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

6 files changed, 136 insertions, 0 deletions

diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest
new file mode 100644
index 000000000000..f9ad87f8424e
--- /dev/null
+++ b/sci-biology/maqview/Manifest
@@ -0,0 +1 @@
+DIST maqview-0.2.5.tar.gz 383410 SHA256 156794f114a00bb455a47ccefa50782441dc1b9668b6e7439ce0674060c085cb SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6 WHIRLPOOL 0ba5a15a1317b4bb78458b9e282348983be9e2c30980aef4e35a9f5dacfff57226eaa4403fb0b9d9d448ba033409d548db224ed544ad365226a8fb59be8b743e
diff --git a/sci-biology/maqview/files/0.2.5-ldflags.patch b/sci-biology/maqview/files/0.2.5-ldflags.patch
new file mode 100644
index 000000000000..92b9a3ed58ac
--- /dev/null
+++ b/sci-biology/maqview/files/0.2.5-ldflags.patch
@@ -0,0 +1,46 @@
+ configure.ac |   18 +++---------------
+ 1 files changed, 3 insertions(+), 15 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 90e612b..5a00d15 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -9,17 +9,10 @@ AC_PROG_INSTALL
+ AC_STDC_HEADERS
+ 
+ is_static=0
+-case ${prefix} in
+-  NONE);;
+-  *) is_static=1
+-     AC_MSG_WARN([Library libglut will be statically linked.])
+-     LDFLAGS="-L${prefix}/lib"
+-     CPPFLAGS="-I${prefix}/include";;
+-esac
+ 
+ # set CFLAGS and LDFLAGS
+ 
+-true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS"
++true_CFLAGS="-DMAQ_LONGREADS"
+ case "${host_os}" in
+   darwin*)
+     GLLIBS="-framework OpenGL -framework GLUT"
+@@ -30,17 +23,12 @@ case "${host_os}" in
+ 	  i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";;
+ 	esac
+ 	AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"])
+-    AC_ARG_ENABLE(static, [  --enable-static         statically link GLUT (Linux Only)],
+-				  [is_static=1])
+-    case $is_static in
+-      1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";;
+-	  0) GLLIBS="-lGL -lglut -lm";;
+-    esac
++	GLLIBS="-lGL -lglut -lm -lGLU"
+ 	AC_SUBST([GLLIBS]);;
+ #  *) AC_MSG_ERROR([OS is not supported]);;
+ esac
+ AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1])
+-CFLAGS=$true_CFLAGS
++CFLAGS="${CFLAGS} $true_CFLAGS"
+ 
+ AC_CONFIG_FILES([Makefile])
+ AC_OUTPUT
diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch
new file mode 100644
index 000000000000..cd35273de66b
--- /dev/null
+++ b/sci-biology/maqview/files/0.2.5-zlib.patch
@@ -0,0 +1,33 @@
+ Makefile.am |    6 +++---
+ zrio.c      |    2 +-
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index dad515a..9617eb7 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,8 +1,8 @@
+ bin_PROGRAMS = zrio maqindex maqview maqindex_socks
+-zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \
+-		   infback.c inftrees.c trees.c uncompr.c zutil.c
+-generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src)
++generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c
++LIBS = -lz
+ zrio_SOURCES = zrio_main.c $(generic_src)
++zrio_LDADD = -lz
+ maqindex_SOURCES = maqmap_index_main.c $(generic_src)
+ maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \
+ 				  $(generic_src)				  
+diff --git a/zrio.c b/zrio.c
+index ffed00a..fe744df 100644
+--- a/zrio.c
++++ b/zrio.c
+@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void
+             totin += strm.avail_in;
+             totout += strm.avail_out;
+ 			tmp = strm.avail_out;
+-            ret = inflate_zr(&strm, Z_BLOCK);      /* return at end of block */
++            ret = inflate(&strm, Z_BLOCK);      /* return at end of block */
+             totin -= strm.avail_in;
+             totout -= strm.avail_out;
+ 			if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout);
diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
new file mode 100644
index 000000000000..043208bb79b5
--- /dev/null
+++ b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
@@ -0,0 +1,16 @@
+ stdhash.hh | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/stdhash.hh b/stdhash.hh
+index eaf98af..f22c5a6 100644
+--- a/stdhash.hh
++++ b/stdhash.hh
+@@ -493,7 +493,7 @@ public:
+ 	inline bool insert(const keytype_t &key, const valtype_t &val) {
+ 		rehash();
+ 		hashint_t i;
+-		int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
++		int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
+ 		vals[i] = val;
+ 		if (ret == 0) return true;
+ 		if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
diff --git a/sci-biology/maqview/maqview-0.2.5-r2.ebuild b/sci-biology/maqview/maqview-0.2.5-r2.ebuild
new file mode 100644
index 000000000000..e549497830bd
--- /dev/null
+++ b/sci-biology/maqview/maqview-0.2.5-r2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler"
+HOMEPAGE="http://maq.sourceforge.net/"
+SRC_URI="mirror://sourceforge/maq/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="
+	media-libs/freeglut
+	sys-libs/zlib"
+RDEPEND="${DEPEND}
+	sci-biology/maq"
+
+S="${WORKDIR}/${PN}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-ldflags.patch
+	"${FILESDIR}"/${PV}-zlib.patch
+	"${FILESDIR}"/${P}-gcc4.7.patch
+	)
diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml
new file mode 100644
index 000000000000..79ebcc09421b
--- /dev/null
+++ b/sci-biology/maqview/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">maq</remote-id>
+  </upstream>
+</pkgmetadata>