Version bump

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 127 insertions, 2 deletions

diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog
index d60721f7ef3e..2c5613175b04 100644
--- a/sci-biology/seaview/ChangeLog
+++ b/sci-biology/seaview/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/seaview
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/ChangeLog,v 1.29 2009/10/07 18:36:07 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/ChangeLog,v 1.30 2009/10/18 22:49:14 weaver Exp $
+
+*seaview-4.2 (18 Oct 2009)
+
+  18 Oct 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/seaview-4.2-gcc44.patch, +seaview-4.2.ebuild:
+  Version bump and gcc-4.4 patch
 
   07 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml,
   +seaview-4.1.ebuild, seaview-20071113.ebuild:
diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
index 4af5c2a96225..e11a2ab70d37 100644
--- a/sci-biology/seaview/Manifest
+++ b/sci-biology/seaview/Manifest
@@ -1,8 +1,11 @@
 AUX seaview-20071113-glibc-2.10.patch 545 RMD160 c8e5f91d20b08a902fc88706a52e6664340f7d1d SHA1 ca1026d79a56ce687bb62237a23a70a9022996ef SHA256 97d670caea6584417851b3da260353043ec73d60349b4a12a2b9fbcbf597f509
+AUX seaview-4.2-gcc44.patch 1291 RMD160 31bab0d688f189266e338038f3c5c37a040cc817 SHA1 6fc02cc3531b935620f12ebd8a698aa75930e7a7 SHA256 84d846adb6ff40ae94e4203c3196aecc8fd85f6865d6c2406b113e1f12826305
 AUX seaview.desktop 207 RMD160 d5b4e57a1866d5f2d384ab1f6acf21292061570f SHA1 38b4a0b0055da291020690e9ac1974d7aed94871 SHA256 314a791477d6059888bce45de2627d58d1b8998a25200d6a9eb8f13c759c7b32
 DIST seaview-20071113.tar.gz 155890 RMD160 1a0b82137e1546eed7e69392a241e7af0e5c3068 SHA1 0928a9729142ebe0fcc32b612150a09ee663eddf SHA256 93335e7e95255a189a5f89cd8fd40a22e3e096727ab30f31b6383c85854c709f
 DIST seaview_4.1.tar.gz 315678 RMD160 de3a7f3e684d73508cf6d9ab0d004549d9abdbf9 SHA1 d8227d0e91dff3221b09ea415e1201d833ead5c5 SHA256 902c6cd8e0f7fb17a4d2849bec3312d9cde94fceb1d7fd02c4242b986f693468
+DIST seaview_4.2.tar.gz 322095 RMD160 b4218953f56d466158e7fee335122ad8893a0aea SHA1 678cbb369e91422426ba66b61287e55e6bad0549 SHA256 eed5620d4462086f6897b7fafd9a40fb62aa4a5791e84c573b975ec65b43fe25
 EBUILD seaview-20071113.ebuild 1505 RMD160 d36b5c3a7941dafdaa9be9219aebe04b31c04578 SHA1 79c84456ff1db956d88b011999264941b4839455 SHA256 0649c61169c8d623461bb8697ce7b2d8f7a9821d23c7eb79afd6882962879068
 EBUILD seaview-4.1.ebuild 2338 RMD160 d2b326d632df2ba6e59f94891a158b0815a73932 SHA1 419a7ef3bcf42c781fff75c7d2a850d8a81a8d94 SHA256 f4880536ce09f67b5686f30f9caacb29e8b0e3a46edd5048a3c9497538ea7deb
-MISC ChangeLog 5247 RMD160 68126a13509ac5b8af0c36da4eeefe8eb8e587cf SHA1 a4070de6a3f38f23bede426dd20ce44df0f3dd5d SHA256 14ac970640e645405972ab9632893a3316d1f114f72788225ce79fa0466254b7
+EBUILD seaview-4.2.ebuild 2455 RMD160 34aebdb6f06809bdd8018fb1c68d3ea4beef5080 SHA1 2ba5359661b9b33e866662cb205ae13a82c6f69e SHA256 c2dd116d6f46f914e05783764b70ac48a56a93f0f45af7a11a4f75d4cf4e4e87
+MISC ChangeLog 5414 RMD160 e2c386f63e919d07a4dd5d68d9397d72a7a0705f SHA1 ce9de0e0ecd5b29575aa9fdc93ee8b9c4721f8e3 SHA256 469ab78703a70327f025a9612019f13f52f57867e901bcc8e8ca8ddb20b1e213
 MISC metadata.xml 619 RMD160 f7bd8491d8c59372963d3f53e322e52d509c0c81 SHA1 d35f32cd0b1171a837f6c9d0dbeb3e396a44fb90 SHA256 ee63d33ca527ca555056c6bc3a7d89fa9b5f32e5f82b7eae27b1c030c80ced9e
diff --git a/sci-biology/seaview/files/seaview-4.2-gcc44.patch b/sci-biology/seaview/files/seaview-4.2-gcc44.patch
new file mode 100644
index 000000000000..e472ea96048c
--- /dev/null
+++ b/sci-biology/seaview/files/seaview-4.2-gcc44.patch
@@ -0,0 +1,36 @@
+diff -durr seaview.orig/seaview.cxx seaview/seaview.cxx
+--- seaview.orig/seaview.cxx	2009-10-12 14:33:40.000000000 +0000
++++ seaview/seaview.cxx	2009-10-18 17:02:56.612201461 +0000
+@@ -3903,7 +3903,7 @@
+ if( clipboard_contains_alignment(clipboard) ) {
+ 	char **seqs, **seqnames, **comments, *p, *message; 
+ 	int i, count, num, changedwname = FALSE;
+-	p = strchr(clipboard, ':') + 1;
++	p = const_cast<char*>(strchr(clipboard, ':')) + 1;
+ 	count = read_mase_seqs_header(p, &seqs, &seqnames, 
+ 		&comments, NULL, &message);
+ 	if(count == 0) return;
+diff -durr seaview.orig/use_mase_files.cxx seaview/use_mase_files.cxx
+--- seaview.orig/use_mase_files.cxx	2009-10-10 15:36:30.000000000 +0000
++++ seaview/use_mase_files.cxx	2009-10-18 17:02:56.612201461 +0000
+@@ -1523,7 +1523,7 @@
+ void inform_prog_dir(const char *arg0)
+ {
+ char *p;
+-if((p = strrchr(arg0, '/')) != NULL) {
++if((p = const_cast<char*>(strrchr(arg0, '/'))) != NULL) {
+ 	memcpy(seaview_prog_dir, arg0, p - arg0 + 1);
+ 	seaview_prog_dir[p - arg0 + 1] = 0;
+ 	}
+@@ -1764,9 +1764,9 @@
+ 	char *p;
+ 	
+ #if defined(WIN32)
+-	p = strrchr(pathname,'\\'); 
++	p = const_cast<char*>(strrchr(pathname,'\\')); 
+ #else
+-	p = strrchr(pathname,'/'); 
++	p = const_cast<char*>(strrchr(pathname,'/')); 
+ #endif
+ 	if(p == NULL) dirname[0] = 0;
+ 	else {
diff --git a/sci-biology/seaview/seaview-4.2.ebuild b/sci-biology/seaview/seaview-4.2.ebuild
new file mode 100644
index 000000000000..9b4964d418be
--- /dev/null
+++ b/sci-biology/seaview/seaview-4.2.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/seaview-4.2.ebuild,v 1.1 2009/10/18 22:49:14 weaver Exp $
+
+EAPI="2"
+
+inherit toolchain-funcs multilib eutils base
+
+DESCRIPTION="A graphical multiple sequence alignment editor"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+pdf +xft"
+
+DEPEND="x11-libs/fltk:1.1
+	pdf? ( media-libs/pdflib )
+	xft? (	x11-libs/libXft
+			x11-libs/fltk[xft] )"
+RDEPEND="${DEPEND}
+	sci-biology/clustalw
+	|| ( sci-libs/libmuscle sci-biology/muscle )
+	sci-biology/phyml"
+
+S="${WORKDIR}/${PN}"
+
+PATCHES=( "${FILESDIR}/seaview-4.2-gcc44.patch" )
+
+src_prepare() {
+	# respect CXXFLAGS (package uses them as CFLAGS)
+	sed -i \
+		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
+		-e "s:\$(OPT):${CXXFLAGS}:" \
+		-e "s:^OPT:#OPT:" \
+		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cxxflags):" \
+		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
+		-e "s:^USE_XFT:#USE_XFT:" \
+		-e "s:^#HELPFILE:HELPFILE:" \
+		-e "s:^#PHYMLNAME:PHYMLNAME:" \
+		Makefile || die "sed failed while editing Makefile"
+
+	if use pdf; then
+		sed -i \
+			-e "s:PDF_PS_FLAGS = -DNO_PDF:#PDF_PS_FLAGS = -DNO_PDF:" \
+			-e "s:PDF_PS = postscript:#PDF_PS = postscript:" \
+			-e "s:#PDF_INC = \$(HOME)/PDFlibLite:PDF_INC = /usr/include:" \
+			-e "s:#PDF_LIB = \$(HOME)/PDFlibLite:PDF_LIB = /usr/lib:" \
+			-e "s:#PDF_PS = pdf:PDF_PS = pdf:" \
+			-e "s:#PDF_PS_FLAGS = -I\$(PDF_INC):PDF_PS_FLAGS = -I\$(PDF_INC):" \
+			-e "s:#LPDF = -L\$(PDF_LIB) -lpdf:LPDF = -L\$(PDF_LIB) -lpdf:" \
+			Makefile || die "sed failed while editing Makefile to enable pdf output"
+	fi
+
+	if use xft; then
+		sed -i \
+			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $(xft-config --cflags):" \
+			-e "s:-lXft:$(xft-config --libs):" \
+			Makefile || die "sed failed while editing Makefile to enable xft"
+	else
+		sed -i -e "s:-lXft::" Makefile || die
+	fi
+	base_src_prepare
+}
+
+src_install() {
+	dobin seaview || die
+
+	# /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
+	insinto /usr/share/seaview
+	doins example.nxs seaview.html
+
+	insinto /usr/share/seaview/images
+	doins seaview.xpm || die
+
+	make_desktop_entry seaview Seaview /usr/share/pixmaps/seaview.xpm || die
+
+	doman seaview.1 || die
+}