e4bbf13a53f1395ccf38e986888b08b8b8f769f22e14b0271e6dd75bc237621ed83434ff9baefabadb8b5bd52a23efd95193d90d1afed7b1f8cfbd40 WHIRLPOOL 528b3bd505228331385e78c42b2b104cf35eea18a6b2a2a3deeefc0def8316bcf8c30babd96deab829a0ee96fcc96922d81528359c7eab738b3772e31d84d7c3
+MISC metadata.xml 313 SHA256 3759536b8696911de250a9c55de7f8e0eb6cffd0517de838f0a571a07d7cc8dc SHA512 d831f8104bf7985944abe20b56f222ae1a4910f13f4e4e749c34073e1998f3157ab0432b9620a6fa87b9dd101af4ca7048623593134047e89cd5b75dd8b9aa6b WHIRLPOOL 0cf0092564e381a0d91ec9e6d403f4b5592334c8885a6071bcb0c81b520491f8d25aea2a49d8923dc1838f71f711db9c5acf57664c0024de6a63da4887678cbd
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.19 (GNU/Linux)
 
-iEYEARECAAYFAkzyGVUACgkQgAnW8HDreRYWmwCglC6OBPnrw4/gk8njy5/oZHPr
-mz0AoIqWJtRr6YJsEId9MftTriH2wJeS
-=cL5F
+iEYEAREIAAYFAlEL11YACgkQgAnW8HDreRZ5LwCbBV0kJeCQVxEtBiSjaaHJcrR+
+Rl8AnA9Qh7W8mrw4djFo9Lbhi4509Myi
+=RHyV
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/readseq/metadata.xml b/sci-biology/readseq/metadata.xml
index 829014583306..b198f044f3f5 100644
--- a/sci-biology/readseq/metadata.xml
+++ b/sci-biology/readseq/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<longdescription>
+  <herd>sci-biology</herd>
+  <longdescription>
 		Reads and writes nucleic/protein sequences in various formats. Data
 		files may have multiple sequences.
 	</longdescription>
diff --git a/sci-biology/readseq/readseq-19930201-r1.ebuild b/sci-biology/readseq/readseq-19930201-r1.ebuild
deleted file mode 100644
index 89add3a9535b..000000000000
--- a/sci-biology/readseq/readseq-19930201-r1.ebuild
+++ /dev/null
@@ -1,37 +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/readseq/readseq-19930201-r1.ebuild,v 1.1 2010/11/28 08:56:48 jlec Exp $
-
-EAPI="3"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Reads and writes nucleic/protein sequences in various formats."
-SRC_URI="mirror://debian/pool/main/r/readseq/readseq_1.orig.tar.gz"
-HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
-LICENSE="public-domain"
-
-KEYWORDS="~amd64 ~sparc ~x86"
-SLOT="0"
-IUSE=""
-
-S="${WORKDIR}/readseq-1"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-getline.patch \
-		"${FILESDIR}"/${PV}-buffer.patch \
-		"${FILESDIR}"/${PV}-impl-dec.patch \
-		"${FILESDIR}"/${PV}-ldflags.patch
-}
-
-src_compile() {
-	emake -e \
-		CC=$(tc-getCC) \
-		build || die
-}
-
-src_install() {
-	dobin readseq || die
-	dodoc Readme Readseq.help || die
-}
diff --git a/sci-biology/readseq/readseq-19930201.ebuild b/sci-biology/readseq/readseq-19930201.ebuild
deleted file mode 100644
index 45251beb271b..000000000000
--- a/sci-biology/readseq/readseq-19930201.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/readseq-19930201.ebuild,v 1.4 2006/08/17 22:20:51 weeve Exp $
-
-DESCRIPTION="Reads and writes nucleic/protein sequences in various formats."
-SRC_URI="mirror://debian/pool/main/r/readseq/readseq_1.orig.tar.gz"
-HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
-LICENSE="public-domain"
-
-KEYWORDS="~amd64 ~sparc x86"
-SLOT="0"
-IUSE=""
-
-S="${WORKDIR}/readseq-1"
-
-src_compile() {
-	make -e || die
-}
-
-src_install() {
-	dobin readseq || die
-	dodoc Readme Readseq.help || die
-}
diff --git a/sci-biology/readseq/readseq-20080420.ebuild b/sci-biology/readseq/readseq-20080420.ebuild
index d91ec3bd4521..173fc172da18 100644
--- a/sci-biology/readseq/readseq-20080420.ebuild
+++ b/sci-biology/readseq/readseq-20080420.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/readseq-20080420.ebuild,v 1.3 2008/07/16 17:00:20 armin76 Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/readseq-20080420.ebuild,v 1.4 2013/02/01 14:55:17 jlec Exp $
 
 EAPI=1
 
@@ -14,13 +14,17 @@ HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
 # Renamed to the date of the modification and mirrored
 SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip"
 #SRC_URI="mirror://gentoo/${MY_P}.zip"
+
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
-COMMON="dev-java/xerces:2
-	dev-java/jaxp"
+
+COMMON="
+	dev-java/jaxp
+	dev-java/xerces:2"
 RDEPEND="${COMMON}
+	!=sci-biology/meme-4.8.1
 	>=virtual/jre-1.4"
 DEPEND="${COMMON}
 	>=virtual/jdk-1.4