New version (fixes bug #191874).

Package-Manager: portage-2.1.3.11

5 files changed, 90 insertions, 15 deletions

diff --git a/sci-biology/probcons/ChangeLog b/sci-biology/probcons/ChangeLog
index a328565fca0e..84b675cf5980 100644
--- a/sci-biology/probcons/ChangeLog
+++ b/sci-biology/probcons/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/probcons
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.5 2007/02/22 01:28:37 jokey Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.6 2007/10/06 11:20:01 markusle Exp $
+
+*probcons-1.12 (06 Oct 2007)
+
+  06 Oct 2007; Markus Dittrich <markusle@gentoo.org> +files/probcons-1.12-cxxflags.patch, +probcons-1.12.ebuild:
+  New version (fixes bug #191874).
 
   22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog:
   Redigest for Manifest2
diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest
index 428ec11506c0..8266d0a560c7 100644
--- a/sci-biology/probcons/Manifest
+++ b/sci-biology/probcons/Manifest
@@ -1,19 +1,25 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX 1.10-fix-cxxflags.patch 845 RMD160 1e04c84b35c245623619c6d5a7128a8ab1c880af SHA1 9d3ecd0da754d899cd4b4016bf2dbffe5e9d87b6 SHA256 73a298114996b5d879b9ec3253d104464cb456d19382668cdf75bfe9f93f11de
 MD5 bcc20b9c5e249f07fb535f0744f816e2 files/1.10-fix-cxxflags.patch 845
 RMD160 1e04c84b35c245623619c6d5a7128a8ab1c880af files/1.10-fix-cxxflags.patch 845
 SHA256 73a298114996b5d879b9ec3253d104464cb456d19382668cdf75bfe9f93f11de files/1.10-fix-cxxflags.patch 845
+AUX probcons-1.12-cxxflags.patch 844 RMD160 c5f07264e5ef9d76baa22b676b26f4a51c76fc73 SHA1 a797284ff9a7df4a7b8bff9ee286594109aabdda SHA256 56e30ce88806c520296e0e06230e4020ac341e91738106aa5392d5fad4975502
+MD5 39dccb33f46968a511b9cb7b39e71810 files/probcons-1.12-cxxflags.patch 844
+RMD160 c5f07264e5ef9d76baa22b676b26f4a51c76fc73 files/probcons-1.12-cxxflags.patch 844
+SHA256 56e30ce88806c520296e0e06230e4020ac341e91738106aa5392d5fad4975502 files/probcons-1.12-cxxflags.patch 844
 DIST probcons_v1_10.tar.gz 43004 RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 SHA1 773d82f6883202ec41e5dee39713b5db649ef5b0 SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518
+DIST probcons_v1_12.tar.gz 43200 RMD160 4d7d9a89c2c95f22056719c8349216ca1ba635c9 SHA1 ee6ce81777c9ce366f575ab4096ff07f39af9829 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383
 EBUILD probcons-1.10.ebuild 1236 RMD160 b24658a6866f556bab2d9ee041540ed65fba961b SHA1 2302f7a9c2a1ba349b3949546187e34e2c7aeafe SHA256 86a6355ad1d5a3bc7914579262047bde097c3228d5ef88ae6a988beb3577c964
 MD5 7ffee477cf8d489117305b770a90d766 probcons-1.10.ebuild 1236
 RMD160 b24658a6866f556bab2d9ee041540ed65fba961b probcons-1.10.ebuild 1236
 SHA256 86a6355ad1d5a3bc7914579262047bde097c3228d5ef88ae6a988beb3577c964 probcons-1.10.ebuild 1236
-MISC ChangeLog 976 RMD160 d9c13d0cae00bf31709c8024423ada92a64c7b2e SHA1 6f8ea7415b67227711267f9df66cb6afa9fa5b21 SHA256 f66c87b3cce49d34e0915132cf1dc1d2ee77c8608602bb5fafdd45f605b24815
-MD5 75d01b3a3c18ea5d78e0df8b34d394cb ChangeLog 976
-RMD160 d9c13d0cae00bf31709c8024423ada92a64c7b2e ChangeLog 976
-SHA256 f66c87b3cce49d34e0915132cf1dc1d2ee77c8608602bb5fafdd45f605b24815 ChangeLog 976
+EBUILD probcons-1.12.ebuild 1231 RMD160 0019e926964f3a729696848b03595023808f4669 SHA1 45b460d558a1e6e0b78649493b0495e2914c8a1d SHA256 4e710630613aecc09a249fcf72fc6596b46c48effd7b918b682a77b426d2233e
+MD5 8c9218fde965456ec99e98dbc7030c50 probcons-1.12.ebuild 1231
+RMD160 0019e926964f3a729696848b03595023808f4669 probcons-1.12.ebuild 1231
+SHA256 4e710630613aecc09a249fcf72fc6596b46c48effd7b918b682a77b426d2233e probcons-1.12.ebuild 1231
+MISC ChangeLog 1158 RMD160 592f21f1ecaa93a50badf58fe06ccfef1f6d63cd SHA1 54254e430007deb64f3319c95a313fc7bedd67e0 SHA256 4fd4359deca24e0130767ef6c686365dfad265f129f3c43fb0243210f58f9198
+MD5 004cb05def7dad610f9c4957ec440455 ChangeLog 1158
+RMD160 592f21f1ecaa93a50badf58fe06ccfef1f6d63cd ChangeLog 1158
+SHA256 4fd4359deca24e0130767ef6c686365dfad265f129f3c43fb0243210f58f9198 ChangeLog 1158
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
 MD5 86813ca8050bc98ba326cb74e88150a5 metadata.xml 164
 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c metadata.xml 164
@@ -21,10 +27,6 @@ SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f metadata
 MD5 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241
 RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241
 SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.1 (GNU/Linux)
-
-iD8DBQFF3PFYz974XjDVpbkRAqjRAKCvF0CqHme2MAZLQk9oCUEp2n/TfACfVeS6
-1CRNfDaMVoIL5akNQ9XEfwA=
-=lZgi
------END PGP SIGNATURE-----
+MD5 f54becdae621af5a5aa441ea2c40c9d9 files/digest-probcons-1.12 241
+RMD160 b5af564aedd7436ed6ba3dae01a376f40675fe23 files/digest-probcons-1.12 241
+SHA256 186a3dfc272aaacf51a6682082f6e7366cb9d07ec847cc84486f4c1e46507f46 files/digest-probcons-1.12 241
diff --git a/sci-biology/probcons/files/digest-probcons-1.12 b/sci-biology/probcons/files/digest-probcons-1.12
new file mode 100644
index 000000000000..655d2ce3110e
--- /dev/null
+++ b/sci-biology/probcons/files/digest-probcons-1.12
@@ -0,0 +1,3 @@
+MD5 a658e24b07aaa9e8194317345133ac9d probcons_v1_12.tar.gz 43200
+RMD160 4d7d9a89c2c95f22056719c8349216ca1ba635c9 probcons_v1_12.tar.gz 43200
+SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383 probcons_v1_12.tar.gz 43200
diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
new file mode 100644
index 000000000000..a2431c4a0936
--- /dev/null
+++ b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
@@ -0,0 +1,21 @@
+diff -Naur probcons/Makefile probcons-new/Makefile
+--- probcons/Makefile	2007-04-03 13:39:23.000000000 -0400
++++ probcons-new/Makefile	2007-10-06 07:07:10.000000000 -0400
+@@ -15,6 +15,8 @@
+ #    c) RELEASE mode
+ ################################################################################
+ 
++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
++
+ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
+ 
+ # debug mode    
+@@ -25,7 +27,7 @@
+ 
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
+-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
+ 
+ ################################################################################
+ # 3) Dependencies
diff --git a/sci-biology/probcons/probcons-1.12.ebuild b/sci-biology/probcons/probcons-1.12.ebuild
new file mode 100644
index 000000000000..d930525be39f
--- /dev/null
+++ b/sci-biology/probcons/probcons-1.12.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/probcons-1.12.ebuild,v 1.1 2007/10/06 11:20:01 markusle Exp $
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}_v${PV/./_}"
+DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
+HOMEPAGE="http://probcons.stanford.edu/"
+SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+# Gnuplot is explicitly runtime-only, it's run using system()
+RDEPEND="sci-visualization/gnuplot"
+DEPEND=""
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+	unpack ${A}
+	epatch ${FILESDIR}/${P}-cxxflags.patch
+}
+
+src_compile() {
+	emake \
+		CXX="$(tc-getCXX)" \
+		OPT_CXXFLAGS="${CXXFLAGS}" \
+		|| die "make failed"
+}
+
+src_install() {
+	DESTTREE="/usr" dobin probcons project makegnuplot
+	# Overlap with imagemagick
+	DESTTREE="/usr" newbin compare compare-probcons
+	dodoc README
+}
+
+pkg_postinst() {
+	ewarn "The 'compare' binary is installed as 'compare-probcons'"
+	ewarn "to avoid overlap with other packages."
+	einfo "You may also want to download the user manual"
+	einfo "from http://probcons.stanford.edu/manual.pdf"
+}