gentoo resync : 15.12.2019

5 files changed, 6 insertions, 113 deletions

diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
index cef1367df245..fa6d7469eacc 100644
--- a/sci-biology/psipred/Manifest
+++ b/sci-biology/psipred/Manifest
@@ -1,13 +1,9 @@
 AUX 3.1-Makefile.patch 1103 BLAKE2B ba9c5a7f60d62d66d1cd5a5e9b0a68ffe5c99124d02eae1924ffe92ecb2d24d7224e5bd0b37db3cf17da4f39d3c8b6b53e04466da8976e71910b9dcea9bc59ab SHA512 6e0daf4478b5b992ed1647bf653320b18cd2582ca69ebe761654bd4bd9c9c46b7de183ae84a28582cb5543603362eb7eb6c306ff562c3ec18c292d89480fd127
 AUX 3.1-path.patch 1128 BLAKE2B ea445427fe2ff574028b3d82ae353da5a1dfe3f5c7fade419287f6dc2e819471b4ec007dfee7cf71a1c958082a8dfa83acd5046208e0a7b16c07d90cdd68073f SHA512 e6201669db910f074bb13d1b781416d8d99300f328147cccd7755d5d6595b25aa45353f6da6566f225a067e94ab8ee41ea89bfd75cf2cdf2c076481707acf88c
 AUX 3.2-fgets.patch 427 BLAKE2B dba911ef9d28c230e38d326336fa7adfae31ffafd225d525968f58b1013df2f5812b0c678f37576714c7bfa396c7378b2e1201f8c6b2bea844c2e042eea7c0ec SHA512 a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb
-DIST psipred3.3.tar.gz 1239746 BLAKE2B b1afa9a6a85f239e02b5affec3a6ff48281f962b94b5b6e5c2f4da496a8f73b3d5103a3e77908976a6423eebcfc4e54d2bcb8f7ab012859a115d6f21d580e9d2 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e
 DIST psipred3.4.tar.gz 1102416 BLAKE2B 9797f4181357bb26455253370aca39857c39a2c4bcd521b10a139784e6fd5dc9e14b76c11d99989ac33c3a01fb62807957f9969daa5ac9d928b0b4e83e943743 SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919
 DIST psipred3.5.tar.gz 1101579 BLAKE2B 2fd86841cbc4bb86045b51f8283550832df8356ee88a6ef2c85281b5810debb23ac53652ddc5ffc9bd6f8e9e7248ce39ccee23400ff8fb49cd05b877d730b553 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2
-DIST psipred321.tar.gz 747151 BLAKE2B 8b58a2c45efc92e049622784e1ca39a622ecfb5f660554cf3a26ab9a7e85feb3e453935fca12f0a68328e5e736becdae737f80407730ea9315f4e79b19f71e8b SHA512 b742f5fd3151bd624452bf37761fa66d364ea5b28d9d005ae6ce6f52fc6f2b17df31d6f1e600bd6c57776a1812f22b1eafbca781b430811a010d74f157a75cd1
 DIST tdbdata.tar.gz 40241247 BLAKE2B c85a2fde9b29a14e1da27be1a7ea5fe1704f72b66cd79514dd50a3a0d2d8aab9341f7d5075f6d1896cefa54ca83948387b902b38780181777dc505a9a15b4aab SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c
-EBUILD psipred-3.2.1.ebuild 1077 BLAKE2B 9964a292420cf395be39b1757e591f2ca76f315c2fc6da8876a9339ec4e305815de1722c6eb4ba602242465a7754a2805159065d21417564c9b2e6fbc85bc127 SHA512 9906fa010d56bbc6b8f0967d4153272a400933ceca83c09e361290e6010d663d90d4099ccac85ed327948aca9f4e337ea839ac58dee97f50163768199b3bd7a0
-EBUILD psipred-3.3.ebuild 1174 BLAKE2B 4b0d3baa6fa748306bb32bea9bd397b4b8f1d009bc78253d4182ec66945b385734d1aa88fa561eef44336d9333e4e9c831c805fc677c7f51fc55a980456048dc SHA512 9a79023c9abbfe9b39243aae76192853ee7efde1bcbeb5a554e3014c86fca08e8f668b543e1c2894538dc37a76fea85755cb0edf871cefdc27db7377e216f7a3
-EBUILD psipred-3.4.ebuild 1191 BLAKE2B a9d1be16864e5bf05c73595648cc161ca508a8e8b6582a50aa76aeda971a4fd79daa5081569b7fc93b854afa9e119fa274befac8c32cbcbd331f3b722a717b41 SHA512 181b9c23a3263ca9febe3a78cfe207b65368d670abbc64b3d084584275d7bf56d0f87076b3ff2e7e9c9b5695145f9ad1e4759e62e090ec174477aab5321ff3fc
-EBUILD psipred-3.5.ebuild 1191 BLAKE2B a9d1be16864e5bf05c73595648cc161ca508a8e8b6582a50aa76aeda971a4fd79daa5081569b7fc93b854afa9e119fa274befac8c32cbcbd331f3b722a717b41 SHA512 181b9c23a3263ca9febe3a78cfe207b65368d670abbc64b3d084584275d7bf56d0f87076b3ff2e7e9c9b5695145f9ad1e4759e62e090ec174477aab5321ff3fc
+EBUILD psipred-3.4.ebuild 1215 BLAKE2B da6e40d6c96916d638aec4343a06be76705d0b0b729ab4332613e998539044780b76b94bdde12ebb01059ba1f5763c070dea0d13f2f1d934e1c3db1aaa4d2dab SHA512 8299f0b758e7192418794fcfaae2d81cc6b4f95dc0507b75b5aeac31c60318c9bfd7d0e9a307f23f163887ebe3af986b2c654d19e27bbf7d4111e56e46a1b649
+EBUILD psipred-3.5.ebuild 1215 BLAKE2B da6e40d6c96916d638aec4343a06be76705d0b0b729ab4332613e998539044780b76b94bdde12ebb01059ba1f5763c070dea0d13f2f1d934e1c3db1aaa4d2dab SHA512 8299f0b758e7192418794fcfaae2d81cc6b4f95dc0507b75b5aeac31c60318c9bfd7d0e9a307f23f163887ebe3af986b2c654d19e27bbf7d4111e56e46a1b649
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/psipred/psipred-3.2.1.ebuild b/sci-biology/psipred/psipred-3.2.1.ebuild
deleted file mode 100644
index 1bcb58744638..000000000000
--- a/sci-biology/psipred/psipred-3.2.1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils prefix toolchain-funcs versionator
-
-MY_P="${PN}$(delete_all_version_separators)"
-
-DESCRIPTION="Protein Secondary Structure Prediction"
-HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
-SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz"
-
-LICENSE="psipred"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	sci-biology/ncbi-tools
-	sci-biology/update-blastdb"
-DEPEND=""
-
-S="${WORKDIR}"
-
-src_prepare() {
-	rm -f bin/*
-	epatch \
-		"${FILESDIR}"/3.1-Makefile.patch \
-		"${FILESDIR}"/3.1-path.patch \
-		"${FILESDIR}"/3.2-fgets.patch
-	eprefixify runpsipred*
-}
-
-src_compile() {
-	emake -C src CC=$(tc-getCC)
-}
-
-src_install() {
-	emake -C src DESTDIR="${D}" install
-	dobin runpsipred* bin/* BLAST+/runpsipred*
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc README
-	newdoc BLAST+/README README-blast
-}
-
-pkg_postinst() {
-	elog "Please use the update_blastdb.pl in order to"
-	elog "maintain your own local blastdb"
-}
diff --git a/sci-biology/psipred/psipred-3.3.ebuild b/sci-biology/psipred/psipred-3.3.ebuild
deleted file mode 100644
index 4e0b0102837b..000000000000
--- a/sci-biology/psipred/psipred-3.3.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils prefix toolchain-funcs versionator
-
-#MY_P="${PN}$(delete_all_version_separators)"
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Protein Secondary Structure Prediction"
-HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
-SRC_URI="
-	http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
-	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
-
-LICENSE="psipred"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	sci-biology/ncbi-tools
-	sci-biology/update-blastdb"
-DEPEND=""
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	rm -f bin/*
-	epatch \
-		"${FILESDIR}"/3.1-Makefile.patch \
-		"${FILESDIR}"/3.1-path.patch \
-		"${FILESDIR}"/3.2-fgets.patch
-	eprefixify runpsipred*
-	emake -C src clean
-}
-
-src_compile() {
-	emake -C src CC=$(tc-getCC)
-}
-
-src_install() {
-	emake -C src DESTDIR="${D}" install
-	dobin runpsipred* bin/* BLAST+/runpsipred*
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc README
-}
-
-pkg_postinst() {
-	elog "Please use the update_blastdb.pl in order to"
-	elog "maintain your own local blastdb"
-}
diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild
index d1d6a547d17f..1fe4c6dced52 100644
--- a/sci-biology/psipred/psipred-3.4.ebuild
+++ b/sci-biology/psipred/psipred-3.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -18,6 +18,7 @@ LICENSE="psipred"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	app-shells/tcsh
diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild
index d1d6a547d17f..1fe4c6dced52 100644
--- a/sci-biology/psipred/psipred-3.5.ebuild
+++ b/sci-biology/psipred/psipred-3.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -18,6 +18,7 @@ LICENSE="psipred"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	app-shells/tcsh