removed old, Version Bump, FORTIFY patch

Package-Manager: portage-2.2_rc97/cvs/Linux x86_64

7 files changed, 57 insertions, 66 deletions

diff --git a/sci-biology/psipred/ChangeLog b/sci-biology/psipred/ChangeLog
index b947e301b829..56dafc64ffbd 100644
--- a/sci-biology/psipred/ChangeLog
+++ b/sci-biology/psipred/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/psipred
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.3 2010/05/16 11:23:30 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.4 2010/10/16 08:50:49 jlec Exp $
+
+*psipred-3.2 (16 Oct 2010)
+
+  16 Oct 2010; Justin Lecher <jlec@gentoo.org> +files/3.1-fgets.patch,
+  -psipred-2.6.1-r1.ebuild, psipred-3.1.ebuild, +files/3.2-fgets.patch,
+  -psipred-3.0.ebuild, +psipred-3.2.ebuild:
+  removed old, Version Bump, FORTIFY patch
 
 *psipred-3.1 (16 May 2010)
 
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
index 435d36a879eb..7c6263f84206 100644
--- a/sci-biology/psipred/Manifest
+++ b/sci-biology/psipred/Manifest
@@ -5,19 +5,19 @@ AUX 2.6.1-Makefile.patch 1295 RMD160 38eb08b77f15db26d60eb9ad5b603df3927f9471 SH
 AUX 2.6.1-path.patch 1114 RMD160 b0982bb972daccd9e4d3dbc0668ad80084929a33 SHA1 d0e1f4a20f114312ab8fcf8faa58b5eb29f7fa1d SHA256 0b2c0cf62c9c8b5fc21ac0c6b537aac52dcf617ffd2bd99724f1ac980efce7a5
 AUX 3.0-path.patch 1124 RMD160 985bc8a52db2df5b7ea0529f69e43d440621829d SHA1 db74c92afa9f9b2849fe65a61259bb8cfc5f9ee4 SHA256 2dc3b531f1bc1ab7e2426b0ec95ff67ec93ac8376e017215b3b2dcd5b1c8804d
 AUX 3.1-Makefile.patch 1103 RMD160 a9ccbf9602a7afa2875a5e43a5e27bec4b17709a SHA1 989fbe7b175ea161c0a314e4c78c3e065d0116b5 SHA256 de49b937edc714ba84ea2ae0900ea92b73c58048fafb8d616e8dfa44b548e927
+AUX 3.1-fgets.patch 427 RMD160 40b3e7de920e05f951ec41268d95f90dce66fed1 SHA1 dd3445540f982f95c2ceada049e94c8ca4254070 SHA256 a1f52692ad3593278718a8d2cc95d176e8bcd773305a6f6769a5c76106cd6423
 AUX 3.1-path.patch 1128 RMD160 2281327e849146a6dc38f035501727e0a30d2d59 SHA1 579b36644c4fd9a23f72177b8ed63e80ccebf751 SHA256 0b91a360760bd27f4ba43639d32e891d5576595451e1f7285632fc9ad38a80fa
-DIST psipred261.tar.gz 873613 RMD160 744e984a21145b6caf312f68de66501ba0ac2d39 SHA1 db3af95091ed745fc956153239016d042e44b62d SHA256 0b39c075493d43e63952535dfed5341d0b81a99e4fb72d5431676d657d027126
-DIST psipred30.tar.gz 724315 RMD160 6aabe85bff8d3a60d3e80d6646ba391c23716edc SHA1 c7d6c4a5a4cc2fe52acb7b2b24eb3b7780c7afca SHA256 24a70fa859ade37d634f2fa8e047061d107ac96ffba8ea96b5bab186f402e62c
+AUX 3.2-fgets.patch 427 RMD160 ed804cd83bbf30b99b59bfa01854a335d8c0ca0b SHA1 9f322d30af56b1aeabbb1e532e52eaf2bace3293 SHA256 95d68881c502c567025eb5e74fcd545bf012ded48ab2731aa70827f0ff449696
 DIST psipred31.tar.gz 746797 RMD160 921f0a0cc8b88a0d8deeaccf05231447122f4237 SHA1 f4ce00879a3dd787df9015636184d777e54d5905 SHA256 2150696cae281bc942a18fc5f1e2057ed70cb6ee7b492c9594cbd99b8f6987dd
-EBUILD psipred-2.6.1-r1.ebuild 1204 RMD160 e45a3e88e973ae58cd553e7d627f6b684b197d43 SHA1 d814f149f3ea10d36a74d111a2369f57a7823d95 SHA256 d66c6f9d91a47e07ceb00e593579a2d351bdffd7aa7ed7478dfbf6c8ce02a4d6
-EBUILD psipred-3.0.ebuild 1199 RMD160 6e1a35188b15cf3f77053df03445e2470c290f3f SHA1 4a8caf825bafe4e5b092b1d2fc56d59944673951 SHA256 12a8bf0ebe5d37922f87b04ec0820903bec0592dd550ff9b963b85bb89b84b90
-EBUILD psipred-3.1.ebuild 1224 RMD160 a3f28901894c035726e37917b0b0092e52bd6168 SHA1 6a6d52c165c26a2f60300210bef7bbd024a0f1c3 SHA256 d4667bc4a25fbe7ad888415a62c06cbbaa672542df563d7422ee7b69f690aaea
-MISC ChangeLog 859 RMD160 a3d2f967909d0ffb8bd7bcbe1ff7bc89514daa9d SHA1 e8a41836bf2d0b9e4ec99c7d78319dc4da93213c SHA256 dad6495fa6d20b01ae6b7c730634fa066f6c077b564dc5047f5dd47c5c93aaa2
+DIST psipred32.tar.gz 747120 RMD160 4416abb730428e87ee766d1bf16409e9d5f3f219 SHA1 496be261ed522dc927d4ce2ad82d23977571265f SHA256 0775b0f07df87b2afd4989a378fc9b47f462507a264aaf2d56dd0243d9d00343
+EBUILD psipred-3.1.ebuild 1270 RMD160 7176556ecb96d45730c3af2f633c32df5b710afa SHA1 d71445cbf8b8697eec3c2b7bb77e4b309c465fcd SHA256 258864043648ffeff37ff370693b5e9272c2611de3523c1443e6f044eee7046c
+EBUILD psipred-3.2.ebuild 1266 RMD160 6995e09fdf7bb8410545dfd4936cb6a5b548fe04 SHA1 7fdd58409aac37b9f52d873468ff8ba0a444a1e6 SHA256 096f80c485417e3b3ab57f04601755fc752777e3fcaf44895a917b8defd78beb
+MISC ChangeLog 1118 RMD160 f8293583268f2ef73b65b8cdc048b55a73d71688 SHA1 359d1484824e6c8630a84c6ceed15464e356e4cf SHA256 ae8fc0bab0896b13eda247c30d0b3c07aa8b00976dbb4d19254991f721eeacbc
 MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAkvv1bgACgkQgAnW8HDreRZ6fgCgmZMhcZl49bomRDc6Q3uXqfE4
-qGIAoMt3DkJr9Jylj6z7qrUn/dzqu9jX
-=8AWe
+iEYEARECAAYFAky5Z2sACgkQgAnW8HDreRbUtgCfQ3yRusnBXQhDDAwejGLkpVMr
+HrwAn1j1KVIWNX0283AJX6EkPq3Patc0
+=mTw5
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/psipred/files/3.1-fgets.patch b/sci-biology/psipred/files/3.1-fgets.patch
new file mode 100644
index 000000000000..e58d677258e0
--- /dev/null
+++ b/sci-biology/psipred/files/3.1-fgets.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
+index 4d8e5ff..0d82483 100644
+--- a/src/sspred_avpred.c
++++ b/src/sspred_avpred.c
+@@ -213,7 +213,7 @@ predict(int argc, char **argv)
+ int             getmtx(FILE *lfil)
+ {
+     int             aa, i, j, naa;
+-    char            buf[256], *p;
++    char            buf[65536], *p;
+     
+     if (fscanf(lfil, "%d", &naa) != 1)
+ 	fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch
new file mode 100644
index 000000000000..ec06d141ee34
--- /dev/null
+++ b/sci-biology/psipred/files/3.2-fgets.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
+index 37b1332..4f04ab6 100644
+--- a/src/sspred_avpred.c
++++ b/src/sspred_avpred.c
+@@ -223,7 +223,7 @@ predict(int argc, char **argv)
+ int             getmtx(FILE *lfil)
+ {
+     int             aa, i, j, naa;
+-    char            buf[256], *p;
++    char            buf[65536], *p;
+     
+     if (fscanf(lfil, "%d", &naa) != 1)
+ 	fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/psipred/psipred-2.6.1-r1.ebuild b/sci-biology/psipred/psipred-2.6.1-r1.ebuild
deleted file mode 100644
index d80c361b20a2..000000000000
--- a/sci-biology/psipred/psipred-2.6.1-r1.ebuild
+++ /dev/null
@@ -1,48 +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/psipred/psipred-2.6.1-r1.ebuild,v 1.1 2010/05/06 18:27:50 jlec Exp $
-
-EAPI="3"
-
-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=""
-
-RDEPEND="
-	sci-biology/ncbi-tools
-	sci-biology/ncbi-tools++"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	rm -f bin/*
-	epatch "${FILESDIR}"/${PV}-Makefile.patch
-	epatch "${FILESDIR}"/${PV}-path.patch
-	eprefixify runpsipred*
-}
-
-src_compile() {
-	emake -C src CC=$(tc-getCC) || die "emake failed"
-}
-
-src_install() {
-	emake -C src DESTDIR="${D}" install || die "installation failed"
-	dobin runpsipred* || die
-	insinto /usr/share/${PN}
-	doins -r data || die "failed to install data"
-	dodoc README || die "nothing to read"
-}
-
-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-3.1.ebuild b/sci-biology/psipred/psipred-3.1.ebuild
index 3201132f6781..e1bcf7908809 100644
--- a/sci-biology/psipred/psipred-3.1.ebuild
+++ b/sci-biology/psipred/psipred-3.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.1.ebuild,v 1.1 2010/05/16 11:23:30 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.1.ebuild,v 1.2 2010/10/16 08:50:49 jlec Exp $
 
 EAPI="3"
 
@@ -20,13 +20,16 @@ IUSE=""
 RDEPEND="
 	sci-biology/ncbi-tools
 	sci-biology/ncbi-tools++"
+DEPEND=""
 
 S="${WORKDIR}"
 
 src_prepare() {
 	rm -f bin/*
-	epatch "${FILESDIR}"/${PV}-Makefile.patch
-	epatch "${FILESDIR}"/${PV}-path.patch
+	epatch \
+		"${FILESDIR}"/${PV}-Makefile.patch \
+		"${FILESDIR}"/${PV}-path.patch \
+		"${FILESDIR}"/${PV}-fgets.patch
 	eprefixify runpsipred*
 }
 
diff --git a/sci-biology/psipred/psipred-3.0.ebuild b/sci-biology/psipred/psipred-3.2.ebuild
index d74553f2952d..566dc1632ede 100644
--- a/sci-biology/psipred/psipred-3.0.ebuild
+++ b/sci-biology/psipred/psipred-3.2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.0.ebuild,v 1.1 2010/05/06 18:27:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.2.ebuild,v 1.1 2010/10/16 08:50:49 jlec Exp $
 
 EAPI="3"
 
@@ -20,13 +20,16 @@ IUSE=""
 RDEPEND="
 	sci-biology/ncbi-tools
 	sci-biology/ncbi-tools++"
+DEPEND=""
 
 S="${WORKDIR}"
 
 src_prepare() {
 	rm -f bin/*
-	epatch "${FILESDIR}"/2.6.1-Makefile.patch
-	epatch "${FILESDIR}"/${PV}-path.patch
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/${PV}-fgets.patch
 	eprefixify runpsipred*
 }
 
@@ -36,7 +39,7 @@ src_compile() {
 
 src_install() {
 	emake -C src DESTDIR="${D}" install || die "installation failed"
-	dobin runpsipred* || die
+	dobin runpsipred* bin/* BLAST+/runpsipred* || die
 	insinto /usr/share/${PN}
 	doins -r data || die "failed to install data"
 	dodoc README || die "nothing to read"