Pruned old version

Package-Manager: portage-2.1.1-r2

9 files changed, 16 insertions, 215 deletions

diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest
index ff445ddaa74c..766ef78b08f0 100644
--- a/sci-biology/aaindex/Manifest
+++ b/sci-biology/aaindex/Manifest
@@ -1,24 +1,16 @@
-DIST aaindex-7.0.tar.bz2 94056 RMD160 a28430d2c78f131fe452e7b4b3c24431aa6a2de9 SHA1 4beee97bfae674394d05b733568d18a4c88252db SHA256 fd65b1d3e82019e8fe9f5c8774aa10b6ecb1e0a094bd54ad8547c99b4b6ed4a6
 DIST aaindex-9.1.tar.bz2 133780 RMD160 6f5bd699de3c84bd366f9747f57712ba8aecf513 SHA1 7215e3dae85cd61919854ba5dd5abff29be91852 SHA256 ae2e5aec2fc47835f26c8d8b5776966464bc08a5fca422c130d8312880382caa
-EBUILD aaindex-7.0.ebuild 1123 RMD160 85b48ff877b75c065feece116e5c479ce4dfc9a5 SHA1 046b2a4b0731d9a2cbd89f4ac4392010dcd1bcc2 SHA256 6b9391cc92d397ced07ab5c09c458b8e7261902a84c222b28239b8e1aaee087c
-MD5 539a262f797cb8a14f7e70657abd0c1e aaindex-7.0.ebuild 1123
-RMD160 85b48ff877b75c065feece116e5c479ce4dfc9a5 aaindex-7.0.ebuild 1123
-SHA256 6b9391cc92d397ced07ab5c09c458b8e7261902a84c222b28239b8e1aaee087c aaindex-7.0.ebuild 1123
 EBUILD aaindex-9.1.ebuild 1165 RMD160 b2ccf34b9a5782992d2e250a7c8d452b61e9813b SHA1 b99d748b7d4ec67809f33b46ca548199fd536281 SHA256 663cb10214f3681665a66c5e4c942031508c2a79557cbac013773bcbfda3822d
 MD5 8dd03fe95e5c9045bf229e9750adc0af aaindex-9.1.ebuild 1165
 RMD160 b2ccf34b9a5782992d2e250a7c8d452b61e9813b aaindex-9.1.ebuild 1165
 SHA256 663cb10214f3681665a66c5e4c942031508c2a79557cbac013773bcbfda3822d aaindex-9.1.ebuild 1165
-MISC ChangeLog 2936 RMD160 44941979c2c04a4ea72810fa4421f6926f3ec18c SHA1 8b6e6c8979d7fcd0f2851f8df3046a6790fa42df SHA256 dda27db02b0642ca2fdfbd897b64b75d3d12ff4ece77b706dc2a5289cb32d205
-MD5 0f12cac39c52bf264f6448f2016a387f ChangeLog 2936
-RMD160 44941979c2c04a4ea72810fa4421f6926f3ec18c ChangeLog 2936
-SHA256 dda27db02b0642ca2fdfbd897b64b75d3d12ff4ece77b706dc2a5289cb32d205 ChangeLog 2936
+MISC ChangeLog 3036 RMD160 5f82268ae4694568690c06640358c8decf93dc0d SHA1 768f475d6f5955b2ca4794ef0271071515c44269 SHA256 b0845e6925e6bd15197a57420d5dff92825919302148b5d186e1332d03735504
+MD5 a7e597720e3063d01ed74f7417360dd8 ChangeLog 3036
+RMD160 5f82268ae4694568690c06640358c8decf93dc0d ChangeLog 3036
+SHA256 b0845e6925e6bd15197a57420d5dff92825919302148b5d186e1332d03735504 ChangeLog 3036
 MISC metadata.xml 1318 RMD160 06733e015e5bea1426d341a5510982f4692da97c SHA1 14d3ef2a711c44b92d0801e1f5ce429e59fbfbf0 SHA256 7ae3adabe021a43e4abedd68d24352718b3d0eca66433d96c700ecfffc091207
 MD5 7b4367ee8d5bb22caff546e4ae7d99c4 metadata.xml 1318
 RMD160 06733e015e5bea1426d341a5510982f4692da97c metadata.xml 1318
 SHA256 7ae3adabe021a43e4abedd68d24352718b3d0eca66433d96c700ecfffc091207 metadata.xml 1318
-MD5 5567d71fb061ca890bd86d0b2efdcc9b files/digest-aaindex-7.0 235
-RMD160 d8ca45eea924b11e56d19223b44e5dbebc1c3ad5 files/digest-aaindex-7.0 235
-SHA256 c787122bcba639feed57d16ab0c5352752b30bfd155b07e1450c3905ca08dcfa files/digest-aaindex-7.0 235
 MD5 7b841c73bc8f99650a8ba6fab51739cb files/digest-aaindex-9.1 238
 RMD160 cd4dd9a4a88c102c672c93a6200b3e2fb2340c62 files/digest-aaindex-9.1 238
 SHA256 ae955fc9a9a798abf186eee38e8e3b8d0122a02ea0ce46efa7786246e526e82d files/digest-aaindex-9.1 238
diff --git a/sci-biology/aaindex/aaindex-7.0.ebuild b/sci-biology/aaindex/aaindex-7.0.ebuild
deleted file mode 100644
index 929310ccd0cc..000000000000
--- a/sci-biology/aaindex/aaindex-7.0.ebuild
+++ /dev/null
@@ -1,39 +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/aaindex/aaindex-7.0.ebuild,v 1.8 2006/11/02 20:16:36 grobian Exp $
-
-DESCRIPTION="Amino acid indices and similarity matrices"
-LICENSE="public-domain"
-HOMEPAGE="http://www.genome.ad.jp/aaindex"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-SLOT="0"
-# Minimal build keeps only the indexed files (if applicable) and the
-# documentation. The non-indexed database is not installed.
-IUSE="emboss minimal"
-KEYWORDS="amd64 ppc ppc64 ~sparc x86"
-
-DEPEND="emboss? ( sci-biology/emboss )"
-
-src_compile() {
-	if use emboss; then
-		mkdir AAINDEX
-		echo
-		einfo "Indexing AAindex for usage with EMBOSS."
-		EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die \
-			"Indexing AAindex failed."
-		echo
-	fi
-}
-
-src_install() {
-	if ! use minimal; then
-		insinto /usr/share/${PN}
-		doins ${PN}{1,2} || die "Failed to install raw database."
-	fi
-	dodoc ${PN}.doc
-	if use emboss; then
-		insinto /usr/share/EMBOSS/data/AAINDEX
-		doins AAINDEX/* || die "Failed to install EMBOSS data files."
-	fi
-}
diff --git a/sci-biology/aaindex/files/digest-aaindex-7.0 b/sci-biology/aaindex/files/digest-aaindex-7.0
deleted file mode 100644
index ef1293bc3d29..000000000000
--- a/sci-biology/aaindex/files/digest-aaindex-7.0
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 5ab27d95b2a4f3756c539333c18ebd54 aaindex-7.0.tar.bz2 94056
-RMD160 a28430d2c78f131fe452e7b4b3c24431aa6a2de9 aaindex-7.0.tar.bz2 94056
-SHA256 fd65b1d3e82019e8fe9f5c8774aa10b6ecb1e0a094bd54ad8547c99b4b6ed4a6 aaindex-7.0.tar.bz2 94056
diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
index 8c68903a58fc..e13fecf83d3f 100644
--- a/sci-biology/cutg/Manifest
+++ b/sci-biology/cutg/Manifest
@@ -1,24 +1,16 @@
-DIST CUTG.150.tar.gz 158138458 RMD160 84ab5640dfdf3a9a6f3e0aeb90fa5c29f4c41eea SHA1 52e25ef85ec0482403728677582668b7ef1e0e2b SHA256 76c32ab56d71002e3054baeb2910b2e37fd6e906d6285646a277abb18394065c
 DIST CUTG.151.tar.gz 165813396 RMD160 77a304321f1535af8bb6eff1ce5c8e559a64535c SHA1 0327ccf522d9e38ab6e261bb0e2077533bf1892b SHA256 8184ac1a99ba54791d4ca672d514daeafd7e6736e76524fbbd7b3930d7d8534f
-EBUILD cutg-150.ebuild 1290 RMD160 1c1e7e0b96a6b6c715b2606cba821b8942d7126c SHA1 6e2d25aab15604cd61ede703acffde0932609df7 SHA256 7f5e677e75be2934ef759113c614d39a4af9153f010f0f620131c06908d2deb7
-MD5 cb31be93a8b2d2affdb9c765938fd404 cutg-150.ebuild 1290
-RMD160 1c1e7e0b96a6b6c715b2606cba821b8942d7126c cutg-150.ebuild 1290
-SHA256 7f5e677e75be2934ef759113c614d39a4af9153f010f0f620131c06908d2deb7 cutg-150.ebuild 1290
 EBUILD cutg-151.ebuild 1295 RMD160 d9f1f0fd111e6b581264b5ef9b49b65ad59f03e3 SHA1 9345c9c39d8e7cf4e7560edbd826a8c5e4005249 SHA256 721a8799721e2a6d223403b7b1932add2755a171d71fa2ebe3fa4a654ecfffb1
 MD5 4cd23123d14e14308e5f911722ddc7f9 cutg-151.ebuild 1295
 RMD160 d9f1f0fd111e6b581264b5ef9b49b65ad59f03e3 cutg-151.ebuild 1295
 SHA256 721a8799721e2a6d223403b7b1932add2755a171d71fa2ebe3fa4a654ecfffb1 cutg-151.ebuild 1295
-MISC ChangeLog 6106 RMD160 de0562cf8dbf3fe20c2b82cab8d89581d70ec407 SHA1 55a34b33c3e54b36ff5e74c5df7f5feac651bc12 SHA256 b04e10b83513bc66e772e68a555a9888cfa318a152a7c3631be091a1049110e5
-MD5 9f2751842e43eb99ec747b10d7296605 ChangeLog 6106
-RMD160 de0562cf8dbf3fe20c2b82cab8d89581d70ec407 ChangeLog 6106
-SHA256 b04e10b83513bc66e772e68a555a9888cfa318a152a7c3631be091a1049110e5 ChangeLog 6106
+MISC ChangeLog 6203 RMD160 498f7fbacfe10913831c78fc3c3203fc77caf0b3 SHA1 68fa5861fa0c21b4557e4285a55a94426b6813fa SHA256 59ddf602e094011d872a718554844de36ce9ac881a4f31f7cb951f249c12ac88
+MD5 b108ac091f4171da827c92c706ff82e2 ChangeLog 6203
+RMD160 498f7fbacfe10913831c78fc3c3203fc77caf0b3 ChangeLog 6203
+SHA256 59ddf602e094011d872a718554844de36ce9ac881a4f31f7cb951f249c12ac88 ChangeLog 6203
 MISC metadata.xml 602 RMD160 0bfaf291f7a1ef2d7c7c3c56b307faeb2d73a14a SHA1 029a446c9375b8a243aa2ef848a6d73144495d81 SHA256 99510df8b62ab52d5ad0a72077f01df7e0e9ccaf374a3456e4a39fb9821aa46a
 MD5 35b8093f40dbeaa81ac2e1da6fb9c7a9 metadata.xml 602
 RMD160 0bfaf291f7a1ef2d7c7c3c56b307faeb2d73a14a metadata.xml 602
 SHA256 99510df8b62ab52d5ad0a72077f01df7e0e9ccaf374a3456e4a39fb9821aa46a metadata.xml 602
-MD5 4e8a803d3dbbd682ad72da2f4efdf0d0 files/digest-cutg-150 235
-RMD160 f59d7b8a24257a6c1ee64de8b533c7a85630d40f files/digest-cutg-150 235
-SHA256 52e76d1e2df33192f485b18cf44236637883baeb632633c611eb562005de8d5c files/digest-cutg-150 235
 MD5 f1527b097ae96fc58677ce4c70027768 files/digest-cutg-151 235
 RMD160 1adc6d33c05fb22b56fe0de042ba749972bee9db files/digest-cutg-151 235
 SHA256 0cd36275bb52878eb43a29bbbdce5479de30275ef352bf6c015745dc2f4cd5b8 files/digest-cutg-151 235
diff --git a/sci-biology/cutg/cutg-150.ebuild b/sci-biology/cutg/cutg-150.ebuild
deleted file mode 100644
index 2ef497807873..000000000000
--- a/sci-biology/cutg/cutg-150.ebuild
+++ /dev/null
@@ -1,46 +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/cutg/cutg-150.ebuild,v 1.7 2006/11/02 21:51:19 grobian Exp $
-
-DESCRIPTION="Codon usage tables calculated from GenBank"
-LICENSE="public-domain"
-HOMEPAGE="http://www.kazusa.or.jp/codon/"
-SRC_URI="ftp://ftp.kazusa.or.jp/pub/codon/current/compressed/CUTG.${PV}.tar.gz"
-
-SLOT="0"
-# Minimal build keeps only the indexed files (if applicable) and the
-# documentation. The non-indexed database is not installed.
-IUSE="emboss minimal"
-KEYWORDS="amd64 ppc ppc64 x86"
-
-DEPEND="emboss? ( sci-biology/emboss )"
-
-S="${WORKDIR}"
-
-src_compile() {
-	if use emboss; then
-		mkdir CODONS
-		echo
-		einfo "Indexing CUTG for usage with EMBOSS."
-		EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \
-			"Indexing CUTG failed."
-		echo
-	fi
-}
-
-src_install() {
-	if ! use minimal; then
-		mkdir -p "${D}"usr/share/${PN}
-		mv *.codon *.spsum "${D}"/usr/share/${PN} || die \
-			"Installing raw CUTG database failed."
-	fi
-	dodoc README
-	if use emboss; then
-		mkdir -p "${D}"/usr/share/EMBOSS/data/CODONS
-		cd CODONS
-		for file in *; do
-			mv ${file} "${D}"/usr/share/EMBOSS/data/CODONS || die \
-				"Installing the EMBOSS-indexed database failed."
-		done
-	fi
-}
diff --git a/sci-biology/cutg/files/digest-cutg-150 b/sci-biology/cutg/files/digest-cutg-150
deleted file mode 100644
index 38a4f012cc1a..000000000000
--- a/sci-biology/cutg/files/digest-cutg-150
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 ceef4467329b766f66039c93484c741c CUTG.150.tar.gz 158138458
-RMD160 84ab5640dfdf3a9a6f3e0aeb90fa5c29f4c41eea CUTG.150.tar.gz 158138458
-SHA256 76c32ab56d71002e3054baeb2910b2e37fd6e906d6285646a277abb18394065c CUTG.150.tar.gz 158138458
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index e6337d2ff91d..264f97ac4eae 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -6,27 +6,19 @@ AUX README.Gentoo 1326 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 SHA1 8cf1
 MD5 615888722f8d6a0c918f936e0cc1cfcd files/README.Gentoo 1326
 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 files/README.Gentoo 1326
 SHA256 33b517b977cc85824847bd6cf4113489a5554fb014f1a6b1d22d6f80c3487e9f files/README.Gentoo 1326
-DIST EMBOSS-3.0.0.tar.gz 16257908 RMD160 4f8a2b0c05f2d77bec27bd3b1886d253b55b1c40 SHA1 5ed529c3a8066e95fe4044d324991a876d906cca SHA256 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
 DIST EMBOSS-4.0.0.tar.gz 17651607 RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 SHA1 784c729f2d2e746339a90048277c9e4f052e036a SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231
-EBUILD emboss-3.0.0-r1.ebuild 2956 RMD160 eaef19d1dda88d7c0843b176fd39937d6b149dac SHA1 c095793682f8e60ab8acea6b421a6913e77542d2 SHA256 2c4c75fba37c145dc6b0ffbc76e0fe9d75670c8b88ab31b5e757780550ed5a83
-MD5 9ec2af538dd9f88c227529490cc7d07f emboss-3.0.0-r1.ebuild 2956
-RMD160 eaef19d1dda88d7c0843b176fd39937d6b149dac emboss-3.0.0-r1.ebuild 2956
-SHA256 2c4c75fba37c145dc6b0ffbc76e0fe9d75670c8b88ab31b5e757780550ed5a83 emboss-3.0.0-r1.ebuild 2956
-EBUILD emboss-4.0.0.ebuild 3046 RMD160 580d0a1580dd3d964f23ee83d189b73e561cdf93 SHA1 d3a1634ff8aed1dba66ce4157562736a23e76212 SHA256 1446c7afa33abc80842cf45381d3015716671dc9baf9b42fd91d07aa061e8b0e
-MD5 ee670b83790c622f50c9483a5f4a3017 emboss-4.0.0.ebuild 3046
-RMD160 580d0a1580dd3d964f23ee83d189b73e561cdf93 emboss-4.0.0.ebuild 3046
-SHA256 1446c7afa33abc80842cf45381d3015716671dc9baf9b42fd91d07aa061e8b0e emboss-4.0.0.ebuild 3046
-MISC ChangeLog 7285 RMD160 128ef44e190d3cd84d210013d2409af53001696f SHA1 5abf661a71fadc0ef56eb7d54d29d9cc3794a852 SHA256 a1b66f182f827980bca943c6ad35f280d9487003d09b031582948e60b640cc15
-MD5 e2e5b98539b696ec7a0c33204b573d33 ChangeLog 7285
-RMD160 128ef44e190d3cd84d210013d2409af53001696f ChangeLog 7285
-SHA256 a1b66f182f827980bca943c6ad35f280d9487003d09b031582948e60b640cc15 ChangeLog 7285
+EBUILD emboss-4.0.0.ebuild 3038 RMD160 0d4477134db67b8ed9edf180d81a8ad545643e5b SHA1 4eae18942dad62860e692dae9b8fb0d6869b2229 SHA256 cc610e2b746878e9452b2293bade9739b26cb6bceb50336671c059c3ba623aa2
+MD5 8ba3872c6752008ee96188053b2d7a49 emboss-4.0.0.ebuild 3038
+RMD160 0d4477134db67b8ed9edf180d81a8ad545643e5b emboss-4.0.0.ebuild 3038
+SHA256 cc610e2b746878e9452b2293bade9739b26cb6bceb50336671c059c3ba623aa2 emboss-4.0.0.ebuild 3038
+MISC ChangeLog 7522 RMD160 9918a042adf79e1b0f4fd9d329971542e18a3bc7 SHA1 51f606216c110d8bcf1ba4f93e7b56610e397144 SHA256 22c025294fb2fed7801a4b0a599fbc027e5d739b3d496f509ab23ce8aa4533c5
+MD5 eee5be80ffd518e7dcf83734ba929260 ChangeLog 7522
+RMD160 9918a042adf79e1b0f4fd9d329971542e18a3bc7 ChangeLog 7522
+SHA256 22c025294fb2fed7801a4b0a599fbc027e5d739b3d496f509ab23ce8aa4533c5 ChangeLog 7522
 MISC metadata.xml 1021 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 SHA1 eff46db435f88e0b457ce2a38e5ff786ae6324e1 SHA256 0c5af548d0483d41a3344695cb04acaf0974fb56b70bc1e2ec0a9749ecbc45a0
 MD5 ecba11e4d50ee5cc740817f5becffa83 metadata.xml 1021
 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 metadata.xml 1021
 SHA256 0c5af548d0483d41a3344695cb04acaf0974fb56b70bc1e2ec0a9749ecbc45a0 metadata.xml 1021
-MD5 ad3e7f9b714ce612677b632c7728f9b9 files/digest-emboss-3.0.0-r1 244
-RMD160 9fa235c91cc4e4a753ad4c7c3fe48c25cd01e43f files/digest-emboss-3.0.0-r1 244
-SHA256 011c076207998316f797d151591daa9ae4afb9494ce7c4d53c6738db025ed35b files/digest-emboss-3.0.0-r1 244
 MD5 868d3a498e023c8ac4cd1ae2504bc8b0 files/digest-emboss-4.0.0 244
 RMD160 9ceca3f11bf27999c9a49c4ae6a438ef8640762f files/digest-emboss-4.0.0 244
 SHA256 4c40525329b260ca9b0ee00d4275b85fd29fc0ea18c51d58dac8534dd19b8179 files/digest-emboss-4.0.0 244
diff --git a/sci-biology/emboss/emboss-3.0.0-r1.ebuild b/sci-biology/emboss/emboss-3.0.0-r1.ebuild
deleted file mode 100644
index d3b05263775d..000000000000
--- a/sci-biology/emboss/emboss-3.0.0-r1.ebuild
+++ /dev/null
@@ -1,81 +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/emboss/emboss-3.0.0-r1.ebuild,v 1.8 2006/11/03 08:40:49 je_fro Exp $
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-HOMEPAGE="http://emboss.sourceforge.net/"
-SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
-LICENSE="GPL-2 LGPL-2"
-
-SLOT="0"
-KEYWORDS="amd64 ppc ppc-macos ppc64 ~sparc x86"
-IUSE="X png minimal"
-
-DEPEND="X? ( || ( x11-libs/libXt virtual/x11 ) )
-	png? (
-		sys-libs/zlib
-		media-libs/libpng
-		>=media-libs/gd-1.8
-	)
-	!minimal? (
-		sci-biology/primer3
-		sci-biology/clustalw
-	)
-	!<dev-util/pscan-20000721-r1"
-
-PDEPEND="!minimal? (
-		sci-biology/aaindex
-		sci-biology/cutg
-		sci-biology/prints
-		>=sci-biology/prosite-19.7
-		>=sci-biology/rebase-601-r1
-		sci-biology/transfac
-	)"
-
-S=${WORKDIR}/EMBOSS-${PV}
-
-src_compile() {
-	EXTRA_CONF="--includedir=${D}/usr/include/emboss"
-	! use X && EXTRA_CONF="${EXTRA_CONF} --without-x"
-	! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver"
-
-	econf ${EXTRA_CONF} || die
-	# Do not install the JEMBOSS component (the --without-java configure option
-	# does not work). JEMBOSS will be available as a separate package.
-	sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' Makefile || die
-	emake || die
-}
-
-src_install() {
-	einstall || die "Failed to install program files."
-	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS "${FILESDIR}"/README.Gentoo \
-		|| die "Failed to install documentation."
-
-	# Install env file for setting libplplot and acd files path.
-	insinto /etc/env.d
-	newins ${FILESDIR}/22emboss-r1 22emboss || \
-		die "Failed to install environment file."
-
-	# Symlink preinstalled docs to /usr/share/doc.
-	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
-	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
-	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
-
-	# Remove useless dummy files from the image.
-	rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \
-		|| die "Failed to remove dummy files."
-
-	# Move the provided codon files to a different directory. This will avoid
-	# user confusion and file collisions on case-insensitive file systems (see
-	# bug #115446). This change is documented in "README.Gentoo".
-	mv "${D}"/usr/share/EMBOSS/data/CODONS \
-		"${D}"/usr/share/EMBOSS/data/CODONS.orig || \
-		die "Failed to move CODON directory."
-
-	# Move the provided restriction enzyme prototypes file to a different name.
-	# This will avoid file collisions with future versions of rebase that will
-	# install their own enzyme prototypes file (see bug #118832).
-	mv "${D}"/usr/share/EMBOSS/data/embossre.equ \
-		"${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \
-		die "Failed to move enzyme equivalence file."
-}
diff --git a/sci-biology/emboss/files/digest-emboss-3.0.0-r1 b/sci-biology/emboss/files/digest-emboss-3.0.0-r1
deleted file mode 100644
index 286e8dad1075..000000000000
--- a/sci-biology/emboss/files/digest-emboss-3.0.0-r1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 fa72feded9ab9272e3e731c09f545dcc EMBOSS-3.0.0.tar.gz 16257908
-RMD160 4f8a2b0c05f2d77bec27bd3b1886d253b55b1c40 EMBOSS-3.0.0.tar.gz 16257908
-SHA256 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea EMBOSS-3.0.0.tar.gz 16257908