sci-biology/emboss: Fix compilation problem with toplplot, #391669, thanks Juergen Rose for the patch

Package-Manager: portage-2.2.0_alpha142/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

4 files changed, 257 insertions, 19 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index fd0dd9332695..c9d8129d2fa4 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/emboss
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.67 2012/04/26 16:35:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.68 2012/11/19 10:36:45 jlec Exp $
+
+*emboss-6.3.1_p4-r1 (19 Nov 2012)
+
+  19 Nov 2012; Justin Lecher <jlec@gentoo.org> +emboss-6.3.1_p4-r1.ebuild,
+  +files/emboss-6.3.1_p4-r1_plcol.patch:
+  Fix compilation problem with toplplot, #391669, thanks Juergen Rose for the
+  patch
 
   26 Apr 2012; Justin Lecher <jlec@gentoo.org> -emboss-6.1.0.ebuild:
   Drop old
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index d3e3eb0b0d10..bc6a1b11e25d 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1,25 +1,27 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA512
 
-AUX 22emboss 110 RMD160 aa416dbfca66cc7822ed162122addadde2756c66 SHA1 c77b477bfdf0e77de4f29794e4fb2e7592557e48 SHA256 cf3bd3b8d2638a0cd14e57839033d63c855114a0e12883bbc7a5106b0cfc01ad
-AUX 6.3.1_p4-unbundle-libs.patch 18988 RMD160 0ecaec78052d8c302717113f4883316db84ba49c SHA1 8d10d947492eea2f338313f3e4c8faabfac747c7 SHA256 1f6170a8f4182792d145fd21b6b23d817ea9f5ea39ba77721947ae67a6b6927d
-AUX README.Gentoo 1326 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 SHA1 8cf13b8aa23c11f0af2aae06916970bf9d8a441f SHA256 33b517b977cc85824847bd6cf4113489a5554fb014f1a6b1d22d6f80c3487e9f
-AUX emboss-5.0.0-as-needed.patch 1751 RMD160 f43faab31a3d5afb4b73704ba597de578668ae48 SHA1 a108e5f68af9c14363bc56c849c9143fcb7675ba SHA256 e57a60d911e32f1aea16c079e2fd0910a5f7ed43752ea71094d3f3b7575617d3
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-DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
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-DIST EMBOSS-6.3.1.tar.gz 23572243 RMD160 5c1e7b82e50a183d6ccb323f6a619f10efb0da1a SHA1 efb2e9c1c9b038432ce6bd81ee4692d5f1dc2f72 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d
-DIST emboss-6.3.1_p4.patch.gz 4070 RMD160 cdfc45a39d33a78453a3f7a18913e18862b2d117 SHA1 5ce862eeaf5be628d64d44179aa37102faf53c85 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c
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+AUX emboss-5.0.0-as-needed.patch 1751 SHA256 e57a60d911e32f1aea16c079e2fd0910a5f7ed43752ea71094d3f3b7575617d3 SHA512 a2d978ce86fc3a63dc691059c4da598ccfb958d51097bc6070204ad6062f257b3ac496b852bb2772041bda087d0732cf03c4a4868462781700705da4faff8b59 WHIRLPOOL 101b8c89052dbc24211363e4fbe45e1407a30f8046013269d360b983a677ad5e62be796baf1d1097ae30dc392dc8db789d784dad51384e9c9b8df526b475a1d6
+AUX emboss-6.3.1_p4-r1_plcol.patch 3638 SHA256 dfaf85cf5c53a42047a75b1544ca44b450f2d4219c458c243bab53166f917b64 SHA512 63feed3dc32769b1c77ee79c4fd2f7d84d3d9bc6b716bc5f8dbef9ecff441432e7c1030b4d42e2da647231a27b6a7ae094b2115730ba8de94a363644d33ee489 WHIRLPOOL 7ba010b3a3a7eb116e4b0b85734648112fd4a6d780d32bde67a459fe23385b5f73a70d69b67b6d775992227ea90fb5edba21db1e4b51624aabfe5831b590e40d
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+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d
+DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c
+EBUILD emboss-6.0.1.ebuild 3464 SHA256 07d3de4ae0a90d0603ad922d7ca6f5a6ecf702980c9ae10ae1b1cb62faac1fc2 SHA512 1f976edc01f212fb86c8622ed76c70669bfbfe10ad7616e7cc644f62696a336e95b0e79620a687dc48e7d97afa4c57b26f098b80f4845711c7f80076cceb8640 WHIRLPOOL 522962459273491ba22e3ea7e2cb7fe110d9a482c7fda96362f3a8aef19f7814fa43d061244b08e3dcbafccab3338eca5da91286368c3044a997b5fb8076806e
+EBUILD emboss-6.1.0-r1.ebuild 3699 SHA256 033af6abb3945862fd2d925435287a70a1b446e370cb5d1d38dc4913fc713517 SHA512 efc8a1178ce1a1115d6d67d9e000d4f435c3005940dc9c7e63aa3a0ae6074f71ae1aec7f6d234b5cfdbbc5510ae8e58341a81af09f9665d9f99b33c6ce9110d4 WHIRLPOOL bd60f5a4f729b0f8c73ca856b350d7cdd4ae1a232a14b1f220ce1deaf66aa52affe9480636074d3320fc841cfe942750c14f3a39acb262d6d6488e552206a328
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diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
new file mode 100644
index 000000000000..119009d24004
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild,v 1.1 2012/11/19 10:36:45 jlec Exp $
+
+EAPI="4"
+
+inherit autotools eutils
+
+MY_PATCH="4"
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="
+	ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz
+	ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz"
+
+LICENSE="GPL-2 LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc minimal mysql pdf png postgres static-libs X"
+
+DEPEND="
+	dev-libs/expat
+	dev-libs/libpcre:3
+	sci-libs/plplot
+	sys-libs/zlib
+	mysql? ( dev-db/mysql )
+	pdf? ( media-libs/libharu )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		media-libs/gd
+		)
+	postgres? ( dev-db/postgresql-base )
+	!minimal? (
+		sci-biology/primer3
+		sci-biology/clustalw
+		)
+	X? ( x11-libs/libXt )"
+RDEPEND="${DEPEND}
+	!sys-devel/cons"
+PDEPEND="
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+		sci-biology/transfac
+		)"
+
+S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}"
+
+src_prepare() {
+	epatch "${WORKDIR}"/${P}.patch
+	epatch \
+		"${FILESDIR}"/${PV}-unbundle-libs.patch \
+		"${FILESDIR}/${PF}_plcol.patch"
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		$(use_with X x) \
+		$(use_with png pngdriver "${EPREFIX}/usr") \
+		$(use_with doc docroot "${EPREFIX}/usr") \
+		$(use_with pdf hpdf "${EPREFIX}/usr") \
+		$(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \
+		$(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \
+		$(use_enable amd64 64) \
+		$(use_enable static-libs static) \
+		--without-java \
+		--enable-large \
+		--enable-systemlibs \
+		--includedir="${ED}/usr/include/emboss"
+}
+
+src_install() {
+	einstall || die "Failed to install program files."
+
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
+	sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
+	dodoc README.Gentoo
+
+	# Install env file for setting libplplot and acd files path.
+	cat <<- EOF > 22emboss
+		# plplot libs dir
+		PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
+		# ACD files location
+		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+	EOF
+	doenvd 22emboss
+
+	# Symlink preinstalled docs to "/usr/share/doc".
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
+	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
+	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
+	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html
+
+	# Clashes #330507
+	mv "${ED}"/usr/bin/{digest,pepdigest} || die
+
+	# Remove useless dummy files from the image.
+	find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
+
+	# Move the provided codon files to a different directory. This will avoid
+	# user confusion and file collisions on case-insensitive file systems (see
+	# bug #115446). This change is documented in "README.Gentoo".
+	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+			die "Failed to move CODON directory."
+
+	# Move the provided restriction enzyme prototypes file to a different name.
+	# This avoids file collisions with versions of rebase that install their
+	# own enzyme prototypes file (see bug #118832).
+	mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
+			die "Failed to move enzyme equivalence file."
+}
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch
new file mode 100644
index 000000000000..0f5e592b77f1
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch
@@ -0,0 +1,112 @@
+--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c	2012-07-19 23:29:05.000000000 +0200
++++ /tmp/ajgraph.c	2012-07-19 23:25:00.000000000 +0200
+@@ -1645,14 +1645,14 @@
+ ** @return [void]
+ ** @@
+ ******************************************************************************/
+ 
+ static void GraphSetPen(ajint colour)
+ {
+-    ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]);
+-    plcol((PLINT)colour);
++    ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]);
++    plcol0((PLINT)colour);
+ 
+     return;
+ }
+ 
+ 
+ 
+--- EMBOSS-6.3.1/plplot/plcore.c	2007-10-24 15:14:43.000000000 +0200
++++ /tmp/plcore.c	2012-07-19 23:25:00.000000000 +0200
+@@ -1709,13 +1709,13 @@
+     if (plsc->zdigmax == 0)
+ 	plsc->zdigmax = 3;
+ 
+ /* Switch to graphics mode and set color and arrow style*/
+ 
+     plgra();
+-    plcol(1);
++    plcol0(1);
+ 
+     plstyl(0, &mk, &sp);
+     plpat(1, &inc, &del);
+ 
+     plsvect(def_arrow_x, def_arrow_y, 6, 0);
+ 
+--- EMBOSS-6.3.1/plplot/plstripc.c	2007-05-08 11:09:37.000000000 +0200
++++ /tmp/plstripc.c	2012-07-19 23:25:00.000000000 +0200
+@@ -153,17 +153,17 @@
+ 
+     plgchr(&sc, &dy);
+     sc = dy = dy/100;
+     plwind(-0.01, 1.01, -0.01, 1.01);
+     for (i=0; i<PEN; i++) {
+ 	if (mystripc->npts[i] || first) {
+-	    plcol(mystripc->colline[i]);
++	    plcol0(mystripc->colline[i]);
+ 	    pllsty(mystripc->styline[i]);
+ 	    pljoin(mystripc->xlpos, mystripc->ylpos - sc,
+ 		   mystripc->xlpos + 0.1, mystripc->ylpos - sc);
+-	    plcol(mystripc->collab);
++	    plcol0(mystripc->collab);
+ 	    plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc,
+ 		   0., 0., 0, mystripc->legline[i]);
+ 	    sc += dy;
+ 	}
+     }
+     plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax);
+@@ -184,34 +184,34 @@
+     PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.};
+ 
+ /* Set up window */
+ 
+     plvpor(0,1,0,1);
+     plwind(0,1,0,1);
+-    plcol(0);plpsty(0);
++    plcol0(0);plpsty(0);
+     plfill(4, &x[0], &y[0]);
+     plvsta();
+ 
+ /* Draw box and same window dimensions */
+     mystrip->wxmin=mystrip->xmin;
+     mystrip->wxmax=mystrip->xmax;
+     mystrip->wymin=mystrip->ymin;
+     mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */
+ 
+     plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax);
+ 
+     pllsty(1);
+-    plcol(mystrip->colbox);
++    plcol0(mystrip->colbox);
+     plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0);
+ 
+-    plcol(mystrip->collab);
++    plcol0(mystrip->collab);
+     pllab(mystrip->labx, mystrip->laby, mystrip->labtop);
+ 
+     for (i=0; i<PEN; i++) {
+         if (mystrip->npts[i] > 0) {
+-            plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]);
++            plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]);
+             plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]);
+         }
+     }
+ 
+     plstrip_legend(mystrip,0);
+ }
+@@ -269,13 +269,13 @@
+         if (stripc->xmax - stripc->xmin < stripc->xlen) {
+             if( yasc == 0) {
+ 
+             /* If user has changed subwindow, make shure we have the correct one */
+                 plvsta();
+                 plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */
+-		plcol(stripc->colline[p]); pllsty(stripc->styline[p]);
++		plcol0(stripc->colline[p]); pllsty(stripc->styline[p]);
+ 		if ((stripc->npts[p]-2) < 0)
+ 		  plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ 		else
+ 		  plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]);
+ 		plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]);
+ 		plflush();