Drop old; fix for format-security; drop broken doc generation, bug #461000

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-biology/eugene/ChangeLog b/sci-biology/eugene/ChangeLog
index 2d7b7d457766686cfecd34ca0464ee4f856e6036..9cf22a2cce9a7d14d62994f7d206425588fea58e 100644 (file)
--- a/sci-biology/eugene/ChangeLog
+++ b/sci-biology/eugene/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/eugene
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.10 2013/03/09 19:24:44 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.11 2015/03/20 16:38:39 jlec Exp $
+
+  20 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +files/eugene-4.1-format-security.patch, -eugene-3.5g.ebuild,
+  eugene-3.6-r1.ebuild, eugene-4.1.ebuild:
+  Drop old; fix for format-security; drop broken doc generation, bug #461000
 
 *eugene-4.1 (09 Mar 2013)
 
@@ -44,4 +49,3 @@
 
   04 Jan 2009; weaver <weaver@gentoo.org> +eugene-3.5d.ebuild:
   Initial commit, ebuild written by me
-

diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
index 373eae5d558e37babbf63f47111a1134fd6f95cd..2f336e68a494fd3cccccda397c978a7552f5d60c 100644 (file)
--- a/sci-biology/eugene/Manifest
+++ b/sci-biology/eugene/Manifest
@@ -3,18 +3,29 @@ Hash: SHA512
 
 AUX eugene-3.6-overflow.patch 252 SHA256 cc8795d5f4525a299bc3e17da1e26c1e5fe3ef0c2371c5bf9de36b5037972fc7 SHA512 ed39c8d4aa73ba9e378a025e740c50f1b431fbb4590e3e9204f789081c8b22aef05fb4ce9ac7a0f22015ee03f73392730894a8dea5f6f16cd4533172e46776ce WHIRLPOOL 775e4167b0efa7dfd1539b01c20f4ce268666840d5c2766222deadacfcc21cf6697c177efde0e777c398ad4c888ee3df1b57113b451b1700ca5965b718c8432f
 AUX eugene-3.6-plugins.patch 1784 SHA256 0ec9c0d2bf6009e89612c3d95711b211aefc267d3eb6b75bc6279318256bc46d SHA512 300601ee6abe469460ebbe29c45468d516e5e781ad4b0542e9590de38ba6e98e3697c5f6f92f83212a1aa6da5e0650636af279d82241277c0b43fb5472028fcc WHIRLPOOL 695b8efe382014c6e1c9c44bebab3ed417b7ad736fd7db5623911971926bab284e9bdfb2ee5061287c99a93433d060040285765f37e0b283ecd83717adca5359
-DIST eugene-3.5g.tar.gz 5439002 SHA256 7837619bcd03b89123e4a03c43fa74060251d98f7bc503de0d92ba78e9efefac
+AUX eugene-4.1-format-security.patch 609 SHA256 391521469ce4c6df425084d9b2df611efe2721f563b15843f495064ed72d4553 SHA512 f4eedd5b70309d4b8eedce8f3a4f79b65e595d407e88fd79e7f4f2f8c98880432366124b7f0a34c9032c9a498a1db607b0cac20304e84ec01f736589924ff362 WHIRLPOOL 5b703b25d049f9f9fb78d543e72cde8130f9f1e116aac26e1c748897fe6558507d22f2ce08fc7c4e65568f5213fe4fc7de111a58043c88ee94586c4aca3f71e0
 DIST eugene-3.6.tar.gz 5589654 SHA256 731757d65f182e2eb2a18ee1fb2e710519a705aa91ef268136053698e07cb227 SHA512 594ad23e215ece2b088a2177304f9eee25411d8b44f1a94dee2079a0a69847cac7053f8675e50dab1cad41bc61135057efb3dce674a9f42156d56acb2ea29968 WHIRLPOOL 50847357a80e3cd149575c569980b050e35997b7a5d3781b4f1cf48f79e05a88c358e186226ff80d56ae090d08ef82f5e9bea779911d96ffb5c983ccf36b09a6
 DIST eugene-4.1.tar.gz 7393361 SHA256 faff769f68e1ab1fdec61be34ec7fef3c73805734199765ba11cf1ea9c02f800 SHA512 f4bcf63103754f8fb577d311d181375732411fa926fb0cef86fcd00c373ed5cc5637f1b55fa375a4bb14c5181f7de1dc244570f74cdd1887b6107d5c6cea37b3 WHIRLPOOL 32f4539456c243dd3c6a9d5a986fea210e53e5566aaa0849a26f34832957100623570a0814193059420d53e553247584360635706844ed0ec55c4cc65e235ad4
-EBUILD eugene-3.5g.ebuild 967 SHA256 2dfb0351ce49e4078d985228461082ed2504baf72cf0260bbf8ed45a5f3a3a78 SHA512 05845888ba1d8d1c895e377cc53f4113d6a789b2dd2795b3f060b2f57ceb79014e7731aa1f7fc195eb8ca8ea5cd8fc5c330734c3ffe907a16149c5760f982b9d WHIRLPOOL 239a89750e1300c51b6efa9bcb496ce57ff94562e2a9f36b2c1f2502b32c2258c13b5b376420d1ce652707b50d55869f9223a8964b17de6afca3f897c00d34d7
-EBUILD eugene-3.6-r1.ebuild 1133 SHA256 fac2a87e98ac975beb46dc1062bfa16462272cf6fadd946fce2a6c5a302a5cca SHA512 c026e57fcb900617029d9aa85e7c9d069f92bc47451b01ba1efbe4177a8384df365e121981a2ea6802f6e8483810ad0e73cf5f48be0107a53c96cdf8cf887529 WHIRLPOOL bcff2158636a67d85a7d64608ae2b0a39ee222d4e19d080d6d84dda448f4b19621ad5929c6804b0a4060c68cc8f29cd29952b723e76eec3e05179c130d973937
-EBUILD eugene-4.1.ebuild 1066 SHA256 42b85e9b8dff96f5b717ee9adc94ddbd0ea85e797dd4281d2808097fcfa710b1 SHA512 819e9357c0d0ad41f57f9f5c871da2f8d612e8f57d2b99547940c1777ddbc324f4b90b954972cc52d3292ed1e8ddbd142b27f9d1b8a8c37492db124a0f3bd286 WHIRLPOOL 5a80fad7aca60116449e20f2bb3439b2e6c1a9941448ea9eb845f0513df80884da7ab07c904532b8bea352f6dbbc58ed0187d2dd0ff18f48d767011ba8423b12
-MISC ChangeLog 1488 SHA256 9e7c60879962ddc8d529ff4e7d85c0b2ca796385471f1a0d5b154afd5e24e2b5 SHA512 00eaac32ac2b2dd1f171e24b1a9ae403a0f1baacdf45a34d2c79d9ea4eac79d18fcc8a5afee2899e720a25ac1b2c2a78d56cc14ac470b3d89f8f0f6e5a0eaf60 WHIRLPOOL e57b9c44177be7f0ba3ada2f2022f9596242182bd4547230f69a92e2e97367cb11cce67dca3e16891047b6bfb605290422a650b59a2fba872742cef0e094604c
+EBUILD eugene-3.6-r1.ebuild 1133 SHA256 d2f29d0f837b5e8043db68b4590b93bb894be11a744c067a3333391bc0b1963d SHA512 88d997ee9a940591b827b2bb921711777177c5178d40b2fe02a161e16fb68c4a76f7e1a8c01da8d45b1330852622bf69c373ed95afe636da49369d903f03b92b WHIRLPOOL 9db7c3d98cc0e8a7f67d114e66ec338bf39bf4000a877258a2553fc4af2ebaf08c19eed736175743d603bc3de5297b7fde2e0c5da9fff4eff98c7b4a84e6e5ae
+EBUILD eugene-4.1.ebuild 904 SHA256 13084e6fff95500ecf0c8edbc1589e305ef18236b9cb1f3d2efb9c9e6257cbb7 SHA512 ae027aebebc13e2682ca60194e6072853149887706c132a3f3a34768e92378fa06ceed8ca8599c5294eb39357ee366914af62c20e023242a62010ff2977e97d9 WHIRLPOOL d8d5214105df9eefd72a7759844fd26a5dc55ebba3e9f74ae64ca05a9eb1e746dbfc15712276626a1d36e405e2f9f1cad212febee451f4d1859b6151271e08ab
+MISC ChangeLog 1719 SHA256 fca910f1eba8f1a96efa41fea06969f9c3f0e7146f0dec1e9ab441f9405d7279 SHA512 d332a20c488f0c0b39f01a97c301b8234501ca6d56f2bf4bb64cc4fe38bd44a0c0e350b3ee1ebeb0e898d2bfa80e5e1aea36294dd8339ce7540120bf5a75d325 WHIRLPOOL 7c3481c44f34bf3282056dba40a03f7c8ef409c0601b982aaf0f36cbc8b51aac1fbc111c85f297b59e388fdc41dfdf7736df0a29ad1b6b06c55a53db1661de81
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.19 (GNU/Linux)
+Version: GnuPG v2.0
 
-iEYEAREKAAYFAlE7jIIACgkQgAnW8HDreRb93ACeK+QCY5aJ/VxaQADuz+uWwkjC
-WAMAoMnsM8zWvHQOBL/+P054XnchOc9v
-=1bkV
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+=IteD
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diff --git a/sci-biology/eugene/eugene-3.5g.ebuild b/sci-biology/eugene/eugene-3.5g.ebuild
deleted file mode 100644 (file)
index 82e3a98..0000000
--- a/sci-biology/eugene/eugene-3.5g.ebuild
+++ /dev/null
@@ -1,42 +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/eugene/eugene-3.5g.ebuild,v 1.2 2009/10/31 17:58:24 maekke Exp $
-
-EAPI=2
-
-inherit autotools
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
-# self-signed https SRC_URI
-#SRC_URI="http://mulcyber.toulouse.inra.fr/gf/download/frsrelease/220/3675/${P}-1.tar.gz"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-RESTRICT="test"
-
-DEPEND="media-libs/gd[png]
-       media-libs/libpng
-       doc? ( dev-lang/tcl
-               dev-texlive/texlive-latex
-               dev-texlive/texlive-latexrecommended
-               dev-texlive/texlive-latexextra
-               )"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-       if ( ! use doc ); then
-               sed -i -e '/SUBDIRS/ s/doc//' \
-                       -e '/INSTALL.*doc/ s/\(.*\)//' \
-                       Makefile.am || die
-               eautoreconf
-       fi
-}
-
-src_install() {
-       emake DESTDIR="${D}" install || die
-}

diff --git a/sci-biology/eugene/eugene-3.6-r1.ebuild b/sci-biology/eugene/eugene-3.6-r1.ebuild
index 088f0bb3b39e3823c2ae77a858c6867dcd9942cf..702b1c551d6d01a293ddf00f09053373b7025c56 100644 (file)
--- a/sci-biology/eugene/eugene-3.6-r1.ebuild
+++ b/sci-biology/eugene/eugene-3.6-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6-r1.ebuild,v 1.4 2011/02/11 19:51:04 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6-r1.ebuild,v 1.5 2015/03/20 16:38:39 jlec Exp $
 
 EAPI=2
 
@@ -20,8 +20,8 @@ KEYWORDS="amd64 x86"
 RESTRICT="test"
 
 DEPEND="media-libs/gd[png]
-       media-libs/libpng
-       doc? ( dev-lang/tcl
+       media-libs/libpng:0
+       doc? ( dev-lang/tcl:0
                dev-texlive/texlive-latex
                dev-texlive/texlive-latexrecommended
                dev-texlive/texlive-latexextra

diff --git a/sci-biology/eugene/eugene-4.1.ebuild b/sci-biology/eugene/eugene-4.1.ebuild
index 15a663c1e63fac2f9a7577b40383c3be0bb8c0d1..acbcbf4a1cd8d033391c117b5605d0a4dc25f854 100644 (file)
--- a/sci-biology/eugene/eugene-4.1.ebuild
+++ b/sci-biology/eugene/eugene-4.1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-4.1.ebuild,v 1.1 2013/03/09 19:24:45 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-4.1.ebuild,v 1.2 2015/03/20 16:38:39 jlec Exp $
 
 EAPI=5
 
@@ -12,17 +12,13 @@ SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1157/${P}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
-IUSE="doc"
 KEYWORDS="~amd64 ~x86"
+IUSE=""
 
 DEPEND="
        media-libs/gd[png]
-       media-libs/libpng
-       doc? ( dev-lang/tcl
-               dev-texlive/texlive-latex
-               dev-texlive/texlive-latexrecommended
-               dev-texlive/texlive-latexextra
-               )"
+       media-libs/libpng:0=
+       "
 RDEPEND="${DEPEND}"
 
 RESTRICT="test"
@@ -31,15 +27,11 @@ src_prepare() {
        # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
        epatch \
                "${FILESDIR}"/${PN}-3.6-overflow.patch \
-               "${FILESDIR}"/${PN}-3.6-plugins.patch
-       if ( ! use doc ); then
-               sed -i -e '/SUBDIRS/ s/doc//' \
-                       -e '/INSTALL.*doc/ s/\(.*\)//' \
-                       Makefile.am || die
-               eautoreconf
-       fi
-}
-
-src_install() {
-       emake DESTDIR="${D}" install || die
+               "${FILESDIR}"/${PN}-3.6-plugins.patch \
+               "${FILESDIR}"/${P}-format-security.patch
+       sed \
+               -e '/SUBDIRS/ s/doc//' \
+               -e '/INSTALL.*doc/ s/\(.*\)//' \
+               -i Makefile.am || die
+       eautoreconf
 }

diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch
new file mode 100644 (file)
index 0000000..e6e4a6c
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-4.1-format-security.patch
@@ -0,0 +1,16 @@
+ src/Hits.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Hits.cc b/src/Hits.cc
+index edfe178..b228be6 100755
+--- a/src/Hits.cc
++++ b/src/Hits.cc
+@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int
+     while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
+                         &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
+     {
+-        if (HSP) fprintf(stderr,HSP);
++        if (HSP) fprintf(stderr, "%s", HSP);
+         if (phase < 0  &&  deb > fin)
+         {
+             int tmp = deb;