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Mon, 16 Sep 2013 18:42:30 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1379356998.d7612ffdd7f827fbf8c835e8d4465091a6261038.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/emboss/files/, sci-biology/emboss/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/emboss/ChangeLog sci-biology/emboss/emboss-6.6.0.ebuild sci-biology/emboss/files/emboss-6.6.0_plcol.patch X-VCS-Directories: sci-biology/emboss/files/ sci-biology/emboss/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: d7612ffdd7f827fbf8c835e8d4465091a6261038 X-VCS-Branch: master Date: Mon, 16 Sep 2013 18:42:30 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 6cba776e-2b38-4c45-9646-d43adc85168f X-Archives-Hash: 05f32845257ab6e2bbaeb0ae8f08985d commit: d7612ffdd7f827fbf8c835e8d4465091a6261038 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Mon Sep 16 18:43:18 2013 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Sep 16 18:43:18 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d7612ffd Mask the 6.6.0 version due to build breakage; add the missing plcol patch copied over from 6.3.1 --- sci-biology/emboss/ChangeLog | 17 ++++ sci-biology/emboss/emboss-6.6.0.ebuild | 14 ++- sci-biology/emboss/files/emboss-6.6.0_plcol.patch | 112 ++++++++++++++++++++++ 3 files changed, 138 insertions(+), 5 deletions(-) diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 76a5b35..1d9c10e 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -2,6 +2,23 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $ + 16 Sep 2013; Martin Mokrejs + emboss-6.6.0.ebuild, +files/emboss-6.6.0_plcol.patch: + emboss-6.6.0.ebuild files/emboss-6.6.0_plcol.patch + Added the misisng patch, disabled searches for Gentoo-patches, + fixed patch-related variable values in the 6.6.0 ebuild, BUT + 1) the ebuild does not work, configure exits after looking for + -lhpdf or later -lpng (that can be obeyed by omitting --with-hpdf + --with-pngdriver) + 2) if one relies on whatever configure detects compilation aborts + while compiling embossversion.c or because -lexpat is not in LIBS. + Well, expat is not in configure flags at all. + + Maybe something is caused by the --enable-systemlibs configure switch, + I think it actually enables inclusion of these from their bundled + copies in the EMBOSS tarball (and not use of the system-wide headers + and libs). + *emboss-6.3.1_p4-r2 (11 Sep 2013) *emboss-6.5.7 (11 Sep 2013) *emboss-6.6.0 (11 Sep 2013) diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild index 4ab7353..1d7b405 100644 --- a/sci-biology/emboss/emboss-6.6.0.ebuild +++ b/sci-biology/emboss/emboss-6.6.0.ebuild @@ -6,8 +6,11 @@ EAPI="4" inherit emboss eutils -EBO_PATCH="4" -EBOV=${PV/_p*} +#EBO_PATCH="4" +#EBOV=${PV/_p*} + +EBO_PATCH="" +EBOV=${PV} DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" SRC_URI=" @@ -18,7 +21,8 @@ SRC_URI=" ##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" #[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" -KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +#KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="" IUSE+=" minimal" RDEPEND+=" !sys-devel/cons" @@ -40,8 +44,8 @@ DOCS+=" FAQ THANKS" src_prepare() { [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch - epatch "${WORKDIR}"/${PF}.patch - epatch "${FILESDIR}/${PF}_plcol.patch" + # epatch "${WORKDIR}"/${PF}.patch + #epatch "${FILESDIR}/${PF}_plcol.patch" emboss_src_prepare } diff --git a/sci-biology/emboss/files/emboss-6.6.0_plcol.patch b/sci-biology/emboss/files/emboss-6.6.0_plcol.patch new file mode 100644 index 0000000..0f5e592 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_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; inpts[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; inpts[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();