sci-biology/trnascan-se: Version BUmp, #532460

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-biology/trnascan-se/ChangeLog b/sci-biology/trnascan-se/ChangeLog
index 3cb787b7d8339b2c2e511b3c594fc4682ec81d7b..c8fc56f8b210e21c62cda757f01e046ed700ae5f 100644 (file)
--- a/sci-biology/trnascan-se/ChangeLog
+++ b/sci-biology/trnascan-se/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/trnascan-se
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/ChangeLog,v 1.13 2010/07/16 22:09:08 hwoarang Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/ChangeLog,v 1.14 2015/01/08 07:42:51 jlec Exp $
+
+*trnascan-se-1.31 (08 Jan 2015)
+
+  08 Jan 2015; Justin Lecher <jlec@gentoo.org> -trnascan-se-1.23-r1.ebuild,
+  +trnascan-se-1.31.ebuild, +files/trnascan-se-1.31-ldflags.patch,
+  metadata.xml:
+  Version BUmp, #532460
 
   16 Jul 2010; Markos Chandras <hwoarang@gentoo.org>
   trnascan-se-1.23-r2.ebuild:

diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
index 24d3ba6abc1c0bd5147702ed25e0ad7541d30462..9108667fc2bfe74f1d109877b90e7cc64867db23 100644 (file)
--- a/sci-biology/trnascan-se/Manifest
+++ b/sci-biology/trnascan-se/Manifest
@@ -1,7 +1,31 @@
-AUX trnascan-se-1.23-glibc-2.10.patch 6702 RMD160 1ac6cf0d4630ae7c9f7cd55c209d3b7d7391b18e SHA1 a2a7017c37e8db122026a2066ae107428b05ac95 SHA256 16c6083f8a2991d22252a23184a45c74e0fd75b5a45085c3dcea7d1cd503cf42
-AUX trnascan-se-1.23-ldflags.patch 971 RMD160 93382a13c9b14e687a884fff06a926abd6ea634c SHA1 0561f26cea27f2ec6268b54383be6aeb07367c1f SHA256 6013162268bc78f6752ce8703d9fd1810f634a9176b55dac67155b8decb8e6e9
-DIST trnascan-se-1.23.tar.bz2 482202 RMD160 41180bc008e64258470a241418467b9b97220669 SHA1 2b35e9b63854bb8ceb9fb602582f7de47d15d095 SHA256 a1d18a0b9decf4a93fa6cf02fb5867367729449fc8e47e3749c91678fc1f344a
-EBUILD trnascan-se-1.23-r1.ebuild 1320 RMD160 dda2944e1d7e44bd5f4f3e0038eed1a923dbc9bb SHA1 4856f02e96e8c06164537f4ef926539bc9923ec7 SHA256 7900c0bdef3751c8552cd67ae04147b2c8679fbce3badbc88ad5fd7e5d6d0290
-EBUILD trnascan-se-1.23-r2.ebuild 1365 RMD160 4df3bafdadbcd809cdaf22023c88f19a0001a223 SHA1 bb2f66bda2d00f4bbd27eeaf5baafc2541306a84 SHA256 56fc2d08e02e5b3bd17a6fe44e99f7aace3f735fabdc524d4374fffdc1c544e6
-MISC ChangeLog 1923 RMD160 6a09a900ec04184f4e6bbee6b6f49d0c59603837 SHA1 a842b2f9974e5e0a2dff06c7c937c535760bfb71 SHA256 2cb61f77aed54dedccbe20a958228f0c0983a9c1da9262433499b9850e2abe75
-MISC metadata.xml 505 RMD160 f2fa2c8de86e9ade0dc4f877b1d196ac68b92e5c SHA1 0f12c05690d0dfcb666e902d7993b7ef0775a74e SHA256 dbc8cc4c1391bf4846f2aa70d6598bc4b40a28568d3cb36e0a8ff8941eee9b23
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
+AUX trnascan-se-1.23-glibc-2.10.patch 6702 SHA256 16c6083f8a2991d22252a23184a45c74e0fd75b5a45085c3dcea7d1cd503cf42 SHA512 2df0a5d6bf633b9b1c1ccce002c5a751a3f5c5eedf755b24a3af1a6d07a93816b6be4195aa3142ebcbd16ad9b373223f398fbac1d91769b26be1d295f080f181 WHIRLPOOL d8bc3d22d50446ffc628276261d091cb0552e564c0d80c9c6fe6e4108c3c036a11fadd48c45a115fef56ac01a49df0b7a0cebb026fcff05344822c29b074f971
+AUX trnascan-se-1.23-ldflags.patch 971 SHA256 6013162268bc78f6752ce8703d9fd1810f634a9176b55dac67155b8decb8e6e9 SHA512 bcfdc71dc8454e110d45f44bf9c4a0b4e77ca85bcf0b501dd2de60c47418bc5d442b1ac976c6a333eb4398a12e4478b8817436246a1f872df208d5eaf64c3ac2 WHIRLPOOL f1afc811efcc061a114ab6b14ac2ef4ce8c7091bdfa6a392ac55dd6f1e38f1d1ded94f218309e2e3abd515ef80bffbefd7e4ed30d993e16603c0477b988f48b3
+AUX trnascan-se-1.31-ldflags.patch 973 SHA256 e103841dfe3f289493c80fc938a3c9318a550e160b3269b9856405ee48dc648a SHA512 ff677ce9ac3ed9299f6a3bf977642e2a6c300a1b801436bb5d3787968cfe28357a0ec23d0438f0b15c06324cd7e1bbbda590c8fb5574577a3f653779316931df WHIRLPOOL 2ba11012cd414d2dc9a523109bfebe726a347558cf1098f52410fc88c652665e6babeaef5581dce12fdd1a83af8ed417d8040ef481d5036a9632838f997333c2
+DIST trnascan-se-1.23.tar.bz2 482202 SHA256 a1d18a0b9decf4a93fa6cf02fb5867367729449fc8e47e3749c91678fc1f344a SHA512 4977febcecf8344fb77aad2eeb278637aebdb1d995fd26823e459b3767d4f40b20f57d343092cc2cb8024b0ccc385879f4b6406c69022f848aa1df0acf1a68d8 WHIRLPOOL 978328857eaef5666fcf38c22afabfb796984b5fa52a02a7167b653164ba0bc32fcb52d35159eef83732046245c598426739cd4ed63bf259ea85130dda17dd70
+DIST trnascan-se-1.31.tar.gz 740960 SHA256 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d WHIRLPOOL aef8b9f8d44799bac134a36af45374cdaba4b30c041e71e3095252aa8272fe9bd0aa76091211ac270ad609f67f388d577a83ec2ed2433997963fd5708c5b6665
+EBUILD trnascan-se-1.23-r2.ebuild 1365 SHA256 56fc2d08e02e5b3bd17a6fe44e99f7aace3f735fabdc524d4374fffdc1c544e6 SHA512 6a302b65e5e0b68da3f77c9221281874803be0ae685d0cd2f7a22668897c2c8ff0f0498dd156aaa0a3e4f117dd7c92b8c6609a93d7db385353ec2928f8ee3db7 WHIRLPOOL ae4f922cc2dcf53032d7d3ef2a18132e0101352c9f444f96f5307627ff1e9bf5985473cb04f97db1c579a498476d138e1be5776299a6cf6cdf0902c2c4d996a6
+EBUILD trnascan-se-1.31.ebuild 1338 SHA256 56001f593ab84f1ee21b55365df1cdb74f62a96839b5eedc21ff987b5979dfef SHA512 c5526359b37ad5157e7a2eb50bf4c2116454a5f40e6c98207e76755e7e190675fcb75b9ca5e8be15dbfaf221fc9db0b42e309095ec12e29c241a163b5af648c5 WHIRLPOOL b9053ae308f65440db90748b91d7e6ec32ba03998bb42c7d143e78d06d32a7fe80564a6d86c9554bf50c222498457f3edb5b29e257536f8d0106d9f92088566e
+MISC ChangeLog 2136 SHA256 92f300b302a4c13d5d024df078b0a4f53a2792ca01eccb4c53e1dc3d319a6d3b SHA512 05cdb586ff5cb5e426ae35c700ddc03155d073becafc4e8c4ab9f2cb813c4218c0793aac458e450b97971fe4d514daea3c5ebd4ae70400bb93b91494c9837301 WHIRLPOOL d2196cc89a8f0e3cfff5c873c72675990f085ea811d90577086c32bf703dc4b56f8e81a89d44e5ffc6b86b8a32f43209446e12546c2a905df2c6231bbf18f2ba
+MISC metadata.xml 507 SHA256 8b986960b3adc36724e73343eea980e16e27312095d977191ca79ed46f56643f SHA512 273d9ecc26b4fe5fc73344461dc0073e0cc0ec416d02f4bb3ae124ace494d9dcfecf7e8cfb2e460479712e4ab51e88c66ec467601788f7000ba308989a6aae2c WHIRLPOOL 791bf63e15d5c2ce12817d6ef231156a7b4740d1a9709d9b282cd82115328b913d46307d1a4a974e4e7941a1c2d7c491a286a2a1f259990ab7c9222e2c52476f
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0
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+=s047
+-----END PGP SIGNATURE-----

diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
new file mode 100644 (file)
index 0000000..f28b1e8
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 53e5c5b..a2d3feb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
+ all:  $(PROGS) tRNAscan-SE setpaths
+ 
+ covels-SE:  $(OBJ) scan_main.o
+-      $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++      $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+ 
+ coves-SE: $(OBJ) score_main.o
+-      $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++      $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+ 
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+-      $(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
++      $(CC) $(CFLAGS)  $(LDFLAGS) -o eufindtRNA eufind_main.o \
+       pavesi.o $(SQUIDOBJ) $(LIBS)
+ 
+ trnascan-1.4: trnascan.o
+-      $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++      $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
+ 
+ tRNAscan-SE:
+       $(PERLDIR)/$(PERLBIN) checkversion.pl

diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml
index 58c1938a82e76d0a008a998126ee03b695fda935..55de1683677fba052d54fa28ca73d8b20a78a9ec 100644 (file)
--- a/sci-biology/trnascan-se/metadata.xml
+++ b/sci-biology/trnascan-se/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>
                tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA
                genes, with a false positive rate of less than one per 15 gigabases,
                and with a search speed of about 30 kb/second. It was implemented for

diff --git a/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild b/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild
deleted file mode 100644 (file)
index b11d1e7..0000000
--- a/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild,v 1.6 2009/08/05 18:45:47 ssuominen Exp $
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="tRNA detection in large-scale genome sequences"
-HOMEPAGE="http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 x86"
-IUSE=""
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND}"
-
-src_unpack() {
-       unpack ${A}
-       cd "${S}"
-       epatch "${FILESDIR}"/${P}-glibc-2.10.patch
-       sed -e "s%BINDIR  = \$(HOME)/bin%BINDIR = /usr/bin%" \
-               -e "s%LIBDIR  = \$(HOME)/lib/tRNAscan-SE%LIBDIR = /usr/lib/${PN}%" \
-               -e "s%MANDIR  = \$(HOME)/man%MANDIR = /usr/share/man%" \
-               -e "s%CC = gcc%CC = $(tc-getCC)%" \
-               -e "s%CFLAGS = -O%CFLAGS = ${CFLAGS}%" \
-               -i Makefile || die
-}
-
-src_compile() {
-       emake || die
-       mv tRNAscan-SE.man tRNAscan-SE.man.1 || die
-}
-
-src_install() {
-       dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 || die
-       doman tRNAscan-SE.man.1 || die
-       dodoc MANUAL README Release.history || die
-       insinto /usr/lib/${PN}/
-       doins *.cm gcode.* Dsignal TPCsignal || die
-       insinto /usr/share/doc/${PF}
-       doins Manual.ps || die
-}
-
-src_test() {
-       make testrun || die
-}

diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
new file mode 100644 (file)
index 0000000..bf80b10
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/trnascan-se-1.31.ebuild,v 1.1 2015/01/08 07:42:51 jlec Exp $
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+
+inherit eutils perl-module toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
+SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S="${WORKDIR}"/tRNAscan-SE-1.3.1/
+
+src_prepare() {
+       epatch \
+               "${FILESDIR}"/${P}-ldflags.patch
+       sed \
+               -e "s:BINDIR  = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
+               -e "s:LIBDIR  = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \
+               -e "s:MANDIR  = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \
+               -e "s:CC = gcc:CC = $(tc-getCC):" \
+               -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \
+               -i Makefile || die
+
+       perl_set_version
+}
+
+src_test() {
+       emake PATH="${S}:${PATH}" testrun
+}
+
+src_install() {
+       dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
+
+       newman tRNAscan-SE.man tRNAscan-SE.man.1
+
+       dodoc MANUAL README Release.history
+
+       insinto /usr/share/${PN}/
+       doins *.cm gcode.* Dsignal TPCsignal
+
+       dodoc Manual.ps
+
+       insinto ${VENDOR_LIB}
+       doins -r tRNAscanSE
+}