From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Q7fk6-0001W7-03 for garchives@archives.gentoo.org; Thu, 07 Apr 2011 03:18:46 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 845191C0B0; Thu, 7 Apr 2011 03:17:33 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 313DD1C0B0 for ; Thu, 7 Apr 2011 03:17:33 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 96D8D1B4101 for ; Thu, 7 Apr 2011 03:17:32 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 0F5C28006A for ; Thu, 7 Apr 2011 03:17:32 +0000 (UTC) From: "Tim Cera" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Tim Cera" Message-ID: <75b2b5ee1422bd2667dba406c4a2d45711ee01ab.timcera@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: timcera X-VCS-Committer-Name: Tim Cera X-VCS-Revision: 75b2b5ee1422bd2667dba406c4a2d45711ee01ab Date: Thu, 7 Apr 2011 03:17:32 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: eced54fd85f5464ddf67954aeb7cbb5a commit: 75b2b5ee1422bd2667dba406c4a2d45711ee01ab Author: timcera earthlink net> AuthorDate: Wed Apr 6 23:55:04 2011 +0000 Commit: Tim Cera earthlink net> CommitDate: Wed Apr 6 23:55:04 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D75b2b5ee Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci dev-python/pyamg/ChangeLog | 8 +- dev-python/pyamg/Manifest | 4 +- .../{pyamg-1.0.0.ebuild =3D> pyamg-2.0.0.ebuild} | 2 +- eclass/emboss.eclass | 157 ++---- eclass/mpi.eclass | 21 +- profiles/updates/1Q-2011 | 2 + sci-biology/embassy-cbstools/ChangeLog | 4 + sci-biology/embassy-cbstools/Manifest | 12 +- .../embassy-cbstools-1.0.0-r2.ebuild | 2 + .../files/embassy-cbstools-1.0.0-r2.patch | 262 ++++++++- sci-biology/embassy-domainatrix/ChangeLog | 5 + sci-biology/embassy-domainatrix/Manifest | 12 +- .../embassy-domainatrix-0.1.0-r5.ebuild | 2 + .../files/embassy-domainatrix-0.1.0-r5.patch | 255 ++++++++- sci-biology/embassy-domalign/ChangeLog | 4 + sci-biology/embassy-domalign/Manifest | 22 +- .../embassy-domalign-0.1.0-r5.ebuild | 2 + .../files/embassy-domalign-0.1.0-r5.patch | 259 ++++++++- sci-biology/embassy-domsearch/ChangeLog | 4 + sci-biology/embassy-domsearch/Manifest | 12 +- .../embassy-domsearch-0.1.0-r5.ebuild | 2 + .../files/embassy-domsearch-0.1.0-r5.patch | 255 ++++++++- sci-biology/embassy-emnu/ChangeLog | 4 + sci-biology/embassy-emnu/Manifest | 12 +- .../embassy-emnu/embassy-emnu-1.05-r7.ebuild | 10 +- .../embassy-emnu/files/embassy-emnu-1.05-r7.patch | 268 +++++++++- sci-biology/embassy-esim4/ChangeLog | 4 + sci-biology/embassy-esim4/Manifest | 12 +- .../embassy-esim4/embassy-esim4-1.0.0-r7.ebuild | 2 + .../files/embassy-esim4-1.0.0-r7.patch | 254 ++++++++- sci-biology/embassy-hmmer/ChangeLog | 4 + sci-biology/embassy-hmmer/Manifest | 12 +- .../embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild | 2 + .../files/embassy-hmmer-2.3.2-r4.patch | 255 ++++++++- sci-biology/embassy-iprscan/ChangeLog | 4 + sci-biology/embassy-iprscan/Manifest | 12 +- .../embassy-iprscan-4.3.1-r2.ebuild | 2 + .../files/embassy-iprscan-4.3.1-r2.patch | 254 ++++++++- sci-biology/embassy-memenew/ChangeLog | 4 + sci-biology/embassy-memenew/Manifest | 12 +- .../embassy-memenew-4.0.0-r1.ebuild | 2 + .../files/embassy-memenew-4.0.0-r1.patch | 255 ++++++++- sci-biology/embassy-mira/ChangeLog | 4 + sci-biology/embassy-mira/Manifest | 12 +- .../embassy-mira/embassy-mira-2.8.2-r2.ebuild | 2 + .../embassy-mira/files/embassy-mira-2.8.2-r2.patch | 254 ++++++++- sci-biology/embassy-mse/ChangeLog | 4 + sci-biology/embassy-mse/Manifest | 16 +- sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild | 8 +- .../embassy-mse/files/embassy-mse-3.0.0.patch | 268 +++++++++- sci-biology/embassy-phylipnew/ChangeLog | 4 + sci-biology/embassy-phylipnew/Manifest | 12 +- .../embassy-phylipnew-3.69.ebuild | 6 +- .../files/embassy-phylipnew-3.69.patch | 255 ++++++++- sci-biology/embassy-signature/ChangeLog | 4 + sci-biology/embassy-signature/Manifest | 12 +- .../embassy-signature-0.1.0-r5.ebuild | 2 + .../files/embassy-signature-0.1.0-r5.patch | 255 ++++++++- sci-biology/embassy-structure/ChangeLog | 4 + sci-biology/embassy-structure/Manifest | 12 +- .../embassy-structure-0.1.0-r5.ebuild | 2 + .../files/embassy-structure-0.1.0-r5.patch | 255 ++++++++- sci-biology/embassy-topo/ChangeLog | 4 + sci-biology/embassy-topo/Manifest | 12 +- sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild | 4 +- .../embassy-topo/files/embassy-topo-2.0.0.patch | 254 ++++++++- sci-biology/embassy-vienna/ChangeLog | 4 + sci-biology/embassy-vienna/Manifest | 12 +- .../embassy-vienna/embassy-vienna-1.7.2-r2.ebuild | 2 + .../files/embassy-vienna-1.7.2-r2.patch | 255 ++++++++- sci-biology/embassy/ChangeLog | 9 + sci-biology/embassy/Manifest | 10 +- sci-biology/embassy/embassy-6.3.1.ebuild | 14 +- sci-biology/emboss/ChangeLog | 17 + sci-biology/emboss/Manifest | 14 +- sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 45 ++- sci-biology/emboss/files/emboss-6.3.1_p4-r1.patch | 600 --------------= ----- sci-chemistry/drawxtl/ChangeLog | 6 +- sci-chemistry/drawxtl/Manifest | 14 +- sci-chemistry/drawxtl/drawxtl-44.ebuild | 4 +- sci-chemistry/drawxtl/drawxtl-54.ebuild | 4 +- sci-chemistry/gromacs/Manifest | 26 +- sci-chemistry/gromacs/gromacs-4.0.9999.ebuild | 4 +- sci-chemistry/inchi/ChangeLog | 10 - sci-chemistry/inchi/Manifest | 6 - .../inchi/files/inchi-1.03-makefile.patch | 66 --- sci-chemistry/inchi/inchi-1.03.ebuild | 48 -- sci-chemistry/inchi/metadata.xml | 8 - sci-chemistry/jmol/ChangeLog | 5 +- sci-chemistry/jmol/Manifest | 4 +- sci-chemistry/jmol/jmol-12.0.34.ebuild | 4 +- sci-chemistry/nmrpipe/ChangeLog | 4 + sci-chemistry/nmrpipe/Manifest | 12 +- sci-chemistry/nmrpipe/files/env-nmrpipe-new | 2 +- .../nmrpipe/nmrpipe-5.5.2011.069.19.56.ebuild | 2 +- sci-chemistry/openbabel-perl/ChangeLog | 35 -- sci-chemistry/openbabel-perl/Manifest | 29 - .../files/openbabel-perl-2.2.0-makefile.patch | 25 - .../files/openbabel-perl-2.2.1-makefile.patch | 25 - .../files/openbabel-perl-2.2.2-makefile.patch | 25 - sci-chemistry/openbabel-perl/metadata.xml | 15 - .../openbabel-perl/openbabel-perl-2.2.1.ebuild | 70 --- .../openbabel-perl/openbabel-perl-2.2.2.ebuild | 70 --- sci-chemistry/openbabel-python/ChangeLog | 57 -- sci-chemistry/openbabel-python/Manifest | 14 - sci-chemistry/openbabel-python/metadata.xml | 15 - .../openbabel-python/openbabel-python-2.3.0.ebuild | 49 -- sci-chemistry/openbabel-ruby/ChangeLog | 34 -- sci-chemistry/openbabel-ruby/Manifest | 26 - sci-chemistry/openbabel-ruby/metadata.xml | 15 - .../openbabel-ruby/openbabel-ruby-2.2.1.ebuild | 49 -- .../openbabel-ruby/openbabel-ruby-2.2.2.ebuild | 49 -- sci-chemistry/openbabel/ChangeLog | 21 - sci-chemistry/openbabel/Manifest | 15 - .../files/openbabel-2.3.0-test_lib_path.patch | 12 - sci-chemistry/openbabel/metadata.xml | 14 - sci-chemistry/openbabel/openbabel-2.3.0.ebuild | 50 -- sci-chemistry/pymol/ChangeLog | 6 +- sci-chemistry/pymol/Manifest | 17 +- .../files/{1.3.0-vmd.patch =3D> 9999-vmd.patch} | 23 +- sci-chemistry/pymol/files/pymol-9999-shaders.patch | 73 ++- sci-chemistry/pymol/metadata.xml | 1 - sci-chemistry/pymol/pymol-9999.ebuild | 47 +- sci-chemistry/stdinchi/ChangeLog | 14 - sci-chemistry/stdinchi/Manifest | 6 - .../stdinchi/files/stdinchi-1.02-makefile.patch | 20 - sci-chemistry/stdinchi/metadata.xml | 8 - sci-chemistry/stdinchi/stdinchi-1.02.ebuild | 45 -- sci-libs/gmsh/ChangeLog | 4 + sci-libs/gmsh/Manifest | 12 +- sci-libs/gmsh/gmsh-2.5.0.ebuild | 2 +- sci-libs/gmsh/gmsh-9999.ebuild | 2 +- sci-mathematics/burrtools/ChangeLog | 5 +- sci-mathematics/burrtools/Manifest | 14 +- .../burrtools/burrtools-0.5.2-r1.ebuild | 5 +- sci-mathematics/hypre/ChangeLog | 11 +- sci-mathematics/hypre/Manifest | 8 +- ...2.6.0b-makefile.patch =3D> makefile-mpicxx.patch} | 0 sci-mathematics/hypre/hypre-2.6.0b.ebuild | 4 +- .../{hypre-2.6.0b.ebuild =3D> hypre-2.7.0b.ebuild} | 4 +- sci-mathematics/petsc/ChangeLog | 6 + sci-mathematics/petsc/Manifest | 5 +- ...-pic.patch =3D> petsc-3.1_p8-configure-pic.patch} | 4 +- .../{petsc-3.1_p7.ebuild =3D> petsc-3.1_p8.ebuild} | 2 +- sci-misc/nco/.#Manifest.1.21 | 6 + sci-misc/nco/Manifest | 3 + sci-misc/nco/metadata.xml | 19 + sci-misc/nco/nco-4.0.7.ebuild | 65 +++ sci-physics/root/ChangeLog | 562 --------------= ---- sci-physics/root/Manifest | 32 - sci-physics/root/files/olbd.confd | 9 - sci-physics/root/files/olbd.initd | 26 - sci-physics/root/files/proofd.confd | 12 - sci-physics/root/files/proofd.initd | 26 - sci-physics/root/files/root-5.28.00-asneeded.patch | 20 - .../root/files/root-5.28.00-configure-paths.patch | 23 - sci-physics/root/files/root-5.28.00-glibc212.patch | 11 - .../root/files/root-5.28.00-nobyte-compile.patch | 138 ----- .../root/files/root-5.28.00-prop-ldflags.patch | 13 - sci-physics/root/files/root-5.28.00-unuran.patch | 39 -- .../files/root-5.28.00-xrootd-prop-flags.patch | 606 --------------= ------ sci-physics/root/files/rootd.confd | 8 - sci-physics/root/files/rootd.initd | 28 - sci-physics/root/files/xrootd.confd | 8 - sci-physics/root/files/xrootd.initd | 26 - sci-physics/root/metadata.xml | 31 - sci-physics/root/root-5.28.00.ebuild | 323 ----------- sys-cluster/mpich2/ChangeLog | 5 +- sys-cluster/mpich2/Manifest | 24 +- sys-cluster/mpich2/mpich2-1.2.1_p1-r2.ebuild | 4 +- sys-cluster/openmpi/ChangeLog | 15 + sys-cluster/openmpi/Manifest | 12 +- .../{openmpi-1.5.2.ebuild =3D> openmpi-1.5.3.ebuild} | 12 +- sys-cluster/scalasca/ChangeLog | 6 + sys-cluster/scalasca/Manifest | 22 +- ...scalasca-1.3.2.ebuild =3D> scalasca-1.3.3.ebuild} | 9 +- 176 files changed, 4802 insertions(+), 3971 deletions(-)