sci-biology/mira: Fix for boost >1.50, #425468

(Portage version: 2.2.0_alpha142/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

4 files changed, 128 insertions, 7 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index a02f37d83202..deab5fc1068a 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.18 2012/07/08 18:01:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.19 2012/11/07 22:10:54 jlec Exp $
+
+*mira-3.2.1-r1 (07 Nov 2012)
+
+  07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild,
+  +mira-3.2.1-r1.ebuild, +files/mira-3.2.1-boost-1.50.patch:
+  Fix for boost >1.50, #425468
 
   08 Jul 2012; Justin Lecher <jlec@gentoo.org> -mira-3.0.5.ebuild,
   -mira-3.2.0.ebuild:
diff --git a/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch
new file mode 100644
index 000000000000..27fb36467c8f
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch
@@ -0,0 +1,52 @@
+ config/m4/ax_boost_regex.m4          | 4 ++--
+ src/examples_programming/Makefile.am | 2 +-
+ src/examples_programming/Makefile.in | 2 +-
+ 3 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 3c4a999..a3bb19b 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,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/src/examples_programming/Makefile.am b/src/examples_programming/Makefile.am
+index d77daaf..09c9965 100644
+--- a/src/examples_programming/Makefile.am
++++ b/src/examples_programming/Makefile.am
+@@ -11,7 +11,7 @@ AM_LDFLAGS= -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L..
+ 
+ mira_101.C: 
+ mira_101_SOURCES= mira_101.C
+-mira_101_LDADD= -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK)
++mira_101_LDADD= -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system
+ 
+ read_101.C: 
+ read_101_SOURCES= read_101.C
+diff --git a/src/examples_programming/Makefile.in b/src/examples_programming/Makefile.in
+index 27e6515..7dae4c4 100644
+--- a/src/examples_programming/Makefile.in
++++ b/src/examples_programming/Makefile.in
+@@ -222,7 +222,7 @@ AM_CXXFLAGS = $(BOOST_CPPFLAGS)
+ INCLUDES = -I$(top_srcdir)/src $(all_includes)
+ AM_LDFLAGS = -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L../EdIt/ -L../caf/ -L../knn_abi373 -L../knn_alf $(BOOST_LDFLAGS)
+ mira_101_SOURCES = mira_101.C
+-mira_101_LDADD = -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK)
++mira_101_LDADD = -lmira  -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB)  $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system
+ read_101_SOURCES = read_101.C
+ read_101_LDADD = -lmirasupport -lmiraerrorhandling  -lmirautil -lmiradptools -lmirafio -lm -lz
+ readpool_101_SOURCES = readpool_101.C
diff --git a/sci-biology/mira/mira-3.2.1-r1.ebuild b/sci-biology/mira/mira-3.2.1-r1.ebuild
new file mode 100644
index 000000000000..c6bddae49f03
--- /dev/null
+++ b/sci-biology/mira/mira-3.2.1-r1.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-3.2.1-r1.ebuild,v 1.1 2012/11/07 22:10:54 jlec Exp $
+
+EAPI=4
+
+MIRA_3RDPARTY_PV="17-04-2010"
+
+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"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+
+CDEPEND="
+	dev-libs/boost
+	dev-util/google-perftools"
+DEPEND="${CDEPEND}
+	dev-libs/expat"
+RDEPEND="${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 \
+		"${FILESDIR}"/${PN}-3.0.0-asneeded.patch \
+		"${FILESDIR}"/${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"
+}
diff --git a/sci-biology/mira/mira-3.2.1.ebuild b/sci-biology/mira/mira-3.2.1.ebuild
index e16486f8073f..097615084e00 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 1.5 2012/06/25 20:26:51 mr_bones_ Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1.ebuild,v 1.6 2012/11/07 22:10:54 jlec Exp $
 
 EAPI="3"
 
@@ -10,15 +10,17 @@ 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/${P}.tar.bz2
+SRC_URI="
+	mirror://sourceforge/mira-assembler/${P}.tar.bz2
 	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
 
-LICENSE="GPL-2"
 SLOT="0"
+LICENSE="GPL-2"
 IUSE=""
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos"
 
-CDEPEND=">=dev-libs/boost-1.41.0-r3
+CDEPEND="
+	dev-libs/boost
 	dev-util/google-perftools"
 DEPEND="${CDEPEND}
 	dev-libs/expat"
@@ -35,8 +37,8 @@ src_prepare() {
 
 src_configure() {
 	econf \
-		--with-boost="${EPREFIX}"/usr/$(get_libdir) \
-		--with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
+		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
+		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
 		--with-boost-thread=boost_thread-mt
 }