proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

7 files changed, 235 insertions, 0 deletions

diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
new file mode 100644
index 000000000000..87d089e34446
--- /dev/null
+++ b/sci-biology/mira/Manifest
@@ -0,0 +1,2 @@
+DIST mira-4.0.2.tar.bz2 10368046 SHA256 a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80 SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e WHIRLPOOL d038472f9b129e97883f59c471df51f07315ee38eda5a9e804cdd2d33988306162b1bb1dde2cb7fd510c82be5734240dfd69364d39865a47af439762c7154747
+DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
new file mode 100644
index 000000000000..9bbd267cf4c8
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
@@ -0,0 +1,56 @@
+http://bugs.gentoo.org/show_bug.cgi?id=305547
+
+--- config/m4/ax_lib_expat.m4
++++ config/m4/ax_lib_expat.m4
+@@ -96,6 +99,7 @@
+ 
+     EXPAT_CFLAGS=""
+     EXPAT_LDFLAGS=""
++    EXPAT_LIBS=""
+     EXPAT_VERSION=""
+ 
+     dnl
+@@ -105,7 +109,8 @@
+ 
+     if test -n "$expat_prefix"; then
+         expat_include_dir="$expat_prefix/include"
+-        expat_lib_flags="-L$expat_prefix/lib -lexpat"
++        expat_lib_flags="-L$expat_prefix/lib"
++        expat_libs="-lexpat"
+         run_expat_test="yes"
+     elif test "$expat_requested" = "yes"; then
+         if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then
+@@ -126,6 +131,8 @@
+         saved_LDFLAGS="$LDFLAGS"
+         LDFLAGS="$LDFLAGS $expat_lib_flags"
+ 
++        saved_LIBS="$LIBS"
++        LIBS="$LIBS $expat_libs"
+         dnl
+         dnl Check Expat headers
+         dnl
+@@ -171,7 +178,8 @@
+                     ]]
+                 )],
+                 [
+                 EXPAT_LDFLAGS="$expat_lib_flags"
++                EXPAT_LIBS="$expat_libs"
+                 expat_lib_found="yes"
+                 AC_MSG_RESULT([found])
+                 ],
+@@ -185,6 +193,7 @@
+ 
+         CPPFLAGS="$saved_CPPFLAGS"
+         LDFLAGS="$saved_LDFLAGS"
++        LIBS="$saved_LIBS"
+     fi
+ 
+     AC_MSG_CHECKING([for Expat XML Parser])
+@@ -194,6 +203,7 @@
+ 
+             AC_SUBST([EXPAT_CFLAGS])
+             AC_SUBST([EXPAT_LDFLAGS])
++            AC_SUBST([EXPAT_LIBS])
+ 
+             HAVE_EXPAT="yes"
+         else
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/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/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch
new file mode 100644
index 000000000000..14feb0284c9f
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cout.patch
@@ -0,0 +1,16 @@
+ src/progs/quirks.C | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/progs/quirks.C b/src/progs/quirks.C
+index 47e5ee8..060b6f3 100644
+--- a/src/progs/quirks.C
++++ b/src/progs/quirks.C
+@@ -25,6 +25,8 @@
+ 
+ #include <boost/filesystem.hpp>
+ 
++#include <iostream>
++
+ // make the "tcmalloc: large alloc" messages from TCMallom disappear
+ // by setting the reporting environment variable to a very large value
+ // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
new file mode 100644
index 000000000000..a2c7c1a0a6a7
--- /dev/null
+++ b/sci-biology/mira/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <upstream>
+    <remote-id type="sourceforge">mira-assembler</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
new file mode 100644
index 000000000000..3fa476c026a2
--- /dev/null
+++ b/sci-biology/mira/mira-4.0.2.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MIRA_3RDPARTY_PV="06-07-2012"
+MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
+
+inherit autotools eutils multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html"
+SRC_URI="
+	http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
+	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+#	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+#	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="doc"
+
+CDEPEND="
+	dev-libs/boost
+	dev-util/google-perftools"
+DEPEND="${CDEPEND}
+	app-editors/vim-core
+	dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+#	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
+
+src_prepare() {
+	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+	epatch \
+		"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
+		"${FILESDIR}"/${P}-cout.patch
+
+	sed \
+		-e "s:-O[23]::g" \
+		-e "s:-funroll-loops::g" \
+		-i configure.ac || die
+
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--with-boost="${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() {
+	default
+	dodoc ${DOCS[@]}
+
+	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
+}
+
+pkg_postinst() {
+	einfo "Documentation is no longer built, you can find it at:"
+	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}