Fix parallel build wrt bug 311919. Thanks to Myckel Habets <m.e.j.habets@biology.leidenuniv.nl> for patch and report. Fix buffer overflow wrt bug 338179 and respect LDFLAGS wrt bug 338177. Thanks to Diego Elio Pettenò for the reports. Drop old.

Package-Manager: portage-2.1.9.24/cvs/Linux x86_64

6 files changed, 92 insertions, 10 deletions

diff --git a/sci-biology/infernal/ChangeLog b/sci-biology/infernal/ChangeLog
index a76b543f0c6d..082d50dec5e4 100644
--- a/sci-biology/infernal/ChangeLog
+++ b/sci-biology/infernal/ChangeLog
@@ -1,6 +1,17 @@
 # ChangeLog for sci-biology/infernal
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/ChangeLog,v 1.7 2010/04/05 12:14:58 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/ChangeLog,v 1.8 2010/11/04 10:06:22 xarthisius Exp $
+
+*infernal-1.0.2-r1 (04 Nov 2010)
+
+  04 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -infernal-1.0.ebuild,
+  +infernal-1.0.2-r1.ebuild, +files/infernal-1.0.2-ldflags.patch,
+  +files/infernal-1.0.2-overflows.patch,
+  +files/infernal-1.0.2-parallel-build.patch:
+  Fix parallel build wrt bug 311919. Thanks to Myckel Habets
+  <m.e.j.habets@biology.leidenuniv.nl> for patch and report. Fix buffer
+  overflow wrt bug 338179 and respect LDFLAGS wrt bug 338177. Thanks to
+  Diego Elio Pettenò for the reports. Drop old.
 
   05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org>
   infernal-1.0.2.ebuild:
diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest
index 106cfecf5d03..86bffc99b8a1 100644
--- a/sci-biology/infernal/Manifest
+++ b/sci-biology/infernal/Manifest
@@ -1,6 +1,8 @@
+AUX infernal-1.0.2-ldflags.patch 440 RMD160 6a9df534b9784f39d768cf62bff406030835ef16 SHA1 c7b796137bef732f84e74d08f1744ec5d150d26f SHA256 397e1fad01f613a4de4679797da5428a8f0d4ebcda0eb68c3044b93d196d6cb0
+AUX infernal-1.0.2-overflows.patch 536 RMD160 fd9434b4291b610053fc0d2a076247eff7799d0c SHA1 8922c7bf904fbf3213231ffc7389645517af1b1b SHA256 ccd5b77323fd769791b1c39f5964fa0a2e29b7710627c16d90eb2b64bb89faa4
+AUX infernal-1.0.2-parallel-build.patch 651 RMD160 4889692cadfd92c96e4b399737374ad7cd401cd1 SHA1 54fadbaca7935c50ec37a1a09318a303de473862 SHA256 5f5aa6fe823640e90bdebe04be99635f1190771df9ea29316d926d3b928878be
 DIST infernal-1.0.2.tar.gz 15205421 RMD160 f56cb970a520b63d60b854f5b397813c342bb81f SHA1 df2454c606eb0f90ab98fc5c988fdd60a6f87903 SHA256 c4f89ac2e865c8b04a53a647703d88f96c31bb1d47d3e06f4b6090d7d15643ad
-DIST infernal-1.0.tar.gz 15032429 RMD160 3438e28ed0cd895a34d6eacc230c34f58b3f95ce SHA1 19c16b32c11fdcfd21a7ff7c5c127c0f9ead08fd SHA256 099d322c1aa1434f9a37379375f24e02cf4eceb102b12690ba1c65958a73999f
+EBUILD infernal-1.0.2-r1.ebuild 992 RMD160 8664d8be60fe11379103b21b908ec9ac519345d8 SHA1 d60084a05cfc8386d255a1bd7fd443f2db57a3ab SHA256 0a83ba8221b4758776ff8f21171089a26fee929c19733a180130223a1822865a
 EBUILD infernal-1.0.2.ebuild 821 RMD160 a79be76a80f518397d0e25714ab740619ca57e77 SHA1 a520349aac4594219ecb0824905546da1336be83 SHA256 7679a24172fae83d28c7dcec64a6ae9cfdd0204185da8b1170c786f0ddd13570
-EBUILD infernal-1.0.ebuild 815 RMD160 857d70c01259971848264183299afb1c5ca07d1d SHA1 c49564b82c66db8e8ae46c304def72dda2fd6db1 SHA256 f0ee121a4cef38a110d05ebfe8fa2d61ebcc583455002d4e8a485810ccc32bb7
-MISC ChangeLog 1094 RMD160 7adcf027e50c44560adcb7a41f8cfad7af7ed7a0 SHA1 9a68551f75447384bb4898630163ec243f642dd7 SHA256 d63fa998a97564e37414e0fe6664ba7293a448a1a8b1b4937513bba6b997c2dc
+MISC ChangeLog 1612 RMD160 2a7e8010e6bfcb6001dd0fa12338e369a58084cf SHA1 f407d851e51876e62a0516eba23a3ed43c323704 SHA256 32f90d0340bbdc4f812f690aa74e9fc33cc93be4ca27584967a0e04bd571519b
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch
new file mode 100644
index 000000000000..5bc5bd008ff6
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch
@@ -0,0 +1,15 @@
+Respect LDFLAGS
+
+http://bugs.gentoo.org/show_bug.cgi?id=338177
+
+--- src/Makefile.in
++++ src/Makefile.in
+@@ -86,7 +86,7 @@
+ all: 	$(PROGS) 
+ 
+ $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS}
+-	$(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
+ 
+ 
+ #################################################################
diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
new file mode 100644
index 000000000000..b9791fa1ca2e
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
@@ -0,0 +1,15 @@
+Fix buffer overflow
+
+http://bugs.gentoo.org/show_bug.cgi?id=338179
+
+--- easel/esl_getopts.c
++++ easel/esl_getopts.c
+@@ -1270,7 +1270,7 @@
+ 		   "Arg looks like option? Use %.24s%.24s if you really mean it.",
+ 		   g->opt[opti].name, *ret_optarg);
+       } else 
+-	ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name);
++	ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name);
+ 
+       g->optstring = NULL;   /* An optchar that takes an arg must terminate an optstring. */
+     }
diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch
new file mode 100644
index 000000000000..004742546f00
--- /dev/null
+++ b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch
@@ -0,0 +1,31 @@
+Fix parallel build 
+
+http://bugs.gentoo.org/show_bug.cgi?id=311919
+
+--- Makefile.in
++++ Makefile.in
+@@ -82,9 +82,10 @@
+ all: core 
+ 
+ core:
+-	(cd easel;     make CC="$(CC)" CFLAGS="$(CFLAGS)"; make)
+-	(cd src;       make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module)
+-	(cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)")
++	$(MAKE) -C easel
++	$(MAKE) -C src 
++	$(MAKE) -C src module
++	$(MAKE) -C testsuite
+ 
+ #.PHONY: $(RIGFILTERS)
+ #$(RIGFILTERS): core
+--- easel/Makefile.in
++++ easel/Makefile.in
+@@ -132,7 +132,7 @@
+ 	esl_wuss.o
+ 
+ all: libeasel.a
+-	(cd miniapps; make)
++	$(MAKE) -C miniapps
+ 
+ .c.o: 
+ 	${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $<		
diff --git a/sci-biology/infernal/infernal-1.0.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
index e7eaf8ff5d83..0930bfea766c 100644
--- a/sci-biology/infernal/infernal-1.0.ebuild
+++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
@@ -1,9 +1,11 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/infernal-1.0.ebuild,v 1.4 2009/09/22 13:05:32 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/infernal-1.0.2-r1.ebuild,v 1.1 2010/11/04 10:06:22 xarthisius Exp $
 
 EAPI="2"
 
+inherit eutils
+
 DESCRIPTION="Inference of RNA alignments"
 HOMEPAGE="http://infernal.janelia.org/"
 SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz"
@@ -11,20 +13,26 @@ SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz"
 LICENSE="GPL-3"
 SLOT="0"
 IUSE="mpi"
-KEYWORDS="amd64 x86"
+KEYWORDS="~amd64 ~x86"
 
 DEPEND="mpi? ( virtual/mpi )"
 RDEPEND="${DEPEND}"
 
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-parallel-build.patch \
+		"${FILESDIR}"/${P}-overflows.patch \
+		"${FILESDIR}"/${P}-ldflags.patch
+}
+
 src_configure() {
 	econf --prefix="${D}/usr" \
-		$(use_enable mpi) || die
+		$(use_enable mpi)
 }
 
 src_install() {
 	emake install || die
 	(cd documentation/manpages; for i in *; do newman ${i} ${i/.man/.1}; done)
 	insinto /usr/share/${PN}
-	doins -r benchmarks tutorial intro matrices
-	dodoc 00README* Userguide.pdf documentation/release-notes/*
+	doins -r benchmarks tutorial intro matrices || die
+	dodoc 00README* Userguide.pdf documentation/release-notes/* || die
 }