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author | Justin Lecher <jlec@gentoo.org> | 2012-11-19 10:36:45 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2012-11-19 10:36:45 +0000 |
commit | d1c0c2184880eb3d4279799f9c279a1725d43175 (patch) | |
tree | b87036103fcf09d927e2806856aafc3f745a5933 /sci-biology/emboss | |
parent | Pull in required virtual/glu and virtual/opengl. (diff) | |
download | gentoo-2-d1c0c2184880eb3d4279799f9c279a1725d43175.tar.gz gentoo-2-d1c0c2184880eb3d4279799f9c279a1725d43175.tar.bz2 gentoo-2-d1c0c2184880eb3d4279799f9c279a1725d43175.zip |
sci-biology/emboss: Fix compilation problem with toplplot, #391669, thanks Juergen Rose for the patch
(Portage version: 2.2.0_alpha142/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)
Diffstat (limited to 'sci-biology/emboss')
-rw-r--r-- | sci-biology/emboss/ChangeLog | 9 | ||||
-rw-r--r-- | sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 117 | ||||
-rw-r--r-- | sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch | 112 |
3 files changed, 237 insertions, 1 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/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(); |