Resepct LDFLAGS, do not link static, unbundle zlib, #298094, #337658, #366197

Package-Manager: portage-2.2.0_alpha31/cvs/Linux x86_64

5 files changed, 132 insertions, 3 deletions

diff --git a/sci-biology/maqview/ChangeLog b/sci-biology/maqview/ChangeLog
index 0c70ed74778d..459d63ce0ac8 100644
--- a/sci-biology/maqview/ChangeLog
+++ b/sci-biology/maqview/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/maqview
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/maqview/ChangeLog,v 1.3 2010/09/16 17:22:19 scarabeus Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/maqview/ChangeLog,v 1.4 2011/05/06 08:42:25 jlec Exp $
+
+*maqview-0.2.5-r1 (06 May 2011)
+
+  06 May 2011; Justin Lecher <jlec@gentoo.org> +files/0.2.5-ldflags.patch,
+  +files/0.2.5-zlib.patch, +maqview-0.2.5-r1.ebuild:
+  Resepct LDFLAGS, do not link static, unbundle zlib, #298094, #337658, #366197
 
   16 Sep 2010; Tomáš Chvátal <scarabeus@gentoo.org> maqview-0.2.5.ebuild:
   virtual/glut -> media-libs/glut
diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest
index 77445dabacd8..11d7a3f3cc8d 100644
--- a/sci-biology/maqview/Manifest
+++ b/sci-biology/maqview/Manifest
@@ -1,4 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 0.2.5-ldflags.patch 1335 RMD160 16ec62f6fbeb18d04faa2007a6f27c6b8c8ba522 SHA1 c93cf468e7832363935370234a3f55273583e2f2 SHA256 0876b98428f7964be91fb27f853458ba557ca8bf7eb313e416ece5a869a31efe
+AUX 0.2.5-zlib.patch 1437 RMD160 5899b4a88ac3abd81d301ff7225ef99ab013ff07 SHA1 8360080bba3ee73f2874f4a378ce3e568c14edc5 SHA256 0952ca78e6ec4474063e2049294f432abe28890e76923fdb69b262a8a0b73d26
 DIST maqview-0.2.5.tar.gz 383410 RMD160 4fbc58f8e015dbe712f2dce4ec074c85b95ebed1 SHA1 567e867d23c3a0855a989a17f1a59814eafef329 SHA256 156794f114a00bb455a47ccefa50782441dc1b9668b6e7439ce0674060c085cb
+EBUILD maqview-0.2.5-r1.ebuild 690 RMD160 853de2f84ffe03397166ab395a1cda92f8a99241 SHA1 b2aaedb3cc168b1834cfe591a9e09cf93a178db0 SHA256 a0c1c32dcd7f469a8df296f385726ccf7b5b0235e094455502da812e2232cf54
 EBUILD maqview-0.2.5.ebuild 693 RMD160 4469f2865c8ce58827583d8b7a739bdd7335a809 SHA1 56b04fb8e9e7c199fd496de030950455c4d19896 SHA256 3ea751f1768b69499e959f239996956c8e36bc2c3023a670053a7b5256a7d38a
-MISC ChangeLog 599 RMD160 0b088c5a7455c9bc9b7b89529a9a518db941cec4 SHA1 08ed6fa239ea377841f19d1d933c835ddd905ce9 SHA256 40a50492597ce05de2a9261f73f6bafd4c1828432b195b7754916cb5a13618c0
+MISC ChangeLog 836 RMD160 e654009652cfc3e1de80b0f44e9a7344233d21a7 SHA1 99f91d34bd2dc9aca2cbe734a21de49e2602459d SHA256 9525545bf8393970dc03c8264b50b9ad680b5ea0c0dbf7c7b4cdb5562dce6f41
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk3DtHcACgkQgAnW8HDreRYzJQCfUeSUi91Uyy6EUYDNXTjfrqLD
+rw0AnRkMRINnbtlRHX4EzxCMFHq85uFB
+=ISLK
+-----END PGP SIGNATURE-----
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/maqview-0.2.5-r1.ebuild b/sci-biology/maqview/maqview-0.2.5-r1.ebuild
new file mode 100644
index 000000000000..08a7885c2337
--- /dev/null
+++ b/sci-biology/maqview/maqview-0.2.5-r1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/maqview/maqview-0.2.5-r1.ebuild,v 1.1 2011/05/06 08:42:25 jlec Exp $
+
+EAPI=4
+
+inherit autotools eutils
+
+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}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-ldflags.patch \
+		"${FILESDIR}"/${PV}-zlib.patch
+	eautoreconf
+}