sci-biology/mira: Version Bump, #377807

Package-Manager: portage-2.2.0_alpha142/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

6 files changed, 107 insertions, 11 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index deab5fc1068a..93cb6f858459 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/mira
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.19 2012/11/07 22:10:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.20 2012/11/07 22:29:55 jlec Exp $
+
+*mira-3.4.0.2 (07 Nov 2012)
+
+  07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild,
+  mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild,
+  +files/mira-3.4.0.2-boost-1.50.patch:
+  Version Bump, #377807
 
 *mira-3.2.1-r1 (07 Nov 2012)
 
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index f40e3908ed84..1540f6a3fb58 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -3,16 +3,20 @@ Hash: SHA512
 
 AUX mira-3.0.0-asneeded.patch 1468 SHA256 17dec784921baccf2c515f7c269209b5cdeb23143b3412e8ad967e74682ee71f SHA512 23f151eb138a216f329b9fefc8b014391915dd5d578b36ac87b4b7f52277313ae8081011b6839882dcb991524ad674ff22bfd7d6d2a91d28f9e5ff19d41e2f3d WHIRLPOOL b3d37aa5b5963cd75a9c9d4d513351c408aa315f40a07acfb8b8c1998f032ad3df50819786e8f31c7c411cd07b08f1609b4e9f78e4305a97eaf23255a3893ec5
 AUX mira-3.2.1-boost-1.50.patch 3672 SHA256 35bebb987d6192889a1cce84fae822e61d607e80cbaadb0ff1703935f8707ead SHA512 5b0cee936ca68ac57c6c8da4b8ab60e582f6ea1b89f5e02eae5562cd299b5f7bffe12454b55088da46d0e04212499aea72f3702619c9854d99792eb27f7b8995 WHIRLPOOL 08636d66e3d1443c392f798d61f7041ffdb727cb96d1a980e6091217577f75c1703cb172f8dc5d511ef2854e531e0af77bc2a8b58126f991010b7fc7e2877718
+AUX mira-3.4.0.2-boost-1.50.patch 1577 SHA256 66edfe52daf8e84844f20d7425b476a8fae95704226493bced687fd1026ec8e6 SHA512 60e8da6d56385114056f16292fb8e6de63498dbd587b12c26724d9007e8f7eea7550f1dac387035768d7fa76fdffcc7c5baac9b0f92b58bec8c269cf3f397cdf WHIRLPOOL 2fe35917e9b7a8f66ef30b19afc495ffba391aef0e64c695d2733959b12119b2b45d6e79390721e794fcb6bc029af71e3c84bf657bf5e485a1ca8295208623ea
 DIST mira-3.2.1.tar.bz2 9626154 SHA256 86a2c00d182573008ef41f7725aec72ea69756ea9f3dc7e798a7d253a47f8bd7 SHA512 56b2bac26d86f1c6a1aef829e168e53d931e6211078966e4ce5464ef26fbce4395c448521bf7d35f74080c00b4efbf6597b2713b276f04683433c32fdcb1199d WHIRLPOOL 85531afa6f7593de938c922e88871104bdd837271448615a23fcd2042b71e1ef9b7900f1906bb64349cad17f4f66f3d958e6aa2148239738e4c45d320a01185f
+DIST mira-3.4.0.2.tar.bz2 10225270 SHA256 5cf24fc6760723b7b8d4d239ee25eb5471e50080aa9bca2c1b01a30be6ae808c SHA512 3d74af98fa1a72892a04579110a74d986170572aca42983e5526ff58a76f2defdacee8d9a5e61cfc685639d41197308493e733aa8b527eba74d21942ca4dc7db WHIRLPOOL 2935ddfe542960d586cfa010cd4e6849d2e9765c4bca384adde38fae4ac95ee654f552958148b3f0d6d27a81246d7443ee6979b5723a959284c5ee39061c78cf
+DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
 DIST mira_3rdparty_17-04-2010.tar.bz2 31296 SHA256 ec2c77508d75b7c28d3d26137ab69648b1ed653af93d486245ad0e4624e332b2 SHA512 7ed99c24b9f01066398e163320d26e5d7028c9cb5e80ba69e733211863a693391e9b203eb9202afaf8f576bff539a80b476a2230ad0e76b6c0b14dfaf668cb27 WHIRLPOOL 34751ad928aa15f58f7806eddaeb5b245c786d6145369167e9f3644450249b8e2b67c37e9014c9eedd64682409faaa77f215cad9fef5c4de69f3352c5bc33d21
-EBUILD mira-3.2.1-r1.ebuild 1713 SHA256 f423aa28f7277d936526c5b54fc1096815b4810c5e140e3717787ee349e11697 SHA512 4c51d572413e30fdffc95dd3b6e9917f9e53256223c43a5b6b9e6cc56ba63123355c5b4fa525bf893cb70286edb06e34f73fb03760b6975f2f91f2c74e98ee53 WHIRLPOOL a958d8db4cfe13fada34ecd281f539d427e151d01760b73a63d9d34e95b62facb83e23c084aaba3c27021e01ec86f1dc2f7bfbf415764f7c3a9f2d7c068f7ba6
-EBUILD mira-3.2.1.ebuild 1673 SHA256 b22e35de2b23cfbfb4cabf2bebe8f9e68f4e2b5ad1238e4ada97e592c231a6c9 SHA512 52d29f5a74e4222e10959adba6b67d148f8015784027241020e1e5e1b2412b510df12172511c15c8ffd29d7b52182ac5c6154fe204335188f1afc7e76a6f0dbb WHIRLPOOL 6eb35bf97efb8c1b655558afc9e81411784c2a8935b8ab27aa173d343e21bfaaa6ccd7fe6caf45629a6eaed3f0fe009be3ecb5364ea874205d61912b530d25a2
-MISC ChangeLog 2714 SHA256 941ebedb8a6d3d3a400f6a10a3770748b8325c456d0083d1996a9ce3bc4c0f47 SHA512 8cab98c5269a4599cc5c21c7691695a525be94d9e6eef6ea900741482eade26d94fe2d9fb2dd734ead7a9459ebcbf1c231674f83fb8544c5ef90239c68229ed7 WHIRLPOOL 02a40f2e4ff9e83b6bdb7640b1af27321b64b48966cfc65c58b1f4cf47903332b0452d1fb1e4a4aafee3026dffe6d0dbec3929233504000db318affabb750317
+EBUILD mira-3.2.1-r1.ebuild 1713 SHA256 9ca51eaec1d05fbb7b90c65f872b9d1be7fd679d5dbcb0195232889a8188ef9e SHA512 e229acd584521c4731d9481fd0c9936a0a2f55067d3b8624eb02ee2b95122927c6a0d22efb4d9bf113020f29cf52f950d3de8ce0f9a78ef2d6d192b62ba7a6d8 WHIRLPOOL 5d6fa960e8df74021b601223c3fb3bd2fd0e1709dae1d4bcbabd49e889252733ca710ff89940e3facc4c031531f284ebb9c75c071b440623be89bf096ae5fc4c
+EBUILD mira-3.2.1.ebuild 1673 SHA256 7129a0691cc3210f29d4dada39a1eb64643661df2b2cbd49471f66bde2bfbd72 SHA512 1d188155ccce9caba3546949b46198d9e3fd79939a5a005b608e86d7b8d6c86550f4e8c65a769407022d0b109b6d0e8e5bab36301db0e9587734b62be966109a WHIRLPOOL a57d63d16a6a2464fbe96498202af3780ecb64b5b1ac1977eb5a84df3dc33f7a4ef36fcb046be596995e7708181c62a22b11c73ee3929cc476fc048e0e70cd7c
+EBUILD mira-3.4.0.2.ebuild 1689 SHA256 3d3a8c5882e7e2d012cc1d1af521c4ad63cfc11b57da84b29bb3fe8aeb06e63a SHA512 2ef505866e0d1d81f981c307082987e4a0d496cec8976f1cd51905d22e818d459e5b5d4cf97d015b2040f46e2f149107a0ca05031fea1c4bee2cf42d0c848779 WHIRLPOOL ef9712b1086cb5280e45396c0a99053227f021d5f8ef19b4bde4ba034a0f2a35b6b065b9eb187a48b3d7330b546929516d65adec4263157fad5341c76fdffea6
+MISC ChangeLog 2920 SHA256 5660ad5cc0b471494888367196f03be3b57e8c628e9e874b79fefa5d3f3cfb2a SHA512 07eacde87247f6775b646af7ce3e7c5bf3716290e17059d7e55f63f6b68069ecd47c5264f748f50ee72431695023d81d649d54efd7c15e754068c9861992c8df WHIRLPOOL 578eb76f1fce5368d2b7be605124ed9965225641d8d9bbb03b16eb7d2dc596c406bfc7c8c5bec70997311272e089fe036252bd2df6531e191ffea885ead542f2
 MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
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diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
new file mode 100644
index 000000000000..427192294c81
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
@@ -0,0 +1,24 @@
+ config/m4/ax_boost_regex.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 1ac06af..5b7be93 100644
+--- a/config/m4/ax_boost_regex.m4
++++ b/config/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
+                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 if test "x$link_regex" != "xyes"; then
+                 for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+                      ax_lib=${libextension}
+ 				    AC_CHECK_LIB($ax_lib, exit,
+-                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+                                  [link_regex="no"])
+ 				done
+                 fi
diff --git a/sci-biology/mira/mira-3.2.1-r1.ebuild b/sci-biology/mira/mira-3.2.1-r1.ebuild
index c6bddae49f03..b4d434df4a9b 100644
--- a/sci-biology/mira/mira-3.2.1-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1-r1.ebuild,v 1.1 2012/11/07 22:10:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1-r1.ebuild,v 1.2 2012/11/07 22:29:55 jlec Exp $
 
 EAPI=4
 
@@ -16,8 +16,8 @@ SRC_URI="
 
 SLOT="0"
 LICENSE="GPL-2"
-IUSE=""
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
 
 CDEPEND="
 	dev-libs/boost
diff --git a/sci-biology/mira/mira-3.2.1.ebuild b/sci-biology/mira/mira-3.2.1.ebuild
index 097615084e00..658a361a1112 100644
--- a/sci-biology/mira/mira-3.2.1.ebuild
+++ b/sci-biology/mira/mira-3.2.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1.ebuild,v 1.6 2012/11/07 22:10:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1.ebuild,v 1.7 2012/11/07 22:29:55 jlec Exp $
 
 EAPI="3"
 
@@ -16,8 +16,8 @@ SRC_URI="
 
 SLOT="0"
 LICENSE="GPL-2"
-IUSE=""
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
 
 CDEPEND="
 	dev-libs/boost
diff --git a/sci-biology/mira/mira-3.4.0.2.ebuild b/sci-biology/mira/mira-3.4.0.2.ebuild
new file mode 100644
index 000000000000..e3582fddd25c
--- /dev/null
+++ b/sci-biology/mira/mira-3.4.0.2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
+
+EAPI=4
+
+MIRA_3RDPARTY_PV="06-07-2012"
+
+inherit autotools base multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html"
+SRC_URI="
+	mirror://sourceforge/mira-assembler/${P}.tar.bz2
+	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
+
+CDEPEND="
+	dev-libs/boost
+	dev-util/google-perftools"
+DEPEND="${CDEPEND}
+	app-editors/vim-core
+	dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+
+src_prepare() {
+	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+	epatch \
+		"${FILESDIR}"/${P}-boost-1.50.patch
+	AT_M4DIR="config/m4" eautoreconf
+}
+
+src_configure() {
+	econf \
+		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
+		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
+		--with-boost-thread=boost_thread-mt
+}
+
+#src_compile() {
+#	base_src_compile
+#	# TODO: resolve docbook incompatibility for building docs
+#	#if use doc; then emake -C doc clean docs || die; fi
+#}
+
+src_install() {
+	base_src_install
+	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
+
+pkg_postinst() {
+	einfo "Documentation is no longer built, you can find it at:"
+	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}