Version bump

(Portage version: 2.2.01.21165-prefix/cvs/Linux x86_64)

4 files changed, 343 insertions, 1 deletions

diff --git a/sci-mathematics/octave/ChangeLog b/sci-mathematics/octave/ChangeLog
index 1cc4beb25435..c0f41bceeb08 100644
--- a/sci-mathematics/octave/ChangeLog
+++ b/sci-mathematics/octave/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-mathematics/octave
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/ChangeLog,v 1.129 2012/10/25 06:20:56 naota Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/ChangeLog,v 1.130 2012/10/26 18:27:13 bicatali Exp $
+
+*octave-3.6.3 (26 Oct 2012)
+
+  26 Oct 2012; Sébastien Fabbro <bicatali@gentoo.org>
+  files/octave-3.4.3-pkgbuilddir.patch, +octave-3.6.3.ebuild,
+  +files/octave-3.6.3-rcond.patch:
+  Version bump
 
   25 Oct 2012;  <naota@gentoo.org> octave-3.6.2-r1.ebuild:
   Add ~x86-fbsd. #303915
diff --git a/sci-mathematics/octave/files/octave-3.4.3-pkgbuilddir.patch b/sci-mathematics/octave/files/octave-3.4.3-pkgbuilddir.patch
index 895fa4932a12..5340c9a19b92 100644
--- a/sci-mathematics/octave/files/octave-3.4.3-pkgbuilddir.patch
+++ b/sci-mathematics/octave/files/octave-3.4.3-pkgbuilddir.patch
@@ -1,3 +1,6 @@
+Description: Allow installation of already extracted packages with pkg.m
+Forwarded: not-needed
+Author: Thomas Weber <tweber@debian.org>
 --- scripts/pkg/pkg.m.orig	2011-02-08 03:00:51.000000000 -0700
 +++ scripts/pkg/pkg.m	2011-03-18 09:31:24.670165643 -0600
 @@ -644,7 +644,14 @@
diff --git a/sci-mathematics/octave/files/octave-3.6.3-rcond.patch b/sci-mathematics/octave/files/octave-3.6.3-rcond.patch
new file mode 100644
index 000000000000..45dcecc07f00
--- /dev/null
+++ b/sci-mathematics/octave/files/octave-3.6.3-rcond.patch
@@ -0,0 +1,210 @@
+Description: Fix rcond function
+ Use new copy of data for full factorization if positive definite cholesky
+ factorization fails.
+Origin: upstream, http://hg.savannah.gnu.org/hgweb/octave/rev/197774b411ec
+Bug: http://savannah.gnu.org/bugs/?37336
+Applied-Upstream: version, 3.6.4
+Last-Update: 2012-09-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+diff --git a/liboctave/CMatrix.cc b/liboctave/CMatrix.cc
+--- a/liboctave/CMatrix.cc
++++ b/liboctave/CMatrix.cc
+@@ -1786,13 +1786,15 @@
+       else if (typ == MatrixType::Full || typ == MatrixType::Hermitian)
+         {
+           double anorm = -1.0;
+-          ComplexMatrix atmp = *this;
+-          Complex *tmp_data = atmp.fortran_vec ();
+ 
+           if (typ == MatrixType::Hermitian)
+             {
+               octave_idx_type info = 0;
+               char job = 'L';
++
++              ComplexMatrix atmp = *this;
++              Complex *tmp_data = atmp.fortran_vec ();
++
+               anorm = atmp.abs().sum().
+                 row(static_cast<octave_idx_type>(0)).max();
+ 
+@@ -1829,6 +1831,9 @@
+             {
+               octave_idx_type info = 0;
+ 
++              ComplexMatrix atmp = *this;
++              Complex *tmp_data = atmp.fortran_vec ();
++
+               Array<octave_idx_type> ipvt (dim_vector (nr, 1));
+               octave_idx_type *pipvt = ipvt.fortran_vec ();
+ 
+@@ -2098,8 +2103,10 @@
+         {
+           info = 0;
+           char job = 'L';
++
+           ComplexMatrix atmp = *this;
+           Complex *tmp_data = atmp.fortran_vec ();
++
+           anorm = atmp.abs().sum().row(static_cast<octave_idx_type>(0)).max();
+ 
+           F77_XFCN (zpotrf, ZPOTRF, (F77_CONST_CHAR_ARG2 (&job, 1), nr,
+diff --git a/liboctave/dMatrix.cc b/liboctave/dMatrix.cc
+--- a/liboctave/dMatrix.cc
++++ b/liboctave/dMatrix.cc
+@@ -1454,13 +1454,15 @@
+       else if (typ == MatrixType::Full || typ == MatrixType::Hermitian)
+         {
+           double anorm = -1.0;
+-          Matrix atmp = *this;
+-          double *tmp_data = atmp.fortran_vec ();
+ 
+           if (typ == MatrixType::Hermitian)
+             {
+               octave_idx_type info = 0;
+               char job = 'L';
++
++              Matrix atmp = *this;
++              double *tmp_data = atmp.fortran_vec ();
++
+               anorm = atmp.abs().sum().
+                 row(static_cast<octave_idx_type>(0)).max();
+ 
+@@ -1495,6 +1497,9 @@
+             {
+               octave_idx_type info = 0;
+ 
++              Matrix atmp = *this;
++              double *tmp_data = atmp.fortran_vec ();
++
+               Array<octave_idx_type> ipvt (dim_vector (nr, 1));
+               octave_idx_type *pipvt = ipvt.fortran_vec ();
+ 
+@@ -1760,8 +1765,10 @@
+         {
+           info = 0;
+           char job = 'L';
++
+           Matrix atmp = *this;
+           double *tmp_data = atmp.fortran_vec ();
++
+           anorm = atmp.abs().sum().row(static_cast<octave_idx_type>(0)).max();
+ 
+           F77_XFCN (dpotrf, DPOTRF, (F77_CONST_CHAR_ARG2 (&job, 1), nr,
+@@ -1838,6 +1845,7 @@
+ 
+           Matrix atmp = *this;
+           double *tmp_data = atmp.fortran_vec ();
++
+           if(anorm < 0.)
+             anorm = atmp.abs().sum().row(static_cast<octave_idx_type>(0)).max();
+ 
+diff --git a/liboctave/fCMatrix.cc b/liboctave/fCMatrix.cc
+--- a/liboctave/fCMatrix.cc
++++ b/liboctave/fCMatrix.cc
+@@ -1782,13 +1782,15 @@
+       else if (typ == MatrixType::Full || typ == MatrixType::Hermitian)
+         {
+           float anorm = -1.0;
+-          FloatComplexMatrix atmp = *this;
+-          FloatComplex *tmp_data = atmp.fortran_vec ();
+ 
+           if (typ == MatrixType::Hermitian)
+             {
+               octave_idx_type info = 0;
+               char job = 'L';
++
++              FloatComplexMatrix atmp = *this;
++              FloatComplex *tmp_data = atmp.fortran_vec ();
++
+               anorm = atmp.abs().sum().
+                 row(static_cast<octave_idx_type>(0)).max();
+ 
+@@ -1825,6 +1827,9 @@
+             {
+               octave_idx_type info = 0;
+ 
++              FloatComplexMatrix atmp = *this;
++              FloatComplex *tmp_data = atmp.fortran_vec ();
++
+               Array<octave_idx_type> ipvt (dim_vector (nr, 1));
+               octave_idx_type *pipvt = ipvt.fortran_vec ();
+ 
+@@ -2094,8 +2099,10 @@
+         {
+           info = 0;
+           char job = 'L';
++
+           FloatComplexMatrix atmp = *this;
+           FloatComplex *tmp_data = atmp.fortran_vec ();
++
+           anorm = atmp.abs().sum().row(static_cast<octave_idx_type>(0)).max();
+ 
+           F77_XFCN (cpotrf, CPOTRF, (F77_CONST_CHAR_ARG2 (&job, 1), nr,
+diff --git a/liboctave/fMatrix.cc b/liboctave/fMatrix.cc
+--- a/liboctave/fMatrix.cc
++++ b/liboctave/fMatrix.cc
+@@ -1454,13 +1454,15 @@
+       else if (typ == MatrixType::Full || typ == MatrixType::Hermitian)
+         {
+           float anorm = -1.0;
+-          FloatMatrix atmp = *this;
+-          float *tmp_data = atmp.fortran_vec ();
+ 
+           if (typ == MatrixType::Hermitian)
+             {
+               octave_idx_type info = 0;
+               char job = 'L';
++
++              FloatMatrix atmp = *this;
++              float *tmp_data = atmp.fortran_vec ();
++
+               anorm = atmp.abs().sum().
+                 row(static_cast<octave_idx_type>(0)).max();
+ 
+@@ -1495,6 +1497,9 @@
+             {
+               octave_idx_type info = 0;
+ 
++              FloatMatrix atmp = *this;
++              float *tmp_data = atmp.fortran_vec ();
++
+               Array<octave_idx_type> ipvt (dim_vector (nr, 1));
+               octave_idx_type *pipvt = ipvt.fortran_vec ();
+ 
+@@ -1760,8 +1765,10 @@
+         {
+           info = 0;
+           char job = 'L';
++
+           FloatMatrix atmp = *this;
+           float *tmp_data = atmp.fortran_vec ();
++
+           anorm = atmp.abs().sum().row(static_cast<octave_idx_type>(0)).max();
+ 
+           F77_XFCN (spotrf, SPOTRF, (F77_CONST_CHAR_ARG2 (&job, 1), nr,
+@@ -1838,6 +1845,7 @@
+ 
+           FloatMatrix atmp = *this;
+           float *tmp_data = atmp.fortran_vec ();
++
+           if(anorm < 0.)
+             anorm = atmp.abs().sum().row(static_cast<octave_idx_type>(0)).max();
+ 
+diff --git a/src/DLD-FUNCTIONS/rcond.cc b/src/DLD-FUNCTIONS/rcond.cc
+--- a/src/DLD-FUNCTIONS/rcond.cc
++++ b/src/DLD-FUNCTIONS/rcond.cc
+@@ -93,4 +93,12 @@
+ %!assert( rcond ([1 1; 2 1]), 1/9)
+ %!assert( rcond (magic (4)), 0, eps)
+ 
++%!shared x, sx
++%! x = [-5.25, -2.25; -2.25, 1] * eps () + ones (2) / 2;
++%! sx = [-5.25, -2.25; -2.25, 1] * eps ("single") + ones (2) / 2;
++%!assert (rcond (x) < eps ());
++%!assert (rcond (sx) < eps ('single'));
++%!assert (rcond (x*i) < eps ());
++%!assert (rcond (sx*i) < eps ('single'));
++
+ */
+
diff --git a/sci-mathematics/octave/octave-3.6.3.ebuild b/sci-mathematics/octave/octave-3.6.3.ebuild
new file mode 100644
index 000000000000..cee10e1f77a5
--- /dev/null
+++ b/sci-mathematics/octave/octave-3.6.3.ebuild
@@ -0,0 +1,122 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-3.6.3.ebuild,v 1.1 2012/10/26 18:27:13 bicatali Exp $
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils toolchain-funcs fortran-2
+
+DESCRIPTION="High-level interactive language for numerical computations"
+LICENSE="GPL-3"
+HOMEPAGE="http://www.octave.org/"
+SRC_URI="mirror://gnu/${PN}/${P}.tar.bz2"
+
+SLOT="0"
+IUSE="curl doc fftw +glpk gnuplot hdf5 +imagemagick opengl +qhull +qrupdate
+	readline +sparse static-libs X zlib"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-fbsd ~x86-linux"
+
+RDEPEND="dev-libs/libpcre
+	app-text/ghostscript-gpl
+	sys-libs/ncurses
+	virtual/lapack
+	curl? ( net-misc/curl )
+	fftw? ( sci-libs/fftw:3.0 )
+	glpk? ( sci-mathematics/glpk )
+	gnuplot? ( sci-visualization/gnuplot )
+	hdf5? ( sci-libs/hdf5 )
+	imagemagick? ( || (
+			media-gfx/graphicsmagick[cxx]
+			media-gfx/imagemagick[cxx] ) )
+	opengl? (
+		media-libs/freetype:2
+		media-libs/fontconfig
+		>=x11-libs/fltk-1.3:1[opengl] )
+	qhull? ( media-libs/qhull )
+	qrupdate? ( sci-libs/qrupdate )
+	readline? ( sys-libs/readline )
+	sparse? (
+		sci-libs/arpack
+		sci-libs/camd
+		sci-libs/ccolamd
+		sci-libs/cholmod
+		sci-libs/colamd
+		sci-libs/cxsparse
+		sci-libs/umfpack )
+	X? ( x11-libs/libX11 )
+	zlib? ( sys-libs/zlib )"
+
+DEPEND="${RDEPEND}
+	doc? (
+		virtual/latex-base
+		dev-texlive/texlive-genericrecommended
+		sys-apps/texinfo )
+	dev-util/gperf
+	virtual/pkgconfig"
+
+PATCHES=( "${FILESDIR}"/${PN}-3.4.3-{pkgbuilddir,help,texi}.patch )
+
+src_prepare() {
+	# nasty prefix hack for fltk:1 linking
+	if use prefix && use opengl; then
+		sed -i \
+			-e "s:ldflags\`:ldflags\` -Wl,-rpath,${EPREFIX}/usr/$(get_libdir)/fltk-1:" \
+			configure.ac
+	fi
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	# occasional fail on install, force regeneration (bug #401189)
+	rm doc/interpreter/contributors.texi || die
+
+	local myconf="--without-magick"
+	if use imagemagick; then
+		if has_version media-gfx/graphicsmagick[cxx]; then
+			myconf="--with-magick=GraphicsMagick"
+		else
+			myconf="--with-magick=ImageMagick"
+		fi
+	fi
+
+	# unfortunate dependency on mpi from hdf5 (bug #302621)
+	use hdf5 && has_version sci-libs/hdf5[mpi] && \
+		export CXX=mpicxx CC=mpicc FC=mpif77 F77=mpif77
+
+	local myeconfargs+=(
+		--localstatedir="${EPREFIX}/var/state/octave"
+		--with-blas="$(pkg-config --libs blas)"
+		--with-lapack="$(pkg-config --libs lapack)"
+		$(use_enable doc docs)
+		$(use_enable readline)
+		$(use_with curl)
+		$(use_with fftw fftw3)
+		$(use_with fftw fftw3f)
+		$(use_with glpk)
+		$(use_with hdf5)
+		$(use_with opengl)
+		$(use_with qhull)
+		$(use_with qrupdate)
+		$(use_with sparse arpack)
+		$(use_with sparse umfpack)
+		$(use_with sparse colamd)
+		$(use_with sparse ccolamd)
+		$(use_with sparse cholmod)
+		$(use_with sparse cxsparse)
+		$(use_with X x)
+		$(use_with zlib z)
+		${myconf}
+	)
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install
+	use doc && dodoc $(find doc -name \*.pdf)
+	[[ -e test/fntests.log ]] && dodoc test/fntests.log
+	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${P}" > 99octave
+	doenvd 99octave
+}