removed old, Version Bump, FORTIFY patch

(Portage version: 2.2_rc97/cvs/Linux x86_64)

6 files changed, 47 insertions, 56 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/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"