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authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-libs
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proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
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-rw-r--r--sci-libs/shogun/shogun-3.2.0.ebuild137
-rw-r--r--sci-libs/silo/Manifest2
-rw-r--r--sci-libs/silo/files/silo-4.10.2-qtlibs.patch66
-rw-r--r--sci-libs/silo/files/silo-4.10.2-tests.patch11
-rw-r--r--sci-libs/silo/files/silo-4.9.1-qtlibs.patch66
-rw-r--r--sci-libs/silo/files/silo-4.9.1-tests.patch11
-rw-r--r--sci-libs/silo/metadata.xml18
-rw-r--r--sci-libs/silo/silo-4.10.2.ebuild38
-rw-r--r--sci-libs/silo/silo-4.9.1.ebuild39
-rw-r--r--sci-libs/spooles/Manifest1
-rw-r--r--sci-libs/spooles/files/Make.inc.in9
-rw-r--r--sci-libs/spooles/files/spooles-2.2-I2Ohash-64bit.patch28
-rw-r--r--sci-libs/spooles/files/spooles-2.2-formats.patch17
-rw-r--r--sci-libs/spooles/files/spooles-2.2-makefiles.patch47
-rw-r--r--sci-libs/spooles/metadata.xml19
-rw-r--r--sci-libs/spooles/spooles-2.2.ebuild68
-rw-r--r--sci-libs/spqr/Manifest2
-rw-r--r--sci-libs/spqr/files/spqr-1.2.3-autotools.patch203
-rw-r--r--sci-libs/spqr/metadata.xml17
-rw-r--r--sci-libs/spqr/spqr-1.2.3-r1.ebuild40
-rw-r--r--sci-libs/spqr/spqr-1.3.1.ebuild32
-rw-r--r--sci-libs/spr/Manifest1
-rw-r--r--sci-libs/spr/files/spr-3.3.2-autotools.patch169
-rw-r--r--sci-libs/spr/files/spr-3.3.2-gcc46.patch33
-rw-r--r--sci-libs/spr/metadata.xml18
-rw-r--r--sci-libs/spr/spr-3.3.2.ebuild38
-rw-r--r--sci-libs/ssm/Manifest2
-rw-r--r--sci-libs/ssm/files/ssm-1.1-mmdb.patch27
-rw-r--r--sci-libs/ssm/files/ssm-1.1-pc.patch19
-rw-r--r--sci-libs/ssm/metadata.xml11
-rw-r--r--sci-libs/ssm/ssm-1.1.ebuild31
-rw-r--r--sci-libs/ssm/ssm-1.4.ebuild26
-rw-r--r--sci-libs/starparse/Manifest1
-rw-r--r--sci-libs/starparse/files/starparse-1.0-guile1.8.patch60
-rw-r--r--sci-libs/starparse/metadata.xml5
-rw-r--r--sci-libs/starparse/starparse-1.0-r1.ebuild33
-rw-r--r--sci-libs/suitesparse/metadata.xml33
-rw-r--r--sci-libs/suitesparse/suitesparse-4.0.2.ebuild28
-rw-r--r--sci-libs/suitesparse/suitesparse-4.2.1.ebuild28
-rw-r--r--sci-libs/suitesparseconfig/Manifest1
-rw-r--r--sci-libs/suitesparseconfig/metadata.xml9
-rw-r--r--sci-libs/suitesparseconfig/suitesparseconfig-4.2.1.ebuild16
-rw-r--r--sci-libs/superlu/Manifest1
-rw-r--r--sci-libs/superlu/files/superlu-4.3-autotools.patch584
-rw-r--r--sci-libs/superlu/files/superlu-4.3-format-security.patch16
-rw-r--r--sci-libs/superlu/metadata.xml21
-rw-r--r--sci-libs/superlu/superlu-4.3-r1.ebuild74
-rw-r--r--sci-libs/szip/Manifest1
-rw-r--r--sci-libs/szip/metadata.xml14
-rw-r--r--sci-libs/szip/szip-2.1-r1.ebuild20
-rw-r--r--sci-libs/szip/szip-2.1.ebuild24
-rw-r--r--sci-libs/ta-lib/Manifest1
-rw-r--r--sci-libs/ta-lib/files/ta-lib-0.4.0-asneeded.patch83
-rw-r--r--sci-libs/ta-lib/metadata.xml10
-rw-r--r--sci-libs/ta-lib/ta-lib-0.4.0.ebuild29
-rw-r--r--sci-libs/tamu_anova/Manifest1
-rw-r--r--sci-libs/tamu_anova/files/0.2.1-gentoo.patch35
-rw-r--r--sci-libs/tamu_anova/files/tamu_anova-0.2.1-texinfo5.1.patch39
-rw-r--r--sci-libs/tamu_anova/metadata.xml8
-rw-r--r--sci-libs/tamu_anova/tamu_anova-0.2.1.ebuild28
-rw-r--r--sci-libs/taucs/Manifest1
-rw-r--r--sci-libs/taucs/files/taucs-2.2-no-test-cilk.patch20
-rw-r--r--sci-libs/taucs/metadata.xml29
-rw-r--r--sci-libs/taucs/taucs-2.2.ebuild94
-rw-r--r--sci-libs/tnt/Manifest3
-rw-r--r--sci-libs/tnt/metadata.xml14
-rw-r--r--sci-libs/tnt/tnt-1.2.6.ebuild32
-rw-r--r--sci-libs/tnt/tnt-3.0.12.ebuild29
-rw-r--r--sci-libs/torch/Manifest2
-rw-r--r--sci-libs/torch/files/3.1-prll.patch40
-rw-r--r--sci-libs/torch/metadata.xml8
-rw-r--r--sci-libs/torch/torch-3.1.ebuild57
-rw-r--r--sci-libs/torch/torch-3.ebuild71
-rw-r--r--sci-libs/udunits/Manifest2
-rw-r--r--sci-libs/udunits/files/udunits-2.1.15-autotools.patch61
-rw-r--r--sci-libs/udunits/metadata.xml11
-rw-r--r--sci-libs/udunits/udunits-2.1.15.ebuild37
-rw-r--r--sci-libs/udunits/udunits-2.1.24.ebuild43
-rw-r--r--sci-libs/ufconfig/Manifest4
-rw-r--r--sci-libs/ufconfig/metadata.xml10
-rw-r--r--sci-libs/ufconfig/ufconfig-3.5.0.ebuild42
-rw-r--r--sci-libs/ufconfig/ufconfig-3.6.1.ebuild41
-rw-r--r--sci-libs/ufconfig/ufconfig-3.7.0.ebuild44
-rw-r--r--sci-libs/ufconfig/ufconfig-3.7.1.ebuild44
-rw-r--r--sci-libs/umfpack/Manifest2
-rw-r--r--sci-libs/umfpack/files/umfpack-5.2.0-autotools.patch531
-rw-r--r--sci-libs/umfpack/metadata.xml15
-rw-r--r--sci-libs/umfpack/umfpack-5.2.0.ebuild47
-rw-r--r--sci-libs/umfpack/umfpack-5.6.2.ebuild34
-rw-r--r--sci-libs/vecmath-objectclub/Manifest1
-rw-r--r--sci-libs/vecmath-objectclub/metadata.xml19
-rw-r--r--sci-libs/vecmath-objectclub/vecmath-objectclub-1.14.ebuild40
-rw-r--r--sci-libs/voro++/Manifest1
-rw-r--r--sci-libs/voro++/files/voro++-0.4.6-cmake.patch141
-rw-r--r--sci-libs/voro++/metadata.xml5
-rw-r--r--sci-libs/voro++/voro++-0.4.6-r1.ebuild26
-rw-r--r--sci-libs/votca-tools/Manifest3
-rw-r--r--sci-libs/votca-tools/metadata.xml15
-rw-r--r--sci-libs/votca-tools/votca-tools-1.2.2.ebuild69
-rw-r--r--sci-libs/votca-tools/votca-tools-1.2.4.ebuild58
-rw-r--r--sci-libs/vtk/Manifest6
-rw-r--r--sci-libs/vtk/files/vtk-5.10.1-ffmpeg-1.patch49
-rw-r--r--sci-libs/vtk/files/vtk-5.10.1-libav-9.patch117
-rw-r--r--sci-libs/vtk/files/vtk-5.10.1-tcl8.6.patch57
-rw-r--r--sci-libs/vtk/files/vtk-5.2.0-tcl-install.patch12
-rw-r--r--sci-libs/vtk/files/vtk-5.4.2-boost-property_map.patch194
-rw-r--r--sci-libs/vtk/files/vtk-5.4.2-cg-path.patch35
-rw-r--r--sci-libs/vtk/files/vtk-5.4.2-libpng14.patch20
-rw-r--r--sci-libs/vtk/files/vtk-5.6.0-R.patch57
-rw-r--r--sci-libs/vtk/files/vtk-5.6.0-boost-property_map.patch13
-rw-r--r--sci-libs/vtk/files/vtk-5.6.0-cg-path.patch36
-rw-r--r--sci-libs/vtk/files/vtk-5.6.0-ffmpeg.patch42
-rw-r--r--sci-libs/vtk/files/vtk-5.6.0-libpng14.patch22
-rw-r--r--sci-libs/vtk/files/vtk-5.6.0-odbc.patch12
-rw-r--r--sci-libs/vtk/files/vtk-5.6.1-ffmpeg.patch42
-rw-r--r--sci-libs/vtk/files/vtk-5.6.1-gcc-46.patch29
-rw-r--r--sci-libs/vtk/files/vtk-5.6.1-libav-0.8.patch66
-rw-r--r--sci-libs/vtk/files/vtk-5.6.1-libpng15.patch22
-rw-r--r--sci-libs/vtk/files/vtk-5.8.0-R.patch45
-rw-r--r--sci-libs/vtk/files/vtk-5.8.0-boost.patch39
-rw-r--r--sci-libs/vtk/files/vtk-6.0.0-cg-path.patch16
-rw-r--r--sci-libs/vtk/files/vtk-6.0.0-install.patch19
-rw-r--r--sci-libs/vtk/files/vtk-6.0.0-netcdf.patch75
-rw-r--r--sci-libs/vtk/files/vtk-6.0.0-system.patch27
-rw-r--r--sci-libs/vtk/files/vtk-6.0.0-vtkpython.patch12
-rw-r--r--sci-libs/vtk/files/vtk-6.1.0-freetype.patch22
-rw-r--r--sci-libs/vtk/files/vtk-6.1.0-glext.patch13
-rw-r--r--sci-libs/vtk/files/vtk-6.1.0-install.patch19
-rw-r--r--sci-libs/vtk/files/vtk-6.1.0-memset.patch147
-rw-r--r--sci-libs/vtk/files/vtk-6.1.0-netcdf.patch29
-rw-r--r--sci-libs/vtk/files/vtk-6.1.0-system.patch27
-rw-r--r--sci-libs/vtk/files/vtk-6.1.0-web.patch25
-rw-r--r--sci-libs/vtk/metadata.xml26
-rw-r--r--sci-libs/vtk/vtk-6.0.0.ebuild323
-rw-r--r--sci-libs/vtk/vtk-6.1.0-r1.ebuild389
-rw-r--r--sci-libs/vtk/vtk-6.1.0.ebuild379
-rw-r--r--sci-libs/vtkdata/Manifest2
-rw-r--r--sci-libs/vtkdata/metadata.xml8
-rw-r--r--sci-libs/vtkdata/vtkdata-6.0.0.ebuild27
-rw-r--r--sci-libs/vtkdata/vtkdata-6.1.0.ebuild27
-rw-r--r--sci-libs/xdmf2/Manifest1
-rw-r--r--sci-libs/xdmf2/files/xdmf2-1.0_p141226-module.patch13
-rw-r--r--sci-libs/xdmf2/metadata.xml8
-rw-r--r--sci-libs/xdmf2/xdmf2-1.0_p141226-r1.ebuild64
-rw-r--r--sci-libs/xdrfile/Manifest1
-rw-r--r--sci-libs/xdrfile/metadata.xml9
-rw-r--r--sci-libs/xdrfile/xdrfile-1.1.1.ebuild24
-rw-r--r--sci-libs/xgks-pmel/Manifest1
-rw-r--r--sci-libs/xgks-pmel/files/aclocal.patch146
-rw-r--r--sci-libs/xgks-pmel/metadata.xml10
-rw-r--r--sci-libs/xgks-pmel/xgks-pmel-2.5.5.ebuild81
-rw-r--r--sci-libs/xkaapi/Manifest3
-rw-r--r--sci-libs/xkaapi/files/xkaapi-2.1-ffi.patch24
-rw-r--r--sci-libs/xkaapi/files/xkaapi-2.1-flags.patch39
-rw-r--r--sci-libs/xkaapi/files/xkaapi-3.0.3-flags.patch31
-rw-r--r--sci-libs/xkaapi/metadata.xml12
-rw-r--r--sci-libs/xkaapi/xkaapi-2.1.ebuild58
-rw-r--r--sci-libs/xkaapi/xkaapi-2.2.ebuild58
-rw-r--r--sci-libs/xkaapi/xkaapi-3.0.3.ebuild52
-rw-r--r--sci-libs/xylib/Manifest2
-rw-r--r--sci-libs/xylib/metadata.xml13
-rw-r--r--sci-libs/xylib/xylib-1.1.ebuild28
-rw-r--r--sci-libs/xylib/xylib-1.2.ebuild31
1322 files changed, 60744 insertions, 0 deletions
diff --git a/sci-libs/Fiona/Fiona-1.5.1.ebuild b/sci-libs/Fiona/Fiona-1.5.1.ebuild
new file mode 100644
index 00000000000..756a8aaa0c5
--- /dev/null
+++ b/sci-libs/Fiona/Fiona-1.5.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit distutils-r1
+
+DESCRIPTION="OGR's neat, nimble, no-nonsense API"
+HOMEPAGE="https://pypi.python.org/pypi/Fiona"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+ >=sci-libs/gdal-1.8
+ dev-python/click[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
+ test? (
+ dev-python/nose[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ )"
+
+PATCHES=( "${FILESDIR}"/scriptname.patch )
+
+python_test() {
+ esetup.py test
+}
diff --git a/sci-libs/Fiona/Fiona-9999.ebuild b/sci-libs/Fiona/Fiona-9999.ebuild
new file mode 100644
index 00000000000..ee2ff80c4e4
--- /dev/null
+++ b/sci-libs/Fiona/Fiona-9999.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit distutils-r1 git-r3
+
+DESCRIPTION="OGR's neat, nimble, no-nonsense API"
+HOMEPAGE="https://pypi.python.org/pypi/Fiona"
+SRC_URI=""
+EGIT_REPO_URI="http://github.com/Toblerity/${PN}.git"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE="test"
+
+RDEPEND="
+ >=sci-libs/gdal-1.8
+ dev-python/click[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
+ test? (
+ dev-python/nose[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ )"
+
+PATCHES=( "${FILESDIR}"/scriptname.patch )
+
+python_test() {
+ esetup.py test
+}
diff --git a/sci-libs/Fiona/Manifest b/sci-libs/Fiona/Manifest
new file mode 100644
index 00000000000..aaea88699c7
--- /dev/null
+++ b/sci-libs/Fiona/Manifest
@@ -0,0 +1 @@
+DIST Fiona-1.5.1.tar.gz 1117361 SHA256 2e2469190107dc671b4aa05d5b8bed5c01ffeb9de79525c91129bad76915e095 SHA512 06a2f091138b455355aa24bdd3cace48a3ccbbcb8b680f8009862a9ef3bdc217b68ba4596c51caaa9d09d2fad606a581d50f2fc9f2d0636bfec459e2022546a7 WHIRLPOOL 47d274f1755aa875273f1c8b4ce8949fe9a22b237fff90bdf71aa3ff7a6a4a18ff9016ebe3cdf8b323a2d67fa45b6cb8c8e8bfc20c2c57e01df0aa7cf8733330
diff --git a/sci-libs/Fiona/files/scriptname.patch b/sci-libs/Fiona/files/scriptname.patch
new file mode 100644
index 00000000000..227e644f075
--- /dev/null
+++ b/sci-libs/Fiona/files/scriptname.patch
@@ -0,0 +1,11 @@
+--- setup.py.orig 2015-03-27 21:34:22.790592037 +0100
++++ setup.py 2015-03-27 21:34:54.247259049 +0100
+@@ -150,7 +150,7 @@
+ packages=['fiona', 'fiona.fio'],
+ entry_points='''
+ [console_scripts]
+- fio=fiona.fio.fio:cli
++ Fiona=fiona.fio.fio:cli
+ ''',
+ install_requires=requirements,
+ tests_require=['nose'],
diff --git a/sci-libs/Fiona/metadata.xml b/sci-libs/Fiona/metadata.xml
new file mode 100644
index 00000000000..027d25f6a2b
--- /dev/null
+++ b/sci-libs/Fiona/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>slis@gentoo.org</email>
+ </maintainer>
+ <upstream>
+ <remote-id type="pypi">Fiona</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/Rtree/Manifest b/sci-libs/Rtree/Manifest
new file mode 100644
index 00000000000..23b42c9017d
--- /dev/null
+++ b/sci-libs/Rtree/Manifest
@@ -0,0 +1 @@
+DIST Rtree-0.8.2.tar.gz 55813 SHA256 064ecd9791fe170a8492f4ae75b0cbe8e62b5392f136a159a24d1b70c86d3c3f SHA512 c0c1091c21e92022540a0aed09c00f3b2b6abb2869757e0cb7a68a120e3a289f275cea824a72172ea5b327696a67024894f5f01354f0cd5ec5b05d9b3ec130e0 WHIRLPOOL 3167258f8a1480b2af65ebe6b6070870f6ad8dd2c5045285cb4babdff64a0bd85a4c434bf9b2a7908e211ec16be268482eacf2de8390afb27f06e8084c7b8db4
diff --git a/sci-libs/Rtree/Rtree-0.8.2.ebuild b/sci-libs/Rtree/Rtree-0.8.2.ebuild
new file mode 100644
index 00000000000..f15d40e7e25
--- /dev/null
+++ b/sci-libs/Rtree/Rtree-0.8.2.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="R-Tree spatial index for Python GIS"
+HOMEPAGE="https://pypi.python.org/pypi/Rtree"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="sci-libs/libspatialindex
+ sci-libs/scipy"
+DEPEND="dev-python/setuptools"
diff --git a/sci-libs/Rtree/metadata.xml b/sci-libs/Rtree/metadata.xml
new file mode 100644
index 00000000000..1d955686c63
--- /dev/null
+++ b/sci-libs/Rtree/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>slis@gentoo.org</email>
+ </maintainer>
+ <upstream>
+ <remote-id type="pypi">Rtree</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/Shapely/Manifest b/sci-libs/Shapely/Manifest
new file mode 100644
index 00000000000..6d0ebde8b8d
--- /dev/null
+++ b/sci-libs/Shapely/Manifest
@@ -0,0 +1,2 @@
+DIST Shapely-1.3.0.tar.gz 118863 SHA256 297df004aec27e38ed93987e93ff5f8187cd0299394fe8b0b9028566015a9bb5 SHA512 106f9773a5b00e7269a84c760f3a2b867c48139c48eebeecd524c8216d75c28daaf46eff45c118c1809999e33a317e9aca278a8d83605dc7273877a7ed3edd82 WHIRLPOOL ddf42cab233b0950a4a955070c5a2a7791a7f259ba857778689944c7799484f7c1aa710926c37c8c66deaae5ab4f03d79fa2f407e8e6d05238217b529e7b1b15
+DIST Shapely-1.3.2.tar.gz 120179 SHA256 9f0de51c71373fcee4962f79f4813d67ea1e711f4394d7636c929a4019c5c2ff SHA512 23d65c5a7137726e05e0399dc49f05e5ad9b582d4adcdf30215f72ae75989e85daf30ea2a5010d6a5a086cb6bbb5b4599b5065080b845c833776812f6e46566d WHIRLPOOL 37836bd5597e485fe4ac8bb0994724fd7cde59bc2d57becd0e89547c0b561d147ff9bea3d99b1429c8a163538a7af7deb8416a4e5dfb8c9f7dff5322e81b2fb6
diff --git a/sci-libs/Shapely/Shapely-1.3.0.ebuild b/sci-libs/Shapely/Shapely-1.3.0.ebuild
new file mode 100644
index 00000000000..aca63508a63
--- /dev/null
+++ b/sci-libs/Shapely/Shapely-1.3.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Geometric objects, predicates, and operations"
+HOMEPAGE="https://pypi.python.org/pypi/Shapely"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND=">=sci-libs/geos-3.1"
+DEPEND="${RDEPEND}
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
+
+PATCHES=( "${FILESDIR}"/setup_unicode.patch )
+
+python_test() {
+ esetup.py test
+}
diff --git a/sci-libs/Shapely/Shapely-1.3.2.ebuild b/sci-libs/Shapely/Shapely-1.3.2.ebuild
new file mode 100644
index 00000000000..aca63508a63
--- /dev/null
+++ b/sci-libs/Shapely/Shapely-1.3.2.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Geometric objects, predicates, and operations"
+HOMEPAGE="https://pypi.python.org/pypi/Shapely"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND=">=sci-libs/geos-3.1"
+DEPEND="${RDEPEND}
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
+
+PATCHES=( "${FILESDIR}"/setup_unicode.patch )
+
+python_test() {
+ esetup.py test
+}
diff --git a/sci-libs/Shapely/Shapely-9999.ebuild b/sci-libs/Shapely/Shapely-9999.ebuild
new file mode 100644
index 00000000000..1b3020d48dd
--- /dev/null
+++ b/sci-libs/Shapely/Shapely-9999.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+inherit distutils-r1 git-r3
+
+DESCRIPTION="Geometric objects, predicates, and operations"
+HOMEPAGE="https://pypi.python.org/pypi/Shapely"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/Toblerity/${PN}.git"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE="test"
+
+RDEPEND=">=sci-libs/geos-3.1"
+DEPEND="${RDEPEND}
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
+
+python_test() {
+ esetup.py test
+}
diff --git a/sci-libs/Shapely/files/setup_unicode.patch b/sci-libs/Shapely/files/setup_unicode.patch
new file mode 100644
index 00000000000..89e1b058f0f
--- /dev/null
+++ b/sci-libs/Shapely/files/setup_unicode.patch
@@ -0,0 +1,23 @@
+--- setup.py.orig 2014-06-20 10:27:26.638779565 +0200
++++ setup.py 2014-06-20 10:27:29.885446151 +0200
+@@ -1,4 +1,5 @@
+ #!/usr/bin/env python
++# -*- coding: utf-8 -*-
+
+ from __future__ import print_function
+
+@@ -74,8 +75,12 @@
+ readme_text = fp.read()
+ readme_text = readme_text.replace(".. include:: CREDITS.txt", "")
+
+-with open('CREDITS.txt', 'r') as fp:
+- credits = fp.read()
++if sys.version_info[0] == 3:
++ with open('CREDITS.txt', 'r', encoding='utf-8') as fp:
++ credits = fp.read()
++elif sys.version_info[0] == 2:
++ with open('CREDITS.txt', 'r') as fp:
++ credits = fp.read().decode('utf-8')
+
+ with open('CHANGES.txt', 'r') as fp:
+ changes_text = fp.read()
diff --git a/sci-libs/Shapely/metadata.xml b/sci-libs/Shapely/metadata.xml
new file mode 100644
index 00000000000..ed7978de6ac
--- /dev/null
+++ b/sci-libs/Shapely/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>slis@gentoo.org</email>
+ </maintainer>
+ <upstream>
+ <remote-id type="pypi">Shapely</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/ViSP/Manifest b/sci-libs/ViSP/Manifest
new file mode 100644
index 00000000000..ee4b922b24a
--- /dev/null
+++ b/sci-libs/ViSP/Manifest
@@ -0,0 +1 @@
+DIST ViSP-2.10.0.tar.gz 20745399 SHA256 1c8a37cadd0012526be9ceaa182eb21fb0d45aac622a1f0f2d255225e85797aa SHA512 485bad6aea1dddf51c1edd162e22f5f00205947b67b57843207902ea3b97b683828031338282861be495d66cc79bde3a7af09c075aa9c6b783652d5d3bd4f9ef WHIRLPOOL d3d7e29076231fd581346f7de37ef49afed22f48198673d08268b1a298121d8a9bd8a9bc6e34cf2a5655cf45575599b09c5cb56e78961340122ca6f95ee275e3
diff --git a/sci-libs/ViSP/ViSP-2.10.0.ebuild b/sci-libs/ViSP/ViSP-2.10.0.ebuild
new file mode 100644
index 00000000000..9bc5ac3e2a0
--- /dev/null
+++ b/sci-libs/ViSP/ViSP-2.10.0.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Visual Servoing Platform: visual tracking and visual servoing library"
+HOMEPAGE="http://www.irisa.fr/lagadic/visp/visp.html"
+SRC_URI="http://gforge.inria.fr/frs/download.php/latestfile/475/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~arm"
+IUSE="
+ demos +dmtx doc examples ffmpeg gsl ieee1394 jpeg lapack ogre ois opencv png
+ test tutorials usb v4l X xml +zbar zlib
+"
+
+RDEPEND="
+ dmtx? ( media-libs/libdmtx )
+ ffmpeg? ( virtual/ffmpeg )
+ gsl? ( sci-libs/gsl )
+ ieee1394? ( media-libs/libdc1394 )
+ jpeg? ( virtual/jpeg:0 )
+ lapack? ( virtual/lapack )
+ ogre? ( dev-games/ogre[ois?] dev-libs/boost:=[threads] )
+ opencv? ( media-libs/opencv )
+ png? ( media-libs/libpng:0= )
+ usb? ( virtual/libusb:1 )
+ v4l? ( media-libs/libv4l )
+ X? ( x11-libs/libX11 )
+ xml? ( dev-libs/libxml2 )
+ zbar? ( media-gfx/zbar )
+ zlib? ( sys-libs/zlib )
+"
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen virtual/latex-base media-gfx/graphviz )
+ virtual/pkgconfig
+ test? ( sci-misc/ViSP-images )
+ v4l? ( virtual/os-headers )"
+RDEPEND="${RDEPEND}
+ demos? ( sci-misc/ViSP-images )"
+REQUIRED_USE="ffmpeg? ( opencv ) ois? ( ogre )"
+PATCHES=( "${FILESDIR}/opencv.patch" "${FILESDIR}/opencv3.patch" )
+
+src_configure() {
+ local mycmakeargs=(
+ "-DBUILD_EXAMPLES=$(usex examples ON OFF)"
+ "-DBUILD_TESTS=$(usex test ON OFF)"
+ "-DBUILD_DEMOS=$(usex demos ON OFF)"
+ "-DBUILD_TUTORIALS=$(usex tutorials ON OFF)"
+ "-DUSE_V4L2=$(usex v4l ON OFF)"
+ "-DUSE_DC1394=$(usex ieee1394 ON OFF)"
+ "-DUSE_LAPACK=$(usex lapack ON OFF)"
+ "-DUSE_GSL=$(usex gsl ON OFF)"
+ "-DUSE_OGRE=$(usex ogre ON OFF)"
+ "-DUSE_OIS=$(usex ois ON OFF)"
+ "-DUSE_LIBUSB_1=$(usex usb ON OFF)"
+ "-DUSE_XML2=$(usex xml ON OFF)"
+ "-DUSE_OPENCV=$(usex opencv ON OFF)"
+ "-DUSE_ZLIB=$(usex zlib ON OFF)"
+ "-DUSE_X11=$(usex X ON OFF)"
+ "-DUSE_LIBJPEG=$(usex jpeg ON OFF)"
+ "-DUSE_LIBPNG=$(usex png ON OFF)"
+ "-DUSE_FFMPEG=$(usex ffmpeg ON OFF)"
+ "-DUSE_ZBAR=$(usex zbar ON OFF)"
+ "-DUSE_DMTX=$(usex dmtx ON OFF)"
+ )
+ cmake-utils_src_configure
+}
+
+src_compile() {
+ cmake-utils_src_compile
+ cd "${BUILD_DIR}"
+ use doc && emake visp_doc
+}
+
+src_install() {
+ cmake-utils_src_install
+ if use tutorials ; then
+ dodoc -r tutorial
+ docompress -x /usr/share/doc/${PF}/tutorial
+ fi
+ cd "${BUILD_DIR}"
+ use doc && dohtml -r doc/html/*
+}
diff --git a/sci-libs/ViSP/files/opencv.patch b/sci-libs/ViSP/files/opencv.patch
new file mode 100644
index 00000000000..c8cafe0a5c9
--- /dev/null
+++ b/sci-libs/ViSP/files/opencv.patch
@@ -0,0 +1,13 @@
+Index: ViSP-2.10.0/CMakeLists.txt
+===================================================================
+--- ViSP-2.10.0.orig/CMakeLists.txt
++++ ViSP-2.10.0/CMakeLists.txt
+@@ -1450,7 +1450,7 @@ if(USE_OPENCV)
+ list(APPEND VISP_EXTERN_LIBRARIES ${OpenCV_LIBS})
+ endif()
+ list(APPEND VISP_EXTERN_INCLUDE_DIRS ${OpenCV_INCLUDE_DIRS})
+- #LIST(APPEND VISP_EXTERN_LIBRARIES ${OpenCV_LIBS})
++ LIST(APPEND VISP_EXTERN_LIBRARIES ${OpenCV_LIBRARIES})
+ #MESSAGE("OpenCV_INCLUDE_DIRS = ${OpenCV_INCLUDE_DIRS}")
+ #MESSAGE("OpenCV_LIBS = ${OpenCV_LIBS}")
+ #MESSAGE("OpenCV_LIB_DIR = ${OpenCV_LIB_DIR}")
diff --git a/sci-libs/ViSP/files/opencv3.patch b/sci-libs/ViSP/files/opencv3.patch
new file mode 100644
index 00000000000..8f7f9ee269c
--- /dev/null
+++ b/sci-libs/ViSP/files/opencv3.patch
@@ -0,0 +1,67 @@
+Index: ViSP-2.10.0/src/key-point/vpKeyPoint.h
+===================================================================
+--- ViSP-2.10.0.orig/src/key-point/vpKeyPoint.h
++++ ViSP-2.10.0/src/key-point/vpKeyPoint.h
+@@ -494,6 +494,7 @@ public:
+ initDetector(detectorName);
+ }
+
++#if (VISP_HAVE_OPENCV_VERSION >= 0x020400 && VISP_HAVE_OPENCV_VERSION < 0x030000)
+ /*!
+ Template function to set to a \p parameterName a value for a specific detector named by his \p detectorName.
+
+@@ -507,6 +508,7 @@ public:
+ m_detectors[detectorName]->set(parameterName, value);
+ }
+ }
++#endif
+
+ /*!
+ Set and initialize a list of detectors denominated by their names \p detectorNames.
+@@ -532,6 +534,7 @@ public:
+ initExtractor(extractorName);
+ }
+
++#if (VISP_HAVE_OPENCV_VERSION >= 0x020400 && VISP_HAVE_OPENCV_VERSION < 0x030000)
+ /*!
+ Template function to set to a \p parameterName a value for a specific extractor named by his \p extractorName.
+
+@@ -545,6 +548,7 @@ public:
+ m_extractors[extractorName]->set(parameterName, value);
+ }
+ }
++#endif
+
+ /*!
+ Set and initialize a list of extractors denominated by their names \p extractorNames.
+@@ -700,7 +704,7 @@ public:
+ m_useAffineDetection = useAffine;
+ }
+
+-#if (VISP_HAVE_OPENCV_VERSION >= 0x020400)
++#if (VISP_HAVE_OPENCV_VERSION >= 0x020400 && VISP_HAVE_OPENCV_VERSION < 0x030000)
+ /*!
+ Set if cross check method must be used to eliminate some false matches with a brute-force matching method.
+
+Index: ViSP-2.10.0/src/key-point/vpKeyPoint.cpp
+===================================================================
+--- ViSP-2.10.0.orig/src/key-point/vpKeyPoint.cpp
++++ ViSP-2.10.0/src/key-point/vpKeyPoint.cpp
+@@ -868,7 +868,7 @@ void vpKeyPoint::detect(const vpImage<un
+ (int) rectangle.getBottom());
+ cv::rectangle(mask, leftTop, rightBottom, cv::Scalar(255), CV_FILLED);
+ } else {
+- mask = cv::Mat::ones(matImg.rows, matImg.cols, CV_8U);
++ mask = cv::Mat::ones(matImg.rows, matImg.cols, CV_8U) * 255;
+ }
+
+ detect(matImg, keyPoints, elapsedTime, mask);
+@@ -1544,7 +1544,7 @@ void vpKeyPoint::initExtractors(const st
+ void vpKeyPoint::initMatcher(const std::string &matcherName) {
+ m_matcher = cv::DescriptorMatcher::create(matcherName);
+
+-#if (VISP_HAVE_OPENCV_VERSION >= 0x020400)
++#if (VISP_HAVE_OPENCV_VERSION >= 0x020400 && VISP_HAVE_OPENCV_VERSION < 0x030000)
+ if(m_matcher != NULL && !m_useKnn && matcherName == "BruteForce") {
+ m_matcher->set("crossCheck", m_useBruteForceCrossCheck);
+ }
diff --git a/sci-libs/ViSP/metadata.xml b/sci-libs/ViSP/metadata.xml
new file mode 100644
index 00000000000..6e275638c4c
--- /dev/null
+++ b/sci-libs/ViSP/metadata.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer>
+<email>aballier@gentoo.org</email>
+<name>Alexis Ballier</name>
+</maintainer>
+<use>
+ <flag name="dmtx">Enables barcode data matrix support.</flag>
+ <flag name="demos">Installs demo programs.</flag>
+ <flag name="ogre">Enables <pkg>dev-games/ogre</pkg> support.</flag>
+ <flag name="ois">Enables <pkg>dev-games/ois</pkg> support via ogre.</flag>
+ <flag name="opencv">Enables <pkg>media-libs/opencv</pkg> support.</flag>
+ <flag name="tutorials">Installs tutorials.</flag>
+ <flag name="zbar">Enables barcodes reading.</flag>
+</use>
+<longdescription lang="en">
+ ViSP standing for Visual Servoing Platform is a modular cross platform library that allows prototyping and developing applications using visual tracking and visual servoing technics at the heart of the researches done by Inria Lagadic team.
+ ViSP is able to compute control laws that can be applied to robotic systems.
+ It provides a set of visual features that can be tracked using real time image processing or computer vision algorithms.
+ ViSP provides also simulation capabilities.
+
+ ViSP can be useful in robotics, computer vision, augmented reality and computer animation.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/acml/Manifest b/sci-libs/acml/Manifest
new file mode 100644
index 00000000000..1bc390d246b
--- /dev/null
+++ b/sci-libs/acml/Manifest
@@ -0,0 +1,6 @@
+DIST acml-4-1-0-gfortran-32bit.tgz 18258099 SHA256 52580576c3a425635eccb19fc5df38c3139fbc44fd669799bc8ffd0e2d82ccc7
+DIST acml-4-1-0-gfortran-64bit-int64.tgz 29351223 SHA256 825ae742df873cf6d41fbaaecff08941badb2b43a7021ba6c8af7abc75a6d14d
+DIST acml-4-1-0-gfortran-64bit.tgz 29995624 SHA256 50f64687b86556123538e1f2bd4c185ff1d018501a5a5834ec8acf7487c817c4
+DIST acml-4-1-0-ifort-32bit.tgz 18797527 SHA256 5dfa768c12e96d2d25678e85cf2e0eea3bd427ddd94f417bcad09abe25369375
+DIST acml-4-1-0-ifort-64bit-int64.tgz 36135363 SHA256 3da0ded50ab25e44f531ac58b469344fed0f6af4ae70aa58b1286cf8de9731a4
+DIST acml-4-1-0-ifort-64bit.tgz 36577689 SHA256 b5b60425fccb624e3baf48f5d51ae68ccdc3e9852a4a50661bb3e45a6f25be40
diff --git a/sci-libs/acml/acml-4.1.0-r2.ebuild b/sci-libs/acml/acml-4.1.0-r2.ebuild
new file mode 100644
index 00000000000..05a9a11930c
--- /dev/null
+++ b/sci-libs/acml/acml-4.1.0-r2.ebuild
@@ -0,0 +1,200 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils fortran-2 multilib toolchain-funcs versionator
+
+MY_P=${PN}-$(replace_all_version_separators -)
+
+DESCRIPTION="AMD Core Math Library for x86 and amd64 CPUs"
+HOMEPAGE="http://developer.amd.com/acml.jsp"
+SRC_URI="
+ amd64? (
+ ifc? ( ${MY_P}-ifort-64bit.tgz
+ int64? ( ${MY_P}-ifort-64bit-int64.tgz ) )
+ gfortran? ( ${MY_P}-gfortran-64bit.tgz
+ int64? ( ${MY_P}-gfortran-64bit-int64.tgz ) )
+ !ifc? (
+ !gfortran? ( ${MY_P}-gfortran-64bit.tgz
+ int64? ( ${MY_P}-gfortran-64bit-int64.tgz ) ) ) )
+ x86? (
+ ifc? ( ${MY_P}-ifort-32bit.tgz )
+ gfortran? ( ${MY_P}-gfortran-32bit.tgz )
+ !ifc? ( !gfortran? ( ${MY_P}-gfortran-32bit.tgz ) ) )"
+
+SLOT="0"
+LICENSE="ACML"
+KEYWORDS="-* ~amd64 ~x86"
+IUSE="doc examples gfortran ifc int64 openmp test"
+
+RESTRICT="strip fetch"
+
+CDEPEND="
+ ifc? ( dev-lang/ifc )
+ gfortran? ( =sys-devel/gcc-4.2* )
+ !gfortran? ( !ifc? ( =sys-devel/gcc-4.2* ) )"
+
+DEPEND="
+ app-eselect/eselect-blas
+ app-eselect/eselect-lapack
+ test? ( ${CDEPEND} )"
+
+RDEPEND="${CDEPEND}
+ app-eselect/eselect-blas
+ app-eselect/eselect-lapack
+ doc? ( app-doc/blas-docs app-doc/lapack-docs )"
+
+S="${WORKDIR}"
+
+pkg_nofetch() {
+ einfo "Please download the ACML from:"
+ einfo "${HOMEPAGE}"
+ einfo "and place it in ${DISTDIR}."
+ einfo "The previous versions could be found at"
+ einfo "http://developer.amd.com/acmlarchive.jsp"
+ einfo "SRC=${A} $SRC_URI"
+}
+
+get_fcomp() {
+ case $(tc-getFC) in
+ *gfortran* )
+ FCOMP="gfortran" ;;
+ ifort )
+ FCOMP="ifc" ;;
+ * )
+ FCOMP=$(tc-getFC) ;;
+ esac
+}
+
+pkg_setup() {
+ if use test; then
+ # work around incomplete fortran eclass
+ if use gfortran &&
+ [[ $(tc-getFC) =~ gfortran ]] &&
+ [[ $(gcc-version) != 4.2 ]]
+ then
+ eerror "You need gfortran-4.2 to test acml"
+ eerror "Please use gcc-config to switch gcc version 4.2"
+ die "gfortran check failed"
+ fi
+ fi
+ if use openmp; then
+ tc-has-openmp || die "Please ensure your compiler has openmp support"
+ FORTRAN_NEED_OPENMP=1
+ fi
+ fortran-2_pkg_setup
+ get_fcomp
+ # construct default profile dprof from default ddir
+ local ddir=gfortran
+ use ifc && ddir=ifort
+ use x86 && ddir=${ddir}32 || ddir=${ddir}64
+ use openmp && ddir=${ddir}_mp
+ use int64 && ddir=${ddir}_int64
+ ACML_DEFAULT_DIR=${ddir}
+}
+
+src_unpack() {
+ unpack ${A}
+ unpack ./contents-acml-*.tgz
+ use openmp || rm -rf *_mp*
+}
+
+src_test() {
+ # only testing with current chosen compiler
+ for fdir in ${ACML_DEFAULT_DIR/_mp}*; do
+ einfo "Testing acml in ${fdir}"
+ for d in . acml_mv; do
+ cd "${S}"/${fdir}/examples/${d}
+ emake \
+ ACMLDIR="${S}"/${fdir} \
+ F77=$(tc-getFC) \
+ CC="$(tc-getCC)" \
+ CPLUSPLUS="$(tc-getCXX)"
+ emake clean
+ done
+ done
+}
+
+make_acml_profile_name() {
+ local fort=${1%%[[:digit:]]*}
+ local opt=${1#*[0-9][0-9]}
+ echo ${PN}-${fort}${opt/mp/openmp} | tr '_' '-'
+}
+
+src_install() {
+ # respect acml default install dir (and FHS)
+ local instdir=/opt/${PN}${PV}
+ dodir ${instdir}
+
+ for lib in */lib; do
+ local fdir=${lib%/*}
+ # install acml
+ use examples || rm -rf "${S}"/${fdir}/examples
+ cp -pPR "${S}"/${fdir} "${D}"${instdir} || die "copy ${fdir} failed"
+
+ # install profiles
+ local prof=$(make_acml_profile_name ${fdir})
+ local acmldir=${instdir}/${fdir}
+ local acmllibs="-lacml"
+ local libname=${acmldir}/lib/libacml
+ local extlibs
+ local extflags
+ [[ ${fdir} =~ int64 ]] && extflags="${extflags} -fdefault-integer-8"
+ [[ ${fdir} =~ gfortran ]] && extlibs="${extlibs} -lgfortran"
+ if [[ ${fdir} =~ _mp ]]; then
+ [[ ${fdir} =~ ifort ]] && extlibs="${extlibs} -lguide"
+ extlibs="${extlibs} -lpthread"
+ extflags="${extflags} -fopenmp"
+ acmllibs="-lacml_mp"
+ libname=${libname}_mp
+ fi
+ use amd64 && acmllibs="${acmllibs} -lacml_mv"
+ for x in blas lapack; do
+ # pkgconfig files
+ sed -e "s:@LIBDIR@:$(get_libdir):" \
+ -e "s:@PV@:${PV}:" \
+ -e "s:@ACMLDIR@:${acmldir}:g" \
+ -e "s:@ACMLLIBS@:${acmllibs}:g" \
+ -e "s:@EXTLIBS@:${extlibs}:g" \
+ -e "s:@EXTFLAGS@:${extflags}:g" \
+ "${FILESDIR}"/${x}.pc.in > ${x}.pc \
+ || die "sed ${x}.pc failed"
+ insinto ${acmldir}/lib
+ doins ${x}.pc
+
+ # eselect files
+ cat > eselect.${prof}.${x} <<-EOF
+ ${libname}.so /usr/@LIBDIR@/lib${x}.so.0
+ ${libname}.so /usr/@LIBDIR@/lib${x}.so
+ ${libname}.a /usr/@LIBDIR@/lib${x}.a
+ ${acmldir}/lib/${x}.pc /usr/@LIBDIR@/pkgconfig/${x}.pc
+ EOF
+ eselect ${x} add $(get_libdir) eselect.${prof}.${x} ${prof}
+ done
+ done
+
+ echo "LDPATH=${instdir}/${ACML_DEFAULT_DIR}/lib" > 35acml
+ doenvd "${S}"/35acml
+ use doc || rm -rf "${S}"/Doc/acml.pdf "${S}"/Doc/html
+ cp -pPR "${S}"/Doc "${D}"${instdir} || die "copy doc failed"
+}
+
+pkg_postinst() {
+ local dprof="$(make_acml_profile_name ${ACML_DEFAULT_DIR})"
+ for x in blas lapack; do
+ local cprof=$(eselect ${x} show | cut -d' ' -f2)
+ if [[ ${cprof} == ${dprof} || -z ${cprof} ]]; then
+ # work around eselect bug #189942
+ local configfile="${ROOT}"/etc/env.d/${x}/$(get_libdir)/config
+ [[ -e ${configfile} ]] && rm -f ${configfile}
+ eselect ${x} set ${dprof}
+ elog "${x} has been eselected to ${dprof}"
+ else
+ elog "Current eselected ${x} implementation is ${cprof}"
+ elog "To use you have one of ${PN}, issue (as root):"
+ elog "\t eselect ${x} set <profile>"
+ fi
+ done
+}
diff --git a/sci-libs/acml/files/blas.pc.in b/sci-libs/acml/files/blas.pc.in
new file mode 100644
index 00000000000..523aabc1204
--- /dev/null
+++ b/sci-libs/acml/files/blas.pc.in
@@ -0,0 +1,11 @@
+prefix=@ACMLDIR@
+exec_prefix=${prefix}
+libdir=${prefix}/lib
+includedir=${prefix}/include
+
+Name: blas
+Description: ACML implementations of the Basic Linear Algebra Subroutines
+Version: @PV@
+URL: http://developer.amd.com/acml.jsp
+Libs: -Wl,--no-as-needed -L${libdir} @ACMLLIBS@ @EXTLIBS@
+Cflags: @EXTFLAGS@
diff --git a/sci-libs/acml/files/lapack.pc.in b/sci-libs/acml/files/lapack.pc.in
new file mode 100644
index 00000000000..48fef122dfe
--- /dev/null
+++ b/sci-libs/acml/files/lapack.pc.in
@@ -0,0 +1,11 @@
+prefix=@ACMLDIR@
+exec_prefix=${prefix}
+libdir=${prefix}/lib
+includedir=${prefix}/include
+
+Name: lapack
+Description: ACML implementation of the F77 Linear Algebra PACKage
+Version: @PV@
+URL: http://developer.amd.com/acml.jsp
+Libs: -Wl,--no-as-needed -L${libdir} @ACMLLIBS@ @EXTLIBS@
+Cflags: @EXTFLAGS@
diff --git a/sci-libs/acml/metadata.xml b/sci-libs/acml/metadata.xml
new file mode 100644
index 00000000000..29546f51523
--- /dev/null
+++ b/sci-libs/acml/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+ The AMD(R) Core Math Library provides an implementation of the "Basic
+ Linear Algebra Subprograms" (BLAS) and the "Linear Algebra PACKage"
+ (LAPACK) as well as a set of "Fast Fourier Transformation" (FFT)
+ routines, all highly optimized for AMD(R) x86 and amd64 CPUs.
+</longdescription>
+ <longdescription lang="de">
+ Die AMD(R) Core Math Library ist ein Ersatz für die "Basic Linear
+ Algebra Subprograms" (BLAS) und das "Linear Algebra PACKage" (LAPACK).
+ Außerdem enthält sie Routinen zur "Fast Fourier Tranformation" (FFT).
+ Alle Routinen sind hoch optimiert für AMD(R) x86 und amd64 CPUs.
+</longdescription>
+ <use>
+ <flag name="gfortran">Fetch and install acml compiled with GNU gfortran</flag>
+ <flag name="ifc">Fetch and install acml compiled with Intel Fortran Compiler
+ (<pkg>dev-lang/ifc</pkg>)</flag>
+ <flag name="int64">Install the 64 bits integer library</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-libs/adolc/Manifest b/sci-libs/adolc/Manifest
new file mode 100644
index 00000000000..39489cbe99b
--- /dev/null
+++ b/sci-libs/adolc/Manifest
@@ -0,0 +1,3 @@
+DIST ADOL-C-2.4.1.tgz 2210414 SHA256 05bf946cc1764e2b3fa7e708ccc4303f289699d9f36b9d525f6a9a6129b4d578 SHA512 5e5135ca587d159510bf77338fdff3d324f4d32c4ec6f8cf64ddc92253b427b8ee26a30bc1d83fe18121bbfdc7454c3536f58849c0c335e1b240e39d46acdccc WHIRLPOOL cd66a895dc3cb1f6f4f705a9fbce5a93dcb6856b6288704c3d3420be7f90e57296acd3fb2ea897ba5362e706429ec56b070bf0baa7094edcbf46c92d535bc492
+DIST ADOL-C-2.5.0.tgz 2313753 SHA256 908753153e0eca31752222150977eabd8ab97c4ab8fcd19f92667aba69a048a6 SHA512 e680565ed911bc15165c27281428c1daf35e95292dc3abc64aab6633068ec0d7e7ae626e692e0574b2c696a0c4aec2c79b2b02c3760acd2bd1b579a4c42d9585 WHIRLPOOL c0301c9a8f1357aa06be8e6a53bee9825a5d56cd31a2734862bcfd1f7c944935a4cd2c8c2ed49028493cb7c998008c9853b2d4bd7f6e0519ed353bbd3b7d0a8c
+DIST ADOL-C-2.5.2.tgz 2320010 SHA256 2fa514d9799989d6379738c2bcf75070d9834e4d227eb32a5b278840893b2af9 SHA512 3d2ef6e42504de9e9c1b5777afda8ece83fa61ab7c22fd471dce6bcb74af0a789d37cd2a6c9c9ead13f6c78e07ba985e7d14e79bcdf35fa56f8e73a2411905b5 WHIRLPOOL 55043cabe44b9913a7fba73ddaf0d64caa234d7002582d78dd9cfc05510ce3fbcb6dd3d1c40a2d6425f5ee1b7cc986d525d065671191096fbb303e122089c954
diff --git a/sci-libs/adolc/adolc-2.4.1.ebuild b/sci-libs/adolc/adolc-2.4.1.ebuild
new file mode 100644
index 00000000000..7adde9df110
--- /dev/null
+++ b/sci-libs/adolc/adolc-2.4.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+AUTOTOOLS_IN_SOURCE_BUILD=yes
+inherit autotools-utils toolchain-funcs
+
+MYPN=ADOL-C
+
+DESCRIPTION="Automatic differentiation system for C/C++"
+HOMEPAGE="https://projects.coin-or.org/ADOL-C/"
+SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz"
+
+LICENSE="|| ( EPL-1.0 GPL-2 )"
+SLOT="0/1"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="sparse static-libs"
+
+RDEPEND="sparse? ( sci-libs/colpack )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MYPN}-${PV}"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.4.0-no-colpack.patch )
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable sparse)
+ $(use_with sparse colpack "${EPREFIX}"/usr)
+ )
+ autotools-utils_src_configure
+}
+
+src_test() {
+ autotools-utils_src_test test
+}
diff --git a/sci-libs/adolc/adolc-2.5.0.ebuild b/sci-libs/adolc/adolc-2.5.0.ebuild
new file mode 100644
index 00000000000..a74e53adb60
--- /dev/null
+++ b/sci-libs/adolc/adolc-2.5.0.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+#AUTOTOOLS_IN_SOURCE_BUILD=yes
+
+inherit autotools-utils toolchain-funcs
+
+MYPN=ADOL-C
+
+DESCRIPTION="Automatic differentiation system for C/C++"
+HOMEPAGE="https://projects.coin-or.org/ADOL-C/"
+SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz"
+
+LICENSE="|| ( EPL-1.0 GPL-2 )"
+SLOT="0/1"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="mpi sparse static-libs"
+
+RDEPEND="mpi? ( sys-cluster/ampi:0= )
+ sparse? ( sci-libs/colpack:0= )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MYPN}-${PV}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.5.0-no-colpack.patch
+ "${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch
+)
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable mpi ampi)
+ $(use_enable sparse)
+ $(use_with sparse colpack "${EPREFIX}"/usr)
+ )
+ autotools-utils_src_configure
+}
+
+src_test() {
+ autotools-utils_src_test test
+}
diff --git a/sci-libs/adolc/adolc-2.5.2.ebuild b/sci-libs/adolc/adolc-2.5.2.ebuild
new file mode 100644
index 00000000000..eacb9e3990e
--- /dev/null
+++ b/sci-libs/adolc/adolc-2.5.2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+#AUTOTOOLS_IN_SOURCE_BUILD=yes
+
+inherit autotools-utils toolchain-funcs
+
+MYPN=ADOL-C
+
+DESCRIPTION="Automatic differentiation system for C/C++"
+HOMEPAGE="https://projects.coin-or.org/ADOL-C/"
+SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz"
+
+LICENSE="|| ( EPL-1.0 GPL-2 )"
+SLOT="0/1"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="mpi sparse static-libs"
+
+RDEPEND="
+ mpi? ( sys-cluster/ampi:0= )
+ sparse? ( sci-libs/colpack:0= )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MYPN}-${PV}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.5.0-no-colpack.patch
+ "${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch
+ "${FILESDIR}"/${P}-dash.patch
+)
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable mpi ampi)
+ $(use_enable sparse)
+ $(use_with sparse colpack "${EPREFIX}"/usr)
+ )
+ autotools-utils_src_configure
+}
+
+src_test() {
+ autotools-utils_src_test test
+}
diff --git a/sci-libs/adolc/files/adolc-2.4.0-no-colpack.patch b/sci-libs/adolc/files/adolc-2.4.0-no-colpack.patch
new file mode 100644
index 00000000000..e3b5a4a2ca5
--- /dev/null
+++ b/sci-libs/adolc/files/adolc-2.4.0-no-colpack.patch
@@ -0,0 +1,24 @@
+do not test colpack when user says no even when it is installed
+
+--- configure.ac.orig 2012-07-19 13:04:37.426461811 -0700
++++ configure.ac 2012-07-19 13:06:06.477916144 -0700
+@@ -281,7 +281,7 @@
+ COLPACK_LIBDIR=""
+ COLPACK_LIBS="-lColPack"
+ ])
+-
++if test x$colpack != xno; then
+ AC_LANG_PUSH([C++])
+ save_CPPFLAGS="$CPPFLAGS"
+ save_LIBS="$LIBS"
+@@ -301,7 +301,9 @@
+ CPPFLAGS="$save_CPPFLAGS"
+ LIBS="$save_LIBS"
+ AC_LANG_POP([C++])
+-
++else
++ have_colpack=no
++fi
+ AM_CONDITIONAL(HAVE_LIBCOLPACK,[test x$have_colpack = xyes])
+ if test x$have_colpack = xyes; then
+ sparse=yes
diff --git a/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch b/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch
new file mode 100644
index 00000000000..779890c8cf2
--- /dev/null
+++ b/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch
@@ -0,0 +1,57 @@
+ autoconf/colpack.m4 | 23 +++++++++++++----------
+ 1 file changed, 13 insertions(+), 10 deletions(-)
+
+diff --git a/autoconf/colpack.m4 b/autoconf/colpack.m4
+index 9792786..bd4ba5e 100644
+--- a/autoconf/colpack.m4
++++ b/autoconf/colpack.m4
+@@ -8,20 +8,20 @@ AC_ARG_WITH(colpack,
+ AS_HELP_STRING([--with-colpack=DIR],[path to the colpack library and headers [default=system libraries]])],
+ [
+ colpack=$withval
+-COLPACK_CFLAGS="-I$colpack/include"
+-if test x${_lib} != xlib ; then
+- D[[0]]="$colpack/${_lib}"
+- D[[1]]="$colpack/lib"
+-else
+- D[[0]]="$colpack/${_lib}"
+-fi
+ ],
+ [
+ COLPACK_CFLAGS=""
+ COLPACK_LIBS="-lColPack"
+ D[[0]]=""
+ ])
+-
++if test x$colpack != xno; then
++COLPACK_CFLAGS="-I$colpack/include"
++if test x${_lib} != xlib ; then
++ D[[0]]="$colpack/${_lib}"
++ D[[1]]="$colpack/lib"
++else
++ D[[0]]="$colpack/${_lib}"
++fi
+ AC_LANG_PUSH([C++])
+ save_CXXFLAGS="$CXXFLAGS"
+ save_CPPFLAGS="$CPPFLAGS"
+@@ -33,8 +33,8 @@ have_colpackheaders=no
+ CPPFLAGS="$save_CPPFLAGS"
+ CXXFLAGS="$save_CXXFLAGS"
+ ])
+-for ((i=0; i < ${#D[@]} ; i++)); do
+-COLPACK_LIBDIR="${D[[$i]]}"
++for i in ${D[@]}; do
++COLPACK_LIBDIR="${i}"
+ if test -n "$COLPACK_LIBDIR" ; then
+ COLPACK_LIBS="-L$COLPACK_LIBDIR -lColPack -Wl,-rpath,$COLPACK_LIBDIR"
+ fi
+@@ -56,6 +56,9 @@ else
+ fi
+ done
+ AC_LANG_POP([C++])
++else
++ have_colpack=no
++fi
+
+ AM_CONDITIONAL(HAVE_LIBCOLPACK,[test x$have_colpack = xyes])
+ if test x$have_colpack = xyes; then
diff --git a/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch b/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch
new file mode 100644
index 00000000000..4a6296e2db7
--- /dev/null
+++ b/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch
@@ -0,0 +1,9 @@
+--- adolclib.pc.in.orig 2014-05-21 09:09:10.060824555 -0700
++++ adolclib.pc.in 2014-05-21 09:09:10.060824555 -0700
+@@ -7,5 +7,5 @@
+ Version: @PACKAGE_VERSION@
+ Description: Algorithmic Differentiation Library for C/C++
+ Requires:
+-Libs: -L${libdir} -l@adolclib@ -Wl,-rpath,${libdir} @LDFLAGS@ @LIBS@
++Libs: -L${libdir} -l@adolclib@ @LIBS@
+ Cflags: -I${includedir}
diff --git a/sci-libs/adolc/files/adolc-2.5.2-dash.patch b/sci-libs/adolc/files/adolc-2.5.2-dash.patch
new file mode 100644
index 00000000000..3aa5a3035a1
--- /dev/null
+++ b/sci-libs/adolc/files/adolc-2.5.2-dash.patch
@@ -0,0 +1,148 @@
+ configure.ac | 45 +++++++++++++++++----------------------------
+ 1 file changed, 17 insertions(+), 28 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 926832c..1310025 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -29,12 +29,12 @@ AM_SILENT_RULES([yes])
+
+ adolclib=adolc
+
+-if test "x$CFLAGS" == x ; then
++if test "x$CFLAGS" = x ; then
+ ac_shell_cflags="not_set"
+ else
+ ac_shell_cflags="$CFLAGS"
+ fi
+-if test "x$CXXFLAGS" == x ; then
++if test "x$CXXFLAGS" = x ; then
+ ac_shell_cxxflags="not_set"
+ else
+ ac_shell_cxxflags="$CXXFLAGS"
+@@ -225,12 +225,12 @@ AS_HELP_STRING([--enable-harddebug],[enable ADOL-C hard debug mode
+ AC_MSG_RESULT(no)
+ ])
+
+-if test x$adolc_harddebug == xyes ; then
++if test x$adolc_harddebug = xyes ; then
+ adolc_debug=yes
+ AC_DEFINE(ADOLC_HARDDEBUG,1,[ADOL-C hard debug mode])
+ fi
+
+-if test x$adolc_debug == xyes ; then
++if test x$adolc_debug = xyes ; then
+ AC_DEFINE(ADOLC_DEBUG,1,[ADOL-C debug mode])
+ fi
+
+@@ -248,7 +248,7 @@ AS_HELP_STRING([--disable-stdczero],[adouble default constructor does not initia
+ AC_MSG_RESULT(yes)
+ ])
+
+-if test x$adolc_stdczero == xyes; then
++if test x$adolc_stdczero = xyes; then
+ AC_DEFINE(ADOLC_ADOUBLE_STDCZERO,1,[ADOL-C adouble zeroing mode])
+ fi
+
+@@ -265,7 +265,7 @@ AS_HELP_STRING([--enable-lateinit],[adouble constructors need to be called. With
+ AC_MSG_RESULT(no)
+ ])
+
+-if test x$adolc_late_init == xyes; then
++if test x$adolc_late_init = xyes; then
+ AC_DEFINE(ADOLC_ADOUBLE_LATEINIT,1,[ADOL-C adouble late initialization mode])
+ fi
+
+@@ -282,7 +282,7 @@ AS_HELP_STRING([--enable-tserrno],[use errno as thread number cache [default=no]
+ AC_MSG_RESULT(no)
+ ])
+
+-if test x$adolc_tserrno == xyes ; then
++if test x$adolc_tserrno = xyes ; then
+ AC_DEFINE(ADOLC_THREADSAVE_ERRNO,1,[ADOL-C thread save errno mode])
+ fi
+
+@@ -351,8 +351,8 @@ AC_ARG_WITH(cflags,
+ [AS_HELP_STRING([--with-cflags=FLAGS],
+ [use CFLAGS=FLAGS (default: -O2)])],
+ [ac_adolc_cflags="$withval"
+- if test x${adolc_debug} == xyes ||
+- test x${adolc_harddebug} == xyes ; then
++ if test "x${adolc_debug}" = xyes ||
++ test "x${adolc_harddebug}" = xyes ; then
+ ac_adolc_cflags="$ac_adolc_cflags -g -O0"
+ fi
+ ac_adolc_cflags="$ac_adolc_cflags $ac_adolc_openmpflag"
+@@ -360,8 +360,8 @@ AC_ARG_WITH(cflags,
+ AC_MSG_RESULT($ac_adolc_cflags)],
+ [if test "$ac_shell_cflags" = "not_set"; then
+ ac_adolc_cflags="-O2"
+- if test x${adolc_debug} == xyes ||
+- test x${adolc_harddebug} == xyes ; then
++ if test "x${adolc_debug}" = xyes ||
++ test "x${adolc_harddebug}" = xyes ; then
+ ac_adolc_cflags="-g -O0 -Wall -ansi"
+ fi
+ else
+@@ -377,8 +377,8 @@ AC_ARG_WITH(cxxflags,
+ [AS_HELP_STRING([--with-cxxflags=FLAGS],
+ [use CXXFLAGS=FLAGS (default: -O2)])],
+ [ac_adolc_cxxflags="$withval"
+- if test x${adolc_debug} == xyes ||
+- test x${adolc_harddebug} == xyes ; then
++ if test x${adolc_debug} = xyes ||
++ test x${adolc_harddebug} = xyes ; then
+ ac_adolc_cxxflags="$ac_adolc_cxxflags -g -O0"
+ fi
+ ac_adolc_cxxflags="$ac_adolc_cxxflags $ac_adolc_openmpflag"
+@@ -386,8 +386,8 @@ AC_ARG_WITH(cxxflags,
+ AC_MSG_RESULT($ac_adolc_cxxflags)],
+ [if test "$ac_shell_cxxflags" = "not_set"; then
+ ac_adolc_cxxflags="-O2"
+- if test x${adolc_debug} == xyes ||
+- test x${adolc_harddebug} == xyes ; then
++ if test x${adolc_debug} = xyes ||
++ test x${adolc_harddebug} = xyes ; then
+ ac_adolc_cxxflags="-g -O0 -Wall"
+ fi
+ else
+@@ -420,7 +420,7 @@ AC_ARG_ENABLE(tapedoc_values,
+ ])
+ AC_MSG_RESULT($tapedoc_values)
+
+-if test x$tapedoc_values == xyes; then
++if test x$tapedoc_values = xyes; then
+ AC_DEFINE(ADOLC_TAPE_DOC_VALUES,1,[ADOL-C tape_doc routine computes values])
+ fi
+
+@@ -583,7 +583,7 @@ while test "x${pdir}" != "x/" ; do
+ break
+ fi
+ done
+-if test "x${pdir}" == "x/" ; then
++if test "x${pdir}" = "x/" ; then
+ writable=false
+ fi
+ if ! ${writable} ; then
+@@ -595,15 +595,6 @@ if ! ${writable} ; then
+ warn=true
+ fi
+
+-case ${prefix} in
+- ${HOME}|${HOME}/*)
+-if $warn ; then
+- for (( i=5; i>0; i-- )); do
+- echo -ne "\rPlease read the above messages carefully, continuing in ${i} seconds"
+- sleep 1
+- done
+- echo -e "\rPlease read the above messages carefully "
+-fi
+ echo \
+ "
+ *****************************************************************************
+@@ -629,5 +620,3 @@ echo \
+
+ *****************************************************************************
+ "
+-;;
+-esac
diff --git a/sci-libs/adolc/metadata.xml b/sci-libs/adolc/metadata.xml
new file mode 100644
index 00000000000..ea1d9dd9ce2
--- /dev/null
+++ b/sci-libs/adolc/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+ The ADOLC system automatically calculates exact derivatives of a
+ C/C++ function. It uses C++ overloading to record arithmetic
+ operations, which it plays back later in various ways to calculate
+ the requested values.
+</longdescription>
+ <use>
+ <flag name="sparse">Add support for sparse matrix algebra with <pkg>sci-libs/colpack</pkg></flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-libs/alglib/Manifest b/sci-libs/alglib/Manifest
new file mode 100644
index 00000000000..76f16145194
--- /dev/null
+++ b/sci-libs/alglib/Manifest
@@ -0,0 +1,2 @@
+DIST alglib-3.7.0.cpp.tgz 1518417 SHA256 62100afea6f3e54606031065d28b484ef82b3a96732265a23d8e0f17e34bd36c SHA512 055a292512eb6b5bdb667a2cfb8fda33237b17f1b900ba086e20a541af0f41bc85aef935c1357d780b45f3b1f2e6acddea23f19cdafa25a08f821aa391fec285 WHIRLPOOL 7dce3c5057c2b356b4f361304f2bfa6281671bb1f45204895864db0013ee18127f9cb4a64b311369debdf1adad4b4cb594514a7387adc6f9b9c21ccb4dc549f6
+DIST alglib-3.8.2.cpp.tgz 1674260 SHA256 c02944558849c8b22f32f8dea03ebf3b77a0aab9aa2518927d25f6bfe7cb06a2 SHA512 3d7b6e3b5a29f25aee476bdd69e583d7504a2e06d390822b4aa2792eeb500e08c13477176be348a9dd560bad358e423465c9086f0c7c12f73dc88024364aed50 WHIRLPOOL 8ec5a51448c00241428f3b6c6191e31f94ee09dc1d94417178a59887edb8b4e8cfd561983bc4b31686971ad27c43e957aa7c1232e500000a0ea84e763f08ddcf
diff --git a/sci-libs/alglib/alglib-3.7.0.ebuild b/sci-libs/alglib/alglib-3.7.0.ebuild
new file mode 100644
index 00000000000..d10eef749b6
--- /dev/null
+++ b/sci-libs/alglib/alglib-3.7.0.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Numerical analysis and data processing library"
+HOMEPAGE="http://www.alglib.net/"
+SRC_URI="http://www.alglib.net/translator/re/${P}.cpp.tgz"
+
+SLOT="0"
+LICENSE="GPL-2+"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+"
+
+S="${WORKDIR}"/cpp/
+
+src_prepare() {
+ cp "${FILESDIR}"/CMakeLists.txt . || die
+ cmake-utils_src_prepare
+}
diff --git a/sci-libs/alglib/alglib-3.8.2.ebuild b/sci-libs/alglib/alglib-3.8.2.ebuild
new file mode 100644
index 00000000000..8a0572f9b59
--- /dev/null
+++ b/sci-libs/alglib/alglib-3.8.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Numerical analysis and data processing library"
+HOMEPAGE="http://www.alglib.net/"
+SRC_URI="http://www.alglib.net/translator/re/${P}.cpp.tgz"
+
+SLOT="0"
+LICENSE="GPL-2+"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+S="${WORKDIR}"/cpp/
+
+src_prepare() {
+ cp "${FILESDIR}"/CMakeLists.txt-${PV} CMakeLists.txt || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=( $(cmake-utils_use_build test) )
+ cmake-utils_src_configure
+}
diff --git a/sci-libs/alglib/files/CMakeLists.txt b/sci-libs/alglib/files/CMakeLists.txt
new file mode 100644
index 00000000000..6455423b0fe
--- /dev/null
+++ b/sci-libs/alglib/files/CMakeLists.txt
@@ -0,0 +1,32 @@
+project(alglib CXX)
+cmake_minimum_required(VERSION 2.8)
+
+INCLUDE(GNUInstallDirs)
+INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src)
+SET(VERSION 3.7.0)
+SET(SOVERSION 3.7)
+
+FILE(GLOB ALGLIB_SRC_LIB "src/*.cpp")
+FILE(GLOB ALGLIB_HDR_LIB "src/*.h")
+
+ADD_LIBRARY(alglib SHARED ${ALGLIB_SRC_LIB})
+SET_TARGET_PROPERTIES(alglib PROPERTIES
+ VERSION ${VERSION}
+ SOVERSION ${SOVERSION})
+
+INSTALL(TARGETS alglib DESTINATION ${CMAKE_INSTALL_LIBDIR}/)
+INSTALL(FILES ${ALGLIB_HDR_LIB} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+#===========================================================
+ADD_EXECUTABLE(test_c tests/test_c.cpp)
+TARGET_LINK_LIBRARIES(test_c alglib)
+#INSTALL(TARGETS test_c DESTINATION ${CMAKE_INSTALL_BINDIR}/)
+#===========================================================
+ADD_EXECUTABLE(test_i tests/test_i.cpp)
+TARGET_LINK_LIBRARIES(test_i alglib)
+#INSTALL(TARGETS test_i DESTINATION ${CMAKE_INSTALL_BINDIR}/)
+#===========================================================
+
+enable_testing()
+add_test( test_c ${CMAKE_BUILD_DIR}/test_c)
+add_test( test_i ${CMAKE_BUILD_DIR}/test_i)
diff --git a/sci-libs/alglib/files/CMakeLists.txt-3.8.2 b/sci-libs/alglib/files/CMakeLists.txt-3.8.2
new file mode 100644
index 00000000000..483c63dc7f5
--- /dev/null
+++ b/sci-libs/alglib/files/CMakeLists.txt-3.8.2
@@ -0,0 +1,36 @@
+project(alglib CXX)
+cmake_minimum_required(VERSION 2.8)
+
+INCLUDE(GNUInstallDirs)
+INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src)
+SET(VERSION 3.8.2)
+SET(SOVERSION 3.8)
+
+option(BUILD_TEST "Build tests" OFF)
+
+FILE(GLOB ALGLIB_SRC_LIB "src/*.cpp")
+FILE(GLOB ALGLIB_HDR_LIB "src/*.h")
+
+ADD_LIBRARY(alglib SHARED ${ALGLIB_SRC_LIB})
+SET_TARGET_PROPERTIES(alglib PROPERTIES
+ VERSION ${VERSION}
+ SOVERSION ${SOVERSION})
+
+INSTALL(TARGETS alglib DESTINATION ${CMAKE_INSTALL_LIBDIR}/)
+INSTALL(FILES ${ALGLIB_HDR_LIB} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+if (BUILD_TEST)
+ #===========================================================
+ ADD_EXECUTABLE(test_c tests/test_c.cpp)
+ TARGET_LINK_LIBRARIES(test_c alglib)
+ #INSTALL(TARGETS test_c DESTINATION ${CMAKE_INSTALL_BINDIR}/)
+ #===========================================================
+ ADD_EXECUTABLE(test_i tests/test_i.cpp)
+ TARGET_LINK_LIBRARIES(test_i alglib)
+ #INSTALL(TARGETS test_i DESTINATION ${CMAKE_INSTALL_BINDIR}/)
+ #===========================================================
+
+ enable_testing()
+endif (BUILD_TEST)
+add_test( test_c ${CMAKE_BUILD_DIR}/test_c)
+add_test( test_i ${CMAKE_BUILD_DIR}/test_i)
diff --git a/sci-libs/alglib/metadata.xml b/sci-libs/alglib/metadata.xml
new file mode 100644
index 00000000000..8fa350bffef
--- /dev/null
+++ b/sci-libs/alglib/metadata.xml
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
+ <longdescription>
+ALGLIB is a cross-platform numerical analysis and data processing library. It
+supports several programming languages (C++, C#, Pascal, VBA) and several
+operating systems (Windows, Linux, Solaris). ALGLIB features include:
+
+* Linear algebra (direct algorithms, EVD/SVD)
+* Solvers (linear and nonlinear)
+* Interpolation
+* Optimization
+* Fast Fourier transforms
+* Numerical integration
+* Linear and nonlinear least-squares fitting
+* Ordinary differential equations
+* Special functions
+* Statistics (descriptive statistics, hypothesis testing)
+* Data analysis (classification/regression, including neural networks)
+* Multiple precision versions of linear algebra, interpolation optimization and
+* others algorithms (using MPFR for floating point computations)
+
+Why to choose ALGLIB? Because it is:
+
+* portable. It can be compiled almost anywhere using almost any compiler
+(see compatibility matrix for more info).
+* easy to use. It supports many programming languages. If you use one language,
+you don't need to study another (FORTRAN, for example) to compile and link an
+external library.
+* open source. It can be used for free under GPL 2+.
+* suited for commercial users too. Those who want to use ALGLIB in commercial
+applications can buy commercial license without copyleft requirement.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/amd/Manifest b/sci-libs/amd/Manifest
new file mode 100644
index 00000000000..5dca5550f72
--- /dev/null
+++ b/sci-libs/amd/Manifest
@@ -0,0 +1 @@
+DIST amd-2.3.1.tar.bz2 339970 SHA256 35f60a47000ec39c8328d621b6d8f249ccf6c12f0ebc809272e16f7d4a8a430c SHA512 19b8c010e0f7a5a96e60fe52904b2b548fb89dfaf9d6f99184df955a732ec3edef04acff01a82a909e030c3bf78c9eccfe0c329731edb29f4b936507e39d885e WHIRLPOOL 737fe5eb785f09bea7a693421b547a0ec18c8428b19efb2890c8573895333862522ece1af00c24156d83ed0888b11c59d9c0ee3ea125ed8cb216d718343f6874
diff --git a/sci-libs/amd/amd-2.3.1.ebuild b/sci-libs/amd/amd-2.3.1.ebuild
new file mode 100644
index 00000000000..a68446a9c76
--- /dev/null
+++ b/sci-libs/amd/amd-2.3.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils fortran-2
+
+DESCRIPTION="Library to order a sparse matrix prior to Cholesky factorization"
+HOMEPAGE="http://www.cise.ufl.edu/research/sparse/amd"
+SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="amd64 ~arm hppa ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="doc fortran static-libs"
+
+RDEPEND="sci-libs/suitesparseconfig"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig
+ doc? ( virtual/latex-base )"
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable fortran)
+ $(use_with doc)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-libs/amd/metadata.xml b/sci-libs/amd/metadata.xml
new file mode 100644
index 00000000000..f4c85ca5986
--- /dev/null
+++ b/sci-libs/amd/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+ AMD is a set of routines for ordering a sparse matrix prior to Cholesky
+ factorization (or for LU factorization with diagonal pivoting). There
+ are versions in both C and Fortran.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest
new file mode 100644
index 00000000000..7dcbe9dfe78
--- /dev/null
+++ b/sci-libs/armadillo/Manifest
@@ -0,0 +1,5 @@
+DIST armadillo-3.4.4.tar.gz 3006964 SHA256 ef94e12556421fa62ba7734f8b18bb12c188f43dd6192d3648a28e8d154e6ba7 SHA512 78fbb107b220d283a2404483ee38720fd8259bbf675d8753d706cc3c3ba9678d47412d156f24a4b3cc95e20ce3c935167e2f7657806b5b8e8b7c95938c4b3f3f WHIRLPOOL 2a1b6426b695569c10b13d3df1183c615fdb4261497eea405e61316a838a5744477db7bfd8344f25d741e69899f64a19c801bd068d366175a2c9898369090093
+DIST armadillo-3.6.2.tar.gz 3016818 SHA256 04f64c632e619989616c7f219310a06cb1618b16274bdac05b4798d49eb4f149 SHA512 0c769caad012f7893cc8ebb46969179f1175edac638f98fd2a0898aed062f7456536eecd12c9720f77caf4859cd0049e00dd71c9f096458b5fd5ce9cea517c66 WHIRLPOOL 898c29f7d0a7b02658f8d95a528be7d321a7d15f95ada6a4296d9822ee873556a49ccaafcaca16cb25e4a05321fa91b9711d7790b0910464b653398fb6ce4738
+DIST armadillo-4.650.4.tar.gz 5408567 SHA256 ccc56580ec932ec9beade5679b07ecbed889e9b602866f673d1a05a7692b4bf8 SHA512 a548150ba5484fce35b0bc6023982939946f2f00b733dff2cd5b46101b1c344342061389cb4363cdaa04c5e3cca3278a40febe2ed705316552dd71f841c46037 WHIRLPOOL 331493d8b9c92b9e1908880c6f6510edb12e93193a9ceb77d0b8ce9d0bfb493dc48e590ea949d39c3c19f6fc3b05446b7e00525512e3055be0f907427c28f7d4
+DIST armadillo-5.100.2.tar.gz 5429961 SHA256 63150f12bf7c7c598ea55b7271d99fce349ff386a3dc2cae3904b244f6e35320 SHA512 2777b525bc62daddfb16eae7b74c29b6b695a7985c56d9dca727ae1e13aa4ea20ee85ea82233a5310b37c738838af07bb0fa7eea782e68e72cbe1cf46a0cc896 WHIRLPOOL df85a508875587651b187520b78900634402f2ca0fc2e64f43bd4a793e382e8cc6abd5b988267645bb02b3133d9aa99ab6d6ff5e200d1277093d4f7ce6e9d240
+DIST armadillo-5.200.2.tar.gz 5430682 SHA256 70c38fd94b4c0559ece1a7313cf85e08197a82dfda4daa5decd89b795bb73079 SHA512 034539d724fd1e4078a709cd616d280178fcfdcb1d3c3ca2f80f5f2ebc4b39b60f11e3bd22773be8a8fd61350a406a6f4056d56f88ed74964f438bed0d224f6f WHIRLPOOL 4d9fb5a5e6ee53db666b7a9b0e437cf18763ba46224ac8425c7aafac4d4c68dbceb272f929ba034c4f738539ea6b52ccc0fdef596e100a226b85239ebd12470b
diff --git a/sci-libs/armadillo/armadillo-3.4.4.ebuild b/sci-libs/armadillo/armadillo-3.4.4.ebuild
new file mode 100644
index 00000000000..a7c75f8948a
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-3.4.4.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+CMAKE_IN_SOURCE_BUILD=1
+
+inherit cmake-utils toolchain-funcs
+
+DESCRIPTION="Streamlined C++ linear algebra library"
+HOMEPAGE="http://arma.sourceforge.net/"
+SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux"
+IUSE="blas doc examples lapack"
+
+RDEPEND="
+ dev-libs/boost
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )"
+
+DEPEND="${DEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ # avoid the automagic cmake macros
+ sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+}
+
+src_configure() {
+ local mycmakeargs=()
+ if use blas; then
+ mycmakeargs+=(
+ -DBLAS_FOUND=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ )
+ fi
+ if use lapack; then
+ mycmakeargs+=(
+ -DLAPACK_FOUND=ON
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+ )
+ fi
+ cmake-utils_src_configure
+}
+
+src_install() {
+ cmake-utils_src_install
+ dodoc README.txt
+ use doc && dodoc *pdf && dohtml *html
+ if use examples; then
+ insinto /usr/share/doc/${PF}
+ doins -r examples
+ fi
+}
diff --git a/sci-libs/armadillo/armadillo-3.6.2.ebuild b/sci-libs/armadillo/armadillo-3.6.2.ebuild
new file mode 100644
index 00000000000..c7d22704bcf
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-3.6.2.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+CMAKE_IN_SOURCE_BUILD=1
+
+inherit cmake-utils toolchain-funcs
+
+DESCRIPTION="Streamlined C++ linear algebra library"
+HOMEPAGE="http://arma.sourceforge.net/"
+SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="blas doc examples lapack"
+
+RDEPEND="
+ dev-libs/boost
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )"
+DEPEND="${DEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ # avoid the automagic cmake macros
+ sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+}
+
+src_configure() {
+ local mycmakeargs=()
+ if use blas; then
+ mycmakeargs+=(
+ -DBLAS_FOUND=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ )
+ fi
+ if use lapack; then
+ mycmakeargs+=(
+ -DLAPACK_FOUND=ON
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+ )
+ fi
+ cmake-utils_src_configure
+}
+
+src_install() {
+ cmake-utils_src_install
+ dodoc README.txt
+ use doc && dodoc *pdf && dohtml *html
+ if use examples; then
+ insinto /usr/share/doc/${PF}
+ doins -r examples
+ fi
+}
diff --git a/sci-libs/armadillo/armadillo-4.650.4.ebuild b/sci-libs/armadillo/armadillo-4.650.4.ebuild
new file mode 100644
index 00000000000..fe855834660
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-4.650.4.ebuild
@@ -0,0 +1,110 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+CMAKE_IN_SOURCE_BUILD=1
+
+inherit cmake-utils toolchain-funcs multilib eutils
+
+DESCRIPTION="Streamlined C++ linear algebra library"
+HOMEPAGE="http://arma.sourceforge.net/"
+SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0/4"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack blas debug doc examples hdf5 lapack mkl tbb test"
+REQUIRED_USE="test? ( lapack )"
+
+RDEPEND="
+ dev-libs/boost
+ arpack? ( sci-libs/arpack )
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+ arpack? ( virtual/pkgconfig )
+ blas? ( virtual/pkgconfig )
+ hdf5? ( sci-libs/hdf5 )
+ lapack? ( virtual/pkgconfig )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+PDEPEND="${RDEPEND}
+ hdf5? ( sci-libs/hdf5 )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+
+src_prepare() {
+ # avoid the automagic cmake macros
+ sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)"
+ $(cmake-utils_use debug ARMA_EXTRA_DEBUG)
+ $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC)
+ $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC)
+ )
+ if use arpack; then
+ mycmakeargs+=(
+ -DARPACK_FOUND=ON
+ -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)"
+ )
+ fi
+# if use atlas; then
+# local c=atlas-cblas l=atlas-clapack
+# $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads
+# $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads
+# mycmakeargs+=(
+# -DCBLAS_FOUND=ON
+# -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')"
+# -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})"
+# -DCLAPACK_FOUND=ON
+# -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')"
+# -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})"
+# )
+# fi
+ if use blas; then
+ mycmakeargs+=(
+ -DBLAS_FOUND=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ )
+ fi
+ if use hdf5; then
+ mycmakeargs+=(
+ -DHDF5_FOUND=ON
+ -DHDF5_LIBRARIES="-lhdf5"
+ )
+ fi
+ if use lapack; then
+ mycmakeargs+=(
+ -DLAPACK_FOUND=ON
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+ )
+ fi
+ cmake-utils_src_configure
+}
+
+src_test() {
+ pushd examples > /dev/null
+ emake \
+ CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \
+ EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)"
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die
+ emake clean
+ popd > /dev/null
+}
+
+src_install() {
+ cmake-utils_src_install
+ dodoc README.txt
+ use doc && dodoc *pdf && dohtml *html
+ if use examples; then
+ insinto /usr/share/examples/${PF}
+ doins -r examples/*
+ fi
+}
diff --git a/sci-libs/armadillo/armadillo-5.100.2.ebuild b/sci-libs/armadillo/armadillo-5.100.2.ebuild
new file mode 100644
index 00000000000..c785a401b00
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-5.100.2.ebuild
@@ -0,0 +1,119 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+CMAKE_IN_SOURCE_BUILD=1
+
+inherit cmake-utils toolchain-funcs multilib eutils
+
+DESCRIPTION="Streamlined C++ linear algebra library"
+HOMEPAGE="http://arma.sourceforge.net/"
+SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0/5"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack blas debug doc examples hdf5 lapack mkl superlu tbb test"
+REQUIRED_USE="test? ( lapack )"
+
+RDEPEND="
+ dev-libs/boost
+ arpack? ( sci-libs/arpack )
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )
+ superlu? ( sci-libs/superlu )
+"
+DEPEND="${RDEPEND}
+ arpack? ( virtual/pkgconfig )
+ blas? ( virtual/pkgconfig )
+ hdf5? ( sci-libs/hdf5 )
+ lapack? ( virtual/pkgconfig )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+PDEPEND="${RDEPEND}
+ hdf5? ( sci-libs/hdf5 )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+
+src_prepare() {
+ # avoid the automagic cmake macros
+ sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)"
+ $(cmake-utils_use debug ARMA_EXTRA_DEBUG)
+ $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC)
+ $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC)
+ )
+ if use arpack; then
+ mycmakeargs+=(
+ -DARPACK_FOUND=ON
+ -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)"
+ )
+ fi
+# if use atlas; then
+# local c=atlas-cblas l=atlas-clapack
+# $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads
+# $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads
+# mycmakeargs+=(
+# -DCBLAS_FOUND=ON
+# -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')"
+# -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})"
+# -DCLAPACK_FOUND=ON
+# -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')"
+# -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})"
+# )
+# fi
+ if use blas; then
+ mycmakeargs+=(
+ -DBLAS_FOUND=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ )
+ fi
+ if use hdf5; then
+ mycmakeargs+=(
+ -DHDF5_FOUND=ON
+ -DHDF5_LIBRARIES="-lhdf5"
+ )
+ fi
+ if use lapack; then
+ mycmakeargs+=(
+ -DLAPACK_FOUND=ON
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+ )
+ fi
+ if use superlu; then
+ mycmakeargs+=(
+ -DSuperLU_FOUND=ON
+ -DSuperLU_LIBRARIES="$($(tc-getPKG_CONFIG) --libs superlu)"
+ )
+ fi
+
+ cmake-utils_src_configure
+}
+
+src_test() {
+ pushd examples > /dev/null
+ emake \
+ CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \
+ EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)"
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die
+ emake clean
+ popd > /dev/null
+}
+
+src_install() {
+ cmake-utils_src_install
+ dodoc README.txt
+ use doc && dodoc *pdf && dohtml *html
+ if use examples; then
+ insinto /usr/share/examples/${PF}
+ doins -r examples/*
+ fi
+}
diff --git a/sci-libs/armadillo/armadillo-5.200.2.ebuild b/sci-libs/armadillo/armadillo-5.200.2.ebuild
new file mode 100644
index 00000000000..c785a401b00
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-5.200.2.ebuild
@@ -0,0 +1,119 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+CMAKE_IN_SOURCE_BUILD=1
+
+inherit cmake-utils toolchain-funcs multilib eutils
+
+DESCRIPTION="Streamlined C++ linear algebra library"
+HOMEPAGE="http://arma.sourceforge.net/"
+SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0/5"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack blas debug doc examples hdf5 lapack mkl superlu tbb test"
+REQUIRED_USE="test? ( lapack )"
+
+RDEPEND="
+ dev-libs/boost
+ arpack? ( sci-libs/arpack )
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )
+ superlu? ( sci-libs/superlu )
+"
+DEPEND="${RDEPEND}
+ arpack? ( virtual/pkgconfig )
+ blas? ( virtual/pkgconfig )
+ hdf5? ( sci-libs/hdf5 )
+ lapack? ( virtual/pkgconfig )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+PDEPEND="${RDEPEND}
+ hdf5? ( sci-libs/hdf5 )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+
+src_prepare() {
+ # avoid the automagic cmake macros
+ sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)"
+ $(cmake-utils_use debug ARMA_EXTRA_DEBUG)
+ $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC)
+ $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC)
+ )
+ if use arpack; then
+ mycmakeargs+=(
+ -DARPACK_FOUND=ON
+ -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)"
+ )
+ fi
+# if use atlas; then
+# local c=atlas-cblas l=atlas-clapack
+# $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads
+# $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads
+# mycmakeargs+=(
+# -DCBLAS_FOUND=ON
+# -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')"
+# -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})"
+# -DCLAPACK_FOUND=ON
+# -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')"
+# -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})"
+# )
+# fi
+ if use blas; then
+ mycmakeargs+=(
+ -DBLAS_FOUND=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ )
+ fi
+ if use hdf5; then
+ mycmakeargs+=(
+ -DHDF5_FOUND=ON
+ -DHDF5_LIBRARIES="-lhdf5"
+ )
+ fi
+ if use lapack; then
+ mycmakeargs+=(
+ -DLAPACK_FOUND=ON
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+ )
+ fi
+ if use superlu; then
+ mycmakeargs+=(
+ -DSuperLU_FOUND=ON
+ -DSuperLU_LIBRARIES="$($(tc-getPKG_CONFIG) --libs superlu)"
+ )
+ fi
+
+ cmake-utils_src_configure
+}
+
+src_test() {
+ pushd examples > /dev/null
+ emake \
+ CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \
+ EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)"
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die
+ emake clean
+ popd > /dev/null
+}
+
+src_install() {
+ cmake-utils_src_install
+ dodoc README.txt
+ use doc && dodoc *pdf && dohtml *html
+ if use examples; then
+ insinto /usr/share/examples/${PF}
+ doins -r examples/*
+ fi
+}
diff --git a/sci-libs/armadillo/metadata.xml b/sci-libs/armadillo/metadata.xml
new file mode 100644
index 00000000000..fb8d262a30e
--- /dev/null
+++ b/sci-libs/armadillo/metadata.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <maintainer>
+ <email>dilfridge@gentoo.org</email>
+ </maintainer>
+ <longdescription lang="en">
+ Armadillo is a C++ linear algebra library (matrix maths) aiming
+ towards a good balance between speed and ease of use. Integer,
+ floating point and complex numbers are supported, as well as a
+ subset of trigonometric and statistics functions. Various matrix
+ decompositions are provided through optional integration with LAPACK
+ and ATLAS libraries.
+ A delayed evaluation approach is employed (during compile time) to
+ combine several operations into one and reduce (or eliminate) the
+ need for temporaries. This is accomplished through recursive
+ templates and template meta-programming.
+</longdescription>
+ <use>
+ <flag name="arpack">
+ Link with <pkg>sci-libs/arpack</pkg> libraries for eigen decomposition
+ </flag>
+ <flag name="mkl">
+ Use matrix allocation from the Intel MKL <pkg>sci-libs/mkl</pkg>
+ </flag>
+ <flag name="tbb">
+ Use matrix allocation from the Threads Building Blocks
+ <pkg>dev-cpp/tbb</pkg>
+ </flag>
+ <flag name="superlu">
+ Use SuperLU for sparse linear equation solving
+ <pkg>sci-libs/superlu</pkg>
+ </flag>
+ </use>
+ <upstream>
+ <remote-id type="sourceforge">arma</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/arpack/Manifest b/sci-libs/arpack/Manifest
new file mode 100644
index 00000000000..2edfb77059b
--- /dev/null
+++ b/sci-libs/arpack/Manifest
@@ -0,0 +1,4 @@
+DIST arpack-ng-3.1.3.tar.gz 1299344 SHA256 4d649b80778e9145b9220f6cdd0d96f589f4c4fb225d385419be87dc863c3c0d SHA512 30bee66edc31d1144d029a4c6c4b03f08782bdcbe1b9627e0c3df8d142121111e9c9dd875158345918931815341a2338cd889a010939016509a7cfdd1e829426 WHIRLPOOL a804e3d85633b39fcd66f853a655a8d2c76daf52f23c0aa5b21b6af16b08f37e6fa0ec30700e6df3f4e52fa55133fcc046595a2ee836f5750edb0aa56840c169
+DIST arpack-ng_3.1.5.tar.gz 1516406 SHA256 a269ce7806bc77ced31ef794d23c3e3aff8543b65550fd7e3e24660f2a79d515 SHA512 4876b0babb89bbcc39e92b63d4537b860e9cd0b8a188937d3ba815041b7261623cdac25c91c8bef20ebce4271f822307c492cf6c9f22ec3d740218405337a515 WHIRLPOOL 6bd202c3bb3c12939bef2178d8e7fe7d7cc96a9dc0e4bb965c241f2c299e0b90d3a383429b94a6bc69bb063d689909e8cc9365091e8aa1d420875fc0c2142331
+DIST tutorial.ps.gz 105599 SHA256 2f745fe80b0a4fcdf1c273995ed67bc6cf03684ccbaa44442ad1187ea41b81c0 SHA512 a7b8fefd1a572ed477ae208d49094c1c65c9368990d12de9b3528e33fed546c947659f74e54a810d04154b4a1b0f9a94bcba4db0cf59d379e20786a261066aa4 WHIRLPOOL 6e1f6901c81993371731861b8c617f9ef22b602e737b3102c2107713b3201362ddd48205aac5814e3a157549f4fa5f280d18e7b84afc8edeadb93d10d8bda5c9
+DIST ug.ps.gz 248543 SHA256 ff1faac74bfc42442955906132756ecd7f0034803898d507dbd1bc960f6f4ab0 SHA512 3349117fb10b07207ffbab2ffa31b406d026855ea4c16e8649b14c7d70bc94e11b5730672e34acd654817799136d4bd76569ac50ec78d787df5582d18ed61328 WHIRLPOOL 83db17d8b1c49d532ca6f4412d110b1973323da5bb526804ab779bc143cf84d8270655b306822e04fa64290f531ed2c4f1e74ffbccbf76529991203e869ca6df
diff --git a/sci-libs/arpack/arpack-3.1.3-r1.ebuild b/sci-libs/arpack/arpack-3.1.3-r1.ebuild
new file mode 100644
index 00000000000..9aa9acbf27f
--- /dev/null
+++ b/sci-libs/arpack/arpack-3.1.3-r1.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P="${PN}-ng-${PV}"
+
+DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems"
+HOMEPAGE="http://www.caam.rice.edu/software/ARPACK/ http://forge.scilab.org/index.php/p/arpack-ng/"
+SRC_URI="
+ http://forge.scilab.org/upload/arpack-ng/files/${MY_P}.tar.gz
+ doc? (
+ http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz
+ http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz )"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="amd64 ~arm hppa ppc ppc64 x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc examples mpi static-libs"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+ mpi? ( virtual/mpi[fortran] )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-pkgconfig.patch
+)
+
+src_configure() {
+ tc-export PKG_CONFIG
+ local myeconfargs=(
+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+ --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
+ $(use_enable mpi)
+ )
+ autotools-utils_src_configure
+}
+
+src_install() {
+ autotools-utils_src_install
+
+ dodoc DOCUMENTS/*.doc
+ newdoc DOCUMENTS/README README.doc
+ use doc && dodoc "${WORKDIR}"/*.ps
+ if use examples; then
+ insinto /usr/share/doc/${PF}
+ doins -r EXAMPLES
+ if use mpi; then
+ insinto /usr/share/doc/${PF}/EXAMPLES/PARPACK
+ doins -r PARPACK/EXAMPLES/MPI
+ fi
+ fi
+}
diff --git a/sci-libs/arpack/arpack-3.1.5.ebuild b/sci-libs/arpack/arpack-3.1.5.ebuild
new file mode 100644
index 00000000000..17640a9af0d
--- /dev/null
+++ b/sci-libs/arpack/arpack-3.1.5.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+#AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P="${PN}-ng_${PV}"
+
+DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems"
+HOMEPAGE="http://www.caam.rice.edu/software/ARPACK/ http://forge.scilab.org/index.php/p/arpack-ng/"
+SRC_URI="
+ http://forge.scilab.org/upload/arpack-ng/files/${MY_P}.tar.gz
+ doc? (
+ http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz
+ http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz )"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc examples mpi static-libs"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+ mpi? ( virtual/mpi[fortran] )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P/_/-}"
+
+src_configure() {
+ tc-export PKG_CONFIG
+ local myeconfargs=(
+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+ --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
+ $(use_enable mpi)
+ )
+ autotools-utils_src_configure
+}
+
+src_test() {
+ cp "${S}"/TESTS/testA.mtx "${BUILD_DIR}"/TESTS || die
+ autotools-utils_src_test
+}
+
+src_install() {
+ autotools-utils_src_install
+
+ dodoc DOCUMENTS/*.doc
+ newdoc DOCUMENTS/README README.doc
+ use doc && dodoc "${WORKDIR}"/*.ps
+ if use examples; then
+ insinto /usr/share/doc/${PF}
+ doins -r EXAMPLES
+ if use mpi; then
+ insinto /usr/share/doc/${PF}/EXAMPLES/PARPACK
+ doins -r PARPACK/EXAMPLES/MPI
+ fi
+ fi
+}
diff --git a/sci-libs/arpack/files/arpack-3.1.3-pkgconfig.patch b/sci-libs/arpack/files/arpack-3.1.3-pkgconfig.patch
new file mode 100644
index 00000000000..437d9034b85
--- /dev/null
+++ b/sci-libs/arpack/files/arpack-3.1.3-pkgconfig.patch
@@ -0,0 +1,14 @@
+ arpack.pc.in | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/arpack.pc.in b/arpack.pc.in
+index 83739bd..996275e 100644
+--- a/arpack.pc.in
++++ b/arpack.pc.in
+@@ -5,5 +5,5 @@ libdir=@libdir@
+ Name: arpack
+ Description: ARPACK-NG
+ Version: @PACKAGE_VERSION@
+-Libs: -L${libdir} -larpack -lblas -latlas
++Libs: -L${libdir} -larpack @LAPACK_LIBS@ @BLAS_LIBS@
+ Cflags:
diff --git a/sci-libs/arpack/metadata.xml b/sci-libs/arpack/metadata.xml
new file mode 100644
index 00000000000..c598daff90b
--- /dev/null
+++ b/sci-libs/arpack/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+ The ARnoldi PACKage is a library of routines capable of solving large scale symmetric,
+ nonsymmetric, and generalized eigenproblems. The software is designed to compute a few
+ eigenvalues with user specified features such as those of largest real
+ part or largest magnitude. Storage requirements are on the order of
+ n*k locations. No auxiliary storage is required. A set of Schur basis
+ vectors for the desired k-dimensional eigen-space is computed which is
+ numerically orthogonal to working precision. Numerically accurate
+ eigenvectors are available on request.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/arprec/Manifest b/sci-libs/arprec/Manifest
new file mode 100644
index 00000000000..87356081d5b
--- /dev/null
+++ b/sci-libs/arprec/Manifest
@@ -0,0 +1,2 @@
+DIST arprec-2.2.16.tar.gz 830227 SHA256 cf71f2a7f3530b57900e67d1282c4a114830d2c00a0fba90819aa8313f11653f SHA512 278bf96402179566d4f2b9a6d69e42d726c81c814f96cd31c19df2c3b61941f3a1858e4a56577548d0fcf526b7db7caca2b7ea7ec57e834e7768d21788e7e672 WHIRLPOOL c55a875af752dfe6700cd714e2d6d34d3100676b8c41d4271065ddb0e754b3c5333cffd7432b45f2dfa0efed8f93dfd3448ac87038b18941a27f6bed1468131c
+DIST arprec-2.2.17.tar.gz 900043 SHA256 87977981c1145465da51f252d04f11d16ee009d9dc7e8d0da71e4ef56b9fc5eb SHA512 d10f7d3e3d61274a36d253d2b50004bbf15447be3ffbd37bb0334ba62bd624e27fb9e26364fa1b89c1d4dfbb4136ab93d865f990ce123ecf94d9614e3ac567d1 WHIRLPOOL 6daeff384cfc9dfbb5771a177166212370ba724850d27ae99de63d1e2f2bc5f76b2be5c28e1fa0bb1d407a29d46212b0896c5e7f6ba66f9c2830e3a53e3e8b31
diff --git a/sci-libs/arprec/arprec-2.2.16.ebuild b/sci-libs/arprec/arprec-2.2.16.ebuild
new file mode 100644
index 00000000000..e467be41e88
--- /dev/null
+++ b/sci-libs/arprec/arprec-2.2.16.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+FORTRAN_NEEDED=fortran
+AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit eutils fortran-2 autotools-utils
+
+DESCRIPTION="Arbitrary precision float arithmetics and functions"
+HOMEPAGE="http://crd.lbl.gov/~dhbailey/mpdist/"
+SRC_URI="http://crd.lbl.gov/~dhbailey/mpdist/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc cpu_flags_x86_fma3 cpu_flags_x86_fma4 fortran qd static-libs"
+
+DEPEND="qd? ( sci-libs/qd[fortran=] )"
+RDEPEND="${DEPEND}"
+
+src_configure() {
+ local myeconfargs=(
+ --docdir="${EPREFIX}/usr/share/doc/${PF}"
+ $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma)
+ $(use_enable fortran)
+ $(use_enable qd)
+ )
+ autotools-utils_src_configure
+}
+
+src_compile() {
+ autotools-utils_src_compile
+ use fortran && autotools-utils_src_compile toolkit
+}
+
+src_install() {
+ autotools-utils_src_install
+ if use fortran; then
+ cd toolkit
+ ./mathinit || die "mathinit failed"
+ exeinto /usr/libexec/${PN}
+ doexe .libs/mathtool
+ insinto /usr/libexec/${PN}
+ doins *.dat
+ echo > mathtool.exe "#!${EROOT}/bin/sh"
+ echo >> mathtool.exe "cd ${EROOT}/usr/libexec/arprec && exec ./mathtool"
+ newbin mathtool.exe mathtool
+ newdoc README README.mathtool
+ fi
+ use doc || rm "${ED}"/usr/share/doc/${PF}/*.pdf
+}
diff --git a/sci-libs/arprec/arprec-2.2.17.ebuild b/sci-libs/arprec/arprec-2.2.17.ebuild
new file mode 100644
index 00000000000..b5e9fe32694
--- /dev/null
+++ b/sci-libs/arprec/arprec-2.2.17.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+FORTRAN_NEEDED=fortran
+FORTRAN_STANDARD="90"
+AUTOTOOLS_AUTORECONF=1
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit eutils fortran-2 autotools-utils
+
+DESCRIPTION="Arbitrary precision float arithmetics and functions"
+HOMEPAGE="http://crd.lbl.gov/~dhbailey/mpdist/"
+SRC_URI="http://crd.lbl.gov/~dhbailey/mpdist/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc cpu_flags_x86_fma3 cpu_flags_x86_fma4 fortran qd static-libs"
+
+DEPEND="qd? ( sci-libs/qd:0=[fortran=] )"
+RDEPEND="${DEPEND}"
+
+src_configure() {
+ local myeconfargs=(
+ --docdir="${EPREFIX}/usr/share/doc/${PF}"
+ $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma)
+ $(use_enable fortran)
+ $(use_enable qd)
+ )
+ autotools-utils_src_configure
+}
+
+src_compile() {
+ autotools-utils_src_compile
+ use fortran && autotools-utils_src_compile toolkit
+}
+
+src_install() {
+ autotools-utils_src_install
+ if use fortran; then
+ cd toolkit
+ ./mathinit || die "mathinit failed"
+ exeinto /usr/libexec/${PN}
+ doexe .libs/mathtool
+ insinto /usr/libexec/${PN}
+ doins *.dat
+ echo > mathtool.exe "#!${EROOT%/}/bin/sh"
+ echo >> mathtool.exe "cd ${EROOT%/}/usr/libexec/arprec && exec ./mathtool"
+ newbin mathtool.exe mathtool
+ newdoc README README.mathtool
+ fi
+ use doc || rm "${ED}"/usr/share/doc/${PF}/*.pdf
+}
diff --git a/sci-libs/arprec/metadata.xml b/sci-libs/arprec/metadata.xml
new file mode 100644
index 00000000000..f5a8029c889
--- /dev/null
+++ b/sci-libs/arprec/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+<maintainer>
+ <email>grozin@gentoo.org</email>
+ <name>Andrey Grozin</name>
+</maintainer>
+<longdescription>
+ Arbitrary precision library for float arithmetics and mathematical functions.
+</longdescription>
+<use>
+ <flag name="qd">Use <pkg>sci-libs/qd</pkg> for quad-double datatype</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest
new file mode 100644
index 00000000000..b8ef93d9df7
--- /dev/null
+++ b/sci-libs/avogadrolibs/Manifest
@@ -0,0 +1 @@
+DIST avogadrolibs-0.7.2.tar.gz 637001 SHA256 217eb5d62082bbaacefe8ad3c8c8ddbbd41931d306038774f761c0155aeccc76 SHA512 a796af1ab3eb77eb2e5484e9e9cb9d7cf68759c9afbd48ddeb237513583e2c207c7c70b2e87b37843886fc737410456ee451e8fe5a21707bdc01fdf600d4cbb8 WHIRLPOOL 81f0d1949c0a93b9efd1f47f276929b01ca761a5875015be3feafb493be3629b0b8e00c0ba930e1ca73b79fc621a67f7e2ab41ae5e4fc10dddd18449238d933f
diff --git a/sci-libs/avogadrolibs/avogadrolibs-0.7.2-r1.ebuild b/sci-libs/avogadrolibs/avogadrolibs-0.7.2-r1.ebuild
new file mode 100644
index 00000000000..d68a539ddce
--- /dev/null
+++ b/sci-libs/avogadrolibs/avogadrolibs-0.7.2-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries"
+HOMEPAGE="http://www.openchemistry.org/"
+SRC_URI="mirror://sourceforge/project/avogadro/avogadro2/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-2+"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc opengl qt4 static-plugins test vtk"
+
+REQUIRED_USE="qt4? ( opengl )"
+
+RDEPEND="
+ >=sci-chemistry/molequeue-0.7
+ sci-libs/chemkit
+ sci-libs/hdf5:=
+ opengl? (
+ dev-qt/qtopengl:4
+ media-libs/glew
+ )
+ qt4? (
+ dev-qt/qtcore:4
+ dev-qt/qtgui:4
+ )
+ vtk? ( sci-libs/vtk )
+"
+DEPEND="${DEPEND}
+ test? ( dev-cpp/gtest )"
+
+PATCHES=( "${FILESDIR}"/${P}-6464.patch )
+
+src_configure() {
+ local mycmakeargs=(
+ -DUSE_PROTOCALL=OFF
+ -DBUILD_GPL_PLUGINS=ON
+ $(cmake-utils_use_build doc DOCUMENTATION)
+ $(cmake-utils_use_use opengl OPENGL)
+ $(cmake-utils_use_use qt4 QT)
+ $(cmake-utils_use_build static-plugins STATIC_PLUGINS)
+ $(cmake-utils_use_enable test TESTING)
+ $(cmake-utils_use_use vtk VTK)
+ )
+ cmake-utils_src_configure
+}
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-0.7.2-6464.patch b/sci-libs/avogadrolibs/files/avogadrolibs-0.7.2-6464.patch
new file mode 100644
index 00000000000..f763c242cc4
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-0.7.2-6464.patch
@@ -0,0 +1,16 @@
+ cmake/AvogadroLibsConfig.cmake.in | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/cmake/AvogadroLibsConfig.cmake.in b/cmake/AvogadroLibsConfig.cmake.in
+index ad57195..8a63400 100644
+--- a/cmake/AvogadroLibsConfig.cmake.in
++++ b/cmake/AvogadroLibsConfig.cmake.in
+@@ -10,7 +10,7 @@ set(AvogadroLibs_VERSION "${AvogadroLibs_VERSION_MAJOR}.${AvogadroLibs_V
+
+ set(AvogadroLibs_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
+ set(AvogadroLibs_INCLUDE_DIRS "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_INCLUDE_DIR@")
+-set(AvogadroLibs_LIBRARY_DIR "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_LIBRARY_DIR@@LIB_SUFFIX@")
++set(AvogadroLibs_LIBRARY_DIR "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_LIBRARY_DIR@")
+ set(AvogadroLibs_RUNTIME_DIR "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_RUNTIME_DIR@")
+ set(AvogadroLibs_CMAKE_DIR "${AvogadroLibs_LIBRARY_DIR}/cmake/avogadrolibs")
+
diff --git a/sci-libs/avogadrolibs/metadata.xml b/sci-libs/avogadrolibs/metadata.xml
new file mode 100644
index 00000000000..e6d586ae920
--- /dev/null
+++ b/sci-libs/avogadrolibs/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
+ <use>
+ <flag name="static-plugins">
+ build all plugins statically into main plugin modules
+ </flag>
+ <flag name="vtk">include vtk support</flag>
+ </use>
+ <upstream>
+ <remote-id type="sourceforge">avogadro</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/balbes-db/Manifest b/sci-libs/balbes-db/Manifest
new file mode 100644
index 00000000000..86fed7e6ab9
--- /dev/null
+++ b/sci-libs/balbes-db/Manifest
@@ -0,0 +1 @@
+DIST ccp4-6.1.3-balbesdb-10-11-08.tar.gz 600856059 SHA256 5606fc5e131138b56fa3a1afce014225a6c07826b99587f132f6c337585f4f0d SHA512 5b7f3b3465312da72ff4816c96244252a6f0bf039fde8ff772ea683e6317053d903cdc2b3b86b78e8edbb1c766d1b3676048ac4e7d4d0db29ed7bf62dfb00ab2 WHIRLPOOL 9a01610c9767aece4c9cc052a8aa2fd5dff9c9967f11688f5e6e206a82e2714751e086a7ddbe6a99da23b70163c7b096f57d281eebe53b8dd7cdb18faed23d63
diff --git a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild b/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild
new file mode 100644
index 00000000000..befa38413e5
--- /dev/null
+++ b/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_P="ccp4-${PV}"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+VERSION="10-11-08"
+
+DESCRIPTION="The database for the BALBES automated crystallographic molecular replacement pipeline"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/"
+SRC_URI="${SRC}/${PV}/${MY_P}-${PN/-/}-${VERSION}.tar.gz"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE=""
+
+RDEPEND="
+ >=dev-python/pyxml-0.8.4
+ sci-libs/monomer-db"
+DEPEND="${RDEPEND}"
+RESTRICT="binchecks strip"
+
+S="${WORKDIR}/${MY_P}"
+
+src_install() {
+ dodir /usr/share/balbes/BALBES_0.0.1
+ rm -rf share/balbes/BALBES_0.0.1/dic || die
+ # We don't want to wait around to copy all this, or suck up double
+ # the disk space
+ einfo "Installing files, which can take some time ..."
+ mv "${S}"/share/balbes/BALBES_0.0.1/* "${ED}"/usr/share/balbes/BALBES_0.0.1/ || die
+ # db files shouldn't be executable
+ find "${ED}"/usr/share/balbes/BALBES_0.0.1/ \
+ -type f \
+ -exec chmod 664 '{}' \; || die
+ dosym ../../ccp4/data/monomers /usr/share/balbes/BALBES_0.0.1/dic
+
+ cat >> "${T}"/20balbes <<- EOF
+ BALBES_ROOT="${EPREFIX}/usr/share/balbes/BALBES_0.0.1/"
+ EOF
+
+ doenvd "${T}"/20balbes
+}
diff --git a/sci-libs/balbes-db/metadata.xml b/sci-libs/balbes-db/metadata.xml
new file mode 100644
index 00000000000..51fdedab1b3
--- /dev/null
+++ b/sci-libs/balbes-db/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-libs/beagle/Manifest b/sci-libs/beagle/Manifest
new file mode 100644
index 00000000000..6e60f608bfc
--- /dev/null
+++ b/sci-libs/beagle/Manifest
@@ -0,0 +1 @@
+DIST beagle-3.0.3.tar.gz 5002994 SHA256 2e481dc180bc1f665ade82f0568db4d67f4b8b3f32bc155f1358fd48630e2935 SHA512 2f8f027f3f24d0fd287e27a80fe5b24e18550144add06fb8157dd03f734f5ce212f62889720c81fd33246fa7086e9b913802ec0c5155df5bd801c36888b346cb WHIRLPOOL 7902d2bf149afb9c2dc1f89fbb6754250950d6df90e63b445939b9c7fdc21b59835ac840d3babb7b56056c24e1f159da9aef27105ff9e05e0298f283e6697bbb
diff --git a/sci-libs/beagle/beagle-3.0.3.ebuild b/sci-libs/beagle/beagle-3.0.3.ebuild
new file mode 100644
index 00000000000..52ba7e8f86b
--- /dev/null
+++ b/sci-libs/beagle/beagle-3.0.3.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils
+
+DESCRIPTION="Open BEAGLE, a versatile EC/GA/GP framework"
+SRC_URI="mirror://sourceforge/beagle/${P}.tar.gz"
+HOMEPAGE="http://beagle.gel.ulaval.ca/"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 x86"
+IUSE="doc static-libs"
+
+RDEPEND="
+ sys-libs/zlib
+ !app-misc/beagle
+ !dev-libs/libbeagle"
+DEPEND="${DEPEND}
+ doc? ( app-doc/doxygen )"
+
+PATCHES=( "${FILESDIR}"/${PN}-3.0.3-gcc43.patch "${FILESDIR}"/${PN}-3.0.3-gcc47.patch )
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+ autotools-utils_src_prepare
+ sed -e "s:@LIBS@:@LIBS@ -lpthread:" \
+ -i PACC/Threading/Makefile.in || \
+ die "Failed to fix threading libs makefile."
+}
+
+src_configure() {
+ local myeconfargs=( --enable-optimization )
+ autotools-utils_src_configure
+}
+
+src_compile() {
+ autotools-utils_src_compile
+
+ use doc && autotools-utils_src_compile doc
+}
+
+src_install () {
+ autotools-utils_src_install
+
+ if use doc; then
+ cp -pPR examples "${D}"/usr/share/doc/${PF} || \
+ die "Failed to install examples."
+ dohtml -r refman/*
+ fi
+}
diff --git a/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch b/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch
new file mode 100644
index 00000000000..608ce388e79
--- /dev/null
+++ b/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch
@@ -0,0 +1,89 @@
+diff -rupN beagle-3.0.3b/PACC/Math/Matrix.cpp beagle-3.0.3/PACC/Math/Matrix.cpp
+--- beagle-3.0.3b/PACC/Math/Matrix.cpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Math/Matrix.cpp 2009-01-21 00:26:46.000000000 -0400
+@@ -40,6 +40,7 @@
+ #include <stdexcept>
+ #include <iomanip>
+ #include <cmath>
++#include <climits>
+
+ using namespace std;
+ using namespace PACC;
+diff -rupN beagle-3.0.3b/PACC/Math/Vector.hpp beagle-3.0.3/PACC/Math/Vector.hpp
+--- beagle-3.0.3b/PACC/Math/Vector.hpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Math/Vector.hpp 2009-01-21 00:26:29.000000000 -0400
+@@ -42,6 +42,7 @@
+ #include "XML/Document.hpp"
+ #include "XML/Streamer.hpp"
+ #include <cmath>
++#include <algorithm>
+
+ namespace PACC {
+
+diff -rupN beagle-3.0.3b/PACC/Socket/Cafe.cpp beagle-3.0.3/PACC/Socket/Cafe.cpp
+--- beagle-3.0.3b/PACC/Socket/Cafe.cpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Socket/Cafe.cpp 2009-01-21 00:31:09.000000000 -0400
+@@ -35,6 +35,7 @@
+
+ #include "Socket/Cafe.hpp"
+ #include <iostream>
++#include <cstring>
+
+ #ifdef WIN32
+ ///////////// specifics for windows /////////////
+diff -rupN beagle-3.0.3b/PACC/Socket/Port.cpp beagle-3.0.3/PACC/Socket/Port.cpp
+--- beagle-3.0.3b/PACC/Socket/Port.cpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Socket/Port.cpp 2009-01-21 00:30:54.000000000 -0400
+@@ -34,6 +34,7 @@
+ */
+
+ #include "Socket/Port.hpp"
++#include <cstring>
+
+ #ifdef WIN32
+ ///////////// specifics for windows /////////////
+diff -rupN beagle-3.0.3b/PACC/Threading/Thread.cpp beagle-3.0.3/PACC/Threading/Thread.cpp
+--- beagle-3.0.3b/PACC/Threading/Thread.cpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Threading/Thread.cpp 2009-01-21 00:28:02.000000000 -0400
+@@ -35,6 +35,7 @@
+
+ #include "Threading/Thread.hpp"
+ #include "Util/Assert.hpp"
++#include <cstdlib>
+
+ #ifdef WIN32
+ #include <windows.h>
+diff -rupN beagle-3.0.3b/PACC/Util/SignalHandler.cpp beagle-3.0.3/PACC/Util/SignalHandler.cpp
+--- beagle-3.0.3b/PACC/Util/SignalHandler.cpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Util/SignalHandler.cpp 2009-01-20 23:44:20.000000000 -0400
+@@ -37,6 +37,7 @@
+ #include "Util/Assert.hpp"
+ #include <signal.h>
+ #include <stdexcept>
++#include <cstdlib>
+
+ using namespace std;
+ using namespace PACC;
+diff -rupN beagle-3.0.3b/PACC/Util/Tokenizer.cpp beagle-3.0.3/PACC/Util/Tokenizer.cpp
+--- beagle-3.0.3b/PACC/Util/Tokenizer.cpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Util/Tokenizer.cpp 2009-01-20 23:44:10.000000000 -0400
+@@ -36,6 +36,8 @@
+ #include "Util/Tokenizer.hpp"
+ #include "Util/Assert.hpp"
+ #include <stdexcept>
++#include <cstring>
++#include <cstdlib>
+
+ using namespace std;
+ using namespace PACC;
+diff -rupN beagle-3.0.3b/PACC/XML/Node.cpp beagle-3.0.3/PACC/XML/Node.cpp
+--- beagle-3.0.3b/PACC/XML/Node.cpp 2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/XML/Node.cpp 2009-01-20 23:45:09.000000000 -0400
+@@ -39,6 +39,7 @@
+ #include "Util/Assert.hpp"
+ #include <sstream>
+ #include <stdexcept>
++#include <cstring>
+
+ using namespace std;
+ using namespace PACC;
diff --git a/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch b/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch
new file mode 100644
index 00000000000..cb3546c68a5
--- /dev/null
+++ b/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch
@@ -0,0 +1,10 @@
+--- beagle/include/beagle/RouletteT.hpp
++++ beagle/include/beagle/RouletteT.hpp
+@@ -87,7 +87,7 @@
+ Beagle_StackTraceBeginM();
+ Beagle_AssertM(inWeight>=0.0);
+ if(VectorType::empty()==false) inWeight += VectorType::back().first;
+- push_back(std::make_pair(inWeight,inValue));
++ this->push_back(std::make_pair(inWeight,inValue));
+ Beagle_StackTraceEndM("void RouletteT<T>::insert(const T& inValue, double inWeight)");
+ }
diff --git a/sci-libs/beagle/metadata.xml b/sci-libs/beagle/metadata.xml
new file mode 100644
index 00000000000..4b2a7479afe
--- /dev/null
+++ b/sci-libs/beagle/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription>
+ Open BEAGLE is a C++ Evolutionary Computation (EC) framework. It provides an high-level software environment to do any kind of EC, with support for tree-based genetic programming, bit string and real-valued genetic algorithms, and evolution strategy.
+ </longdescription>
+ <upstream>
+ <remote-id type="sourceforge">beagle</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/blas-reference/Manifest b/sci-libs/blas-reference/Manifest
new file mode 100644
index 00000000000..d8ee8dc4240
--- /dev/null
+++ b/sci-libs/blas-reference/Manifest
@@ -0,0 +1 @@
+DIST lapack-lite-3.1.1.tgz 5332509 SHA256 505a13272d0d71c45ea52be2de74b0562b234ea3ccf5160665c7a2ee74a58437 SHA512 492b932ef313339ce6b4e63ac8f778489e6870b0eb85f7b086f3c844e75f98e7f85382c7556dfa368ab8320b6f02d1df8ccfcb40b5c0b7c2d74518b7c309e75c WHIRLPOOL 11145043d16b8c2972229e17a24e92e62987c08e84d91b81a7f4767b80f13844faffb2a2798b321a78c7127d849a0fd60cbb1605f03e150b4eaa6c230f0e7fdd
diff --git a/sci-libs/blas-reference/blas-reference-20070226-r2.ebuild b/sci-libs/blas-reference/blas-reference-20070226-r2.ebuild
new file mode 100644
index 00000000000..6c6e0a9e373
--- /dev/null
+++ b/sci-libs/blas-reference/blas-reference-20070226-r2.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils fortran-2 autotools multilib flag-o-matic toolchain-funcs
+
+LAPACKPV="3.1.1"
+LAPACKPN="lapack-lite"
+
+DESCRIPTION="Basic Linear Algebra Subprograms F77 reference implementations"
+HOMEPAGE="http://www.netlib.org/blas/"
+SRC_URI="http://www.netlib.org/lapack/${LAPACKPN}-${LAPACKPV}.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris"
+IUSE="doc"
+
+DEPEND="app-eselect/eselect-blas"
+RDEPEND="${DEPEND}
+ doc? ( app-doc/blas-docs )"
+
+S="${WORKDIR}/${LAPACKPN}-${LAPACKPV}"
+
+src_prepare() {
+ ESELECT_PROF=reference
+ epatch \
+ "${FILESDIR}"/${P}-autotool.patch \
+ "${FILESDIR}"/${P}-pkg-config.patch
+ eautoreconf
+
+ cp "${FILESDIR}"/eselect.blas.reference "${T}"/
+ sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.blas.reference || die
+ if [[ ${CHOST} == *-darwin* ]] ; then
+ sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \
+ "${T}"/eselect.blas.reference || die
+ fi
+}
+
+src_configure() {
+ econf \
+ --libdir="${EPREFIX}"/usr/$(get_libdir)/blas/reference
+}
+
+src_compile() {
+ emake LDFLAGS="${LDFLAGS}" || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ eselect blas add $(get_libdir) "${T}"/eselect.blas.reference ${ESELECT_PROF}
+}
+
+pkg_postinst() {
+ local p=blas
+ local current_lib=$(eselect ${p} show | cut -d' ' -f2)
+ if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then
+ # work around eselect bug #189942
+ local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config
+ [[ -e ${configfile} ]] && rm -f ${configfile}
+ eselect ${p} set ${ESELECT_PROF}
+ elog "${p} has been eselected to ${ESELECT_PROF}"
+ else
+ elog "Current eselected ${p} is ${current_lib}"
+ elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):"
+ elog "\t eselect ${p} set ${ESELECT_PROF}"
+ fi
+}
diff --git a/sci-libs/blas-reference/blas-reference-20070226-r3.ebuild b/sci-libs/blas-reference/blas-reference-20070226-r3.ebuild
new file mode 100644
index 00000000000..6317d3d99dd
--- /dev/null
+++ b/sci-libs/blas-reference/blas-reference-20070226-r3.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=3
+
+inherit eutils fortran-2 autotools multilib flag-o-matic toolchain-funcs
+
+LAPACKPV="3.1.1"
+LAPACKPN="lapack-lite"
+
+DESCRIPTION="Basic Linear Algebra Subprograms F77 reference implementations"
+HOMEPAGE="http://www.netlib.org/blas/"
+SRC_URI="http://www.netlib.org/lapack/${LAPACKPN}-${LAPACKPV}.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE="doc"
+
+DEPEND="app-eselect/eselect-blas"
+RDEPEND="${DEPEND}
+ doc? ( app-doc/blas-docs )"
+
+S="${WORKDIR}/${LAPACKPN}-${LAPACKPV}"
+
+src_prepare() {
+ ESELECT_PROF=reference
+ epatch \
+ "${FILESDIR}"/${P}-autotool.patch \
+ "${FILESDIR}"/${P}-pkg-config.patch
+ eautoreconf
+
+ cp "${FILESDIR}"/eselect.blas.reference-ng "${T}"/eselect.blas.reference || die
+ sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.blas.reference || die
+ if [[ ${CHOST} == *-darwin* ]] ; then
+ sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \
+ "${T}"/eselect.blas.reference || die
+ fi
+}
+
+src_configure() {
+ econf \
+ --libdir="${EPREFIX}"/usr/$(get_libdir)/blas/reference
+}
+
+src_compile() {
+ emake LDFLAGS="${LDFLAGS}" || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ eselect blas add $(get_libdir) "${T}"/eselect.blas.reference ${ESELECT_PROF}
+}
+
+pkg_postinst() {
+ local p=blas
+ local current_lib=$(eselect ${p} show | cut -d' ' -f2)
+ if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then
+ # work around eselect bug #189942
+ local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config
+ [[ -e ${configfile} ]] && rm -f ${configfile}
+ eselect ${p} set ${ESELECT_PROF}
+ elog "${p} has been eselected to ${ESELECT_PROF}"
+ else
+ elog "Current eselected ${p} is ${current_lib}"
+ elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):"
+ elog "\t eselect ${p} set ${ESELECT_PROF}"
+ fi
+}
diff --git a/sci-libs/blas-reference/blas-reference-20070226.ebuild b/sci-libs/blas-reference/blas-reference-20070226.ebuild
new file mode 100644
index 00000000000..b062b5b6a6f
--- /dev/null
+++ b/sci-libs/blas-reference/blas-reference-20070226.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils fortran-2 autotools multilib flag-o-matic toolchain-funcs
+
+LAPACKPV="3.1.1"
+LAPACKPN="lapack-lite"
+
+DESCRIPTION="Basic Linear Algebra Subprograms F77 reference implementations"
+HOMEPAGE="http://www.netlib.org/blas/"
+SRC_URI="http://www.netlib.org/lapack/${LAPACKPN}-${LAPACKPV}.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="alpha amd64 hppa ia64 ppc ppc64 s390 sparc x86 ~x86-fbsd"
+IUSE="doc"
+
+DEPEND="app-eselect/eselect-blas"
+RDEPEND="${DEPEND}
+ doc? ( app-doc/blas-docs )"
+
+S="${WORKDIR}/${LAPACKPN}-${LAPACKPV}"
+
+src_unpack() {
+ ESELECT_PROF=reference
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-autotool.patch
+ eautoreconf
+}
+
+src_compile() {
+ econf \
+ --libdir=/usr/$(get_libdir)/blas/reference
+ emake LDFLAGS="${LDFLAGS}" || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ eselect blas add $(get_libdir) "${FILESDIR}"/eselect.blas.reference ${ESELECT_PROF}
+}
+
+pkg_postinst() {
+ local p=blas
+ local current_lib=$(eselect ${p} show | cut -d' ' -f2)
+ if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then
+ # work around eselect bug #189942
+ local configfile="${ROOT}"/etc/env.d/${p}/$(get_libdir)/config
+ [[ -e ${configfile} ]] && rm -f ${configfile}
+ eselect ${p} set ${ESELECT_PROF}
+ elog "${p} has been eselected to ${ESELECT_PROF}"
+ else
+ elog "Current eselected ${p} is ${current_lib}"
+ elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):"
+ elog "\t eselect ${p} set ${ESELECT_PROF}"
+ fi
+}
diff --git a/sci-libs/blas-reference/files/blas-reference-20070226-autotool.patch b/sci-libs/blas-reference/files/blas-reference-20070226-autotool.patch
new file mode 100644
index 00000000000..8d8192fc025
--- /dev/null
+++ b/sci-libs/blas-reference/files/blas-reference-20070226-autotool.patch
@@ -0,0 +1,243 @@
+--- configure.ac 1970-01-01 01:00:00.000000000 +0100
++++ configure.ac 2007-07-16 10:14:29.000000000 +0100
+@@ -0,0 +1,14 @@
++AC_PREREQ(2.59)
++AC_INIT(blas, 20070226, lapack@cs.utk.edu)
++AM_INIT_AUTOMAKE([foreign])
++
++AC_LANG(Fortran 77)
++AC_PROG_F77
++AC_PROG_LIBTOOL
++
++AC_CONFIG_FILES([Makefile
++ BLAS/Makefile
++ BLAS/SRC/Makefile
++ BLAS/TESTING/Makefile
++ BLAS/blas.pc])
++AC_OUTPUT
+--- Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ Makefile.am 2007-07-16 01:51:11.000000000 +0100
+@@ -0,0 +1 @@
++SUBDIRS = BLAS
+--- BLAS/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ BLAS/Makefile.am 2007-08-14 11:38:42.000000000 +0100
+@@ -0,0 +1,7 @@
++SUBDIRS = SRC TESTING
++
++pkgconfigdir = $(libdir)
++pkgconfig_DATA = blas.pc
++
++EXTRA = blas.pc
++
+--- BLAS/blas.pc.in 1970-01-01 01:00:00.000000000 +0100
++++ BLAS/blas.pc.in 2007-08-17 11:38:23.000000000 +0100
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: @PACKAGE_NAME@
++Description: Basic Linear Algebra Subprograms F77 reference implementations
++Version: @PACKAGE_VERSION@
++URL: http://www.netlib.org/blas
++Libs: -lblas
++Libs.private: -lm
+--- BLAS/SRC/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ BLAS/SRC/Makefile.am 2007-07-16 01:50:12.000000000 +0100
+@@ -0,0 +1,153 @@
++lib_LTLIBRARIES = libblas.la
++
++libblas_la_SOURCES = \
++ caxpy.f \
++ ccopy.f \
++ cdotc.f \
++ cdotu.f \
++ cgbmv.f \
++ cgemm.f \
++ cgemv.f \
++ cgerc.f \
++ cgeru.f \
++ chbmv.f \
++ chemm.f \
++ chemv.f \
++ cher2.f \
++ cher2k.f \
++ cher.f \
++ cherk.f \
++ chpmv.f \
++ chpr2.f \
++ chpr.f \
++ crotg.f \
++ cscal.f \
++ csrot.f \
++ csscal.f \
++ cswap.f \
++ csymm.f \
++ csyr2k.f \
++ csyrk.f \
++ ctbmv.f \
++ ctbsv.f \
++ ctpmv.f \
++ ctpsv.f \
++ ctrmm.f \
++ ctrmv.f \
++ ctrsm.f \
++ ctrsv.f \
++ dasum.f \
++ daxpy.f \
++ dcabs1.f \
++ dcopy.f \
++ ddot.f \
++ dgbmv.f \
++ dgemm.f \
++ dgemv.f \
++ dger.f \
++ dnrm2.f \
++ drot.f \
++ drotg.f \
++ drotm.f \
++ drotmg.f \
++ dsbmv.f \
++ dscal.f \
++ dsdot.f \
++ dspmv.f \
++ dspr2.f \
++ dspr.f \
++ dswap.f \
++ dsymm.f \
++ dsymv.f \
++ dsyr2.f \
++ dsyr2k.f \
++ dsyr.f \
++ dsyrk.f \
++ dtbmv.f \
++ dtbsv.f \
++ dtpmv.f \
++ dtpsv.f \
++ dtrmm.f \
++ dtrmv.f \
++ dtrsm.f \
++ dtrsv.f \
++ dzasum.f \
++ dznrm2.f \
++ icamax.f \
++ idamax.f \
++ isamax.f \
++ izamax.f \
++ lsame.f \
++ scabs1.f \
++ sasum.f \
++ saxpy.f \
++ scasum.f \
++ scnrm2.f \
++ scopy.f \
++ sdot.f \
++ sdsdot.f \
++ sgbmv.f \
++ sgemm.f \
++ sgemv.f \
++ sger.f \
++ snrm2.f \
++ srot.f \
++ srotg.f \
++ srotm.f \
++ srotmg.f \
++ ssbmv.f \
++ sscal.f \
++ sspmv.f \
++ sspr2.f \
++ sspr.f \
++ sswap.f \
++ ssymm.f \
++ ssymv.f \
++ ssyr2.f \
++ ssyr2k.f \
++ ssyr.f \
++ ssyrk.f \
++ stbmv.f \
++ stbsv.f \
++ stpmv.f \
++ stpsv.f \
++ strmm.f \
++ strmv.f \
++ strsm.f \
++ strsv.f \
++ xerbla.f \
++ zaxpy.f \
++ zcopy.f \
++ zdotc.f \
++ zdotu.f \
++ zdrot.f \
++ zdscal.f \
++ zgbmv.f \
++ zgemm.f \
++ zgemv.f \
++ zgerc.f \
++ zgeru.f \
++ zhbmv.f \
++ zhemm.f \
++ zhemv.f \
++ zher2.f \
++ zher2k.f \
++ zher.f \
++ zherk.f \
++ zhpmv.f \
++ zhpr2.f \
++ zhpr.f \
++ zrotg.f \
++ zscal.f \
++ zswap.f \
++ zsymm.f \
++ zsyr2k.f \
++ zsyrk.f \
++ ztbmv.f \
++ ztbsv.f \
++ ztpmv.f \
++ ztpsv.f \
++ ztrmm.f \
++ ztrmv.f \
++ ztrsm.f \
++ ztrsv.f
+--- BLAS/TESTING/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ BLAS/TESTING/Makefile.am 2007-07-16 01:50:12.000000000 +0100
+@@ -0,0 +1,27 @@
++TESTS = blas_tests
++
++blas_tests:
++ @install -m0755 blas_tests.sh blas_tests
++
++check_PROGRAMS = \
++ xsblat1 xdblat1 xcblat1 xzblat1 \
++ xsblat2 xdblat2 xcblat2 xzblat2 \
++ xsblat3 xdblat3 xcblat3 xzblat3
++
++LDADD = $(top_builddir)/BLAS/SRC/libblas.la
++
++xsblat1_SOURCES = sblat1.f
++xdblat1_SOURCES = dblat1.f
++xcblat1_SOURCES = cblat1.f
++xzblat1_SOURCES = zblat1.f
++
++xsblat2_SOURCES = sblat2.f
++xdblat2_SOURCES = dblat2.f
++xcblat2_SOURCES = cblat2.f
++xzblat2_SOURCES = zblat2.f
++
++xsblat3_SOURCES = sblat3.f
++xdblat3_SOURCES = dblat3.f
++xcblat3_SOURCES = cblat3.f
++xzblat3_SOURCES = zblat3.f
++
+--- BLAS/TESTING/blas_tests.sh 1970-01-01 01:00:00.000000000 +0100
++++ BLAS/TESTING/blas_tests.sh 2007-07-16 01:50:12.000000000 +0100
+@@ -0,0 +1,9 @@
++#!/bin/sh
++
++for t in cblat1 sblat1 dblat1 zblat1; do
++ ./x${t}
++done
++
++for t in cblat2 sblat2 dblat2 zblat2 cblat3 sblat3 dblat3 zblat3; do
++ ./x${t} < ../${t}.in
++done
diff --git a/sci-libs/blas-reference/files/blas-reference-20070226-pkg-config.patch b/sci-libs/blas-reference/files/blas-reference-20070226-pkg-config.patch
new file mode 100644
index 00000000000..14190f41e7d
--- /dev/null
+++ b/sci-libs/blas-reference/files/blas-reference-20070226-pkg-config.patch
@@ -0,0 +1,11 @@
+diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in
+index 367c87b..44b86db 100644
+--- a/BLAS/blas.pc.in
++++ b/BLAS/blas.pc.in
+@@ -7,5 +7,5 @@ Name: @PACKAGE_NAME@
+ Description: Basic Linear Algebra Subprograms F77 reference implementations
+ Version: @PACKAGE_VERSION@
+ URL: http://www.netlib.org/blas
+-Libs: -lblas
++Libs: -L@libdir@ -lblas
+ Libs.private: -lm
diff --git a/sci-libs/blas-reference/files/eselect.blas.reference b/sci-libs/blas-reference/files/eselect.blas.reference
new file mode 100644
index 00000000000..edb10ddd10d
--- /dev/null
+++ b/sci-libs/blas-reference/files/eselect.blas.reference
@@ -0,0 +1,4 @@
+blas/reference/libblas.so /usr/@LIBDIR@/libblas.so
+blas/reference/libblas.so.0 /usr/@LIBDIR@/libblas.so.0
+blas/reference/libblas.a /usr/@LIBDIR@/libblas.a
+../blas/reference/blas.pc /usr/@LIBDIR@/pkgconfig/blas.pc
diff --git a/sci-libs/blas-reference/files/eselect.blas.reference-ng b/sci-libs/blas-reference/files/eselect.blas.reference-ng
new file mode 100644
index 00000000000..840389479fe
--- /dev/null
+++ b/sci-libs/blas-reference/files/eselect.blas.reference-ng
@@ -0,0 +1 @@
+../blas/reference/blas.pc /usr/@LIBDIR@/pkgconfig/blas.pc
diff --git a/sci-libs/blas-reference/metadata.xml b/sci-libs/blas-reference/metadata.xml
new file mode 100644
index 00000000000..6d6f67c0371
--- /dev/null
+++ b/sci-libs/blas-reference/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+The BLAS (Basic Linear Algebra Subprograms) are high quality "building
+block" routines for performing basic vector and matrix operations. Level 1
+BLAS do vector-vector operations, Level 2 BLAS do matrix-vector operations,
+and Level 3 BLAS do matrix-matrix operations. Because the BLAS are
+efficient, portable, and widely available, they're commonly used in the
+development of high quality linear algebra software, LAPACK for
+example. This packages implements the reference FORTRAN 77 library.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/bliss/Manifest b/sci-libs/bliss/Manifest
new file mode 100644
index 00000000000..be3eecb6e27
--- /dev/null
+++ b/sci-libs/bliss/Manifest
@@ -0,0 +1 @@
+DIST bliss-0.72.zip 90970 SHA256 528d192b1e30722fc60f5f12c9d6c12b374d838198ae7f18fb41bedabf735ed3 SHA512 a09b3cea26e3ff5f5733f10bfaadaf6fb5a3f443e1cc306fad16af2f7b4cd97c90652315f911a324d6d71426a3d098cd5c7e5721f69c599fe2e0d6d34caa0ef5 WHIRLPOOL afbc41c04e843d383a2da8d5e26ec2882c847e8e5f1e71c05f884396fcc79eab764df628523336b88e0c6ef4fbf073a52870e2c68ded428002d9391894cb53d6
diff --git a/sci-libs/bliss/bliss-0.72.ebuild b/sci-libs/bliss/bliss-0.72.ebuild
new file mode 100644
index 00000000000..dea3e3c0c72
--- /dev/null
+++ b/sci-libs/bliss/bliss-0.72.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+
+inherit autotools-utils
+
+SRC_URI="http://www.tcs.hut.fi/Software/${PN}/${P}.zip"
+DESCRIPTION="A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs"
+HOMEPAGE="http://www.tcs.hut.fi/Software/bliss/index.shtml"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc gmp static-libs"
+
+RDEPEND="gmp? ( dev-libs/gmp:0= )"
+
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+AUTOTOOLS_PRUNE_LIBTOOL_FILES="all" #comes with pkg-config file
+
+PATCHES=(
+ "${FILESDIR}/${P}-fedora.patch"
+ "${FILESDIR}/${P}-autotools.patch"
+)
+
+src_configure() {
+ local myeconfargs=( $(use_with gmp) )
+ autotools-utils_src_configure
+}
+
+src_compile() {
+ autotools-utils_src_compile all $(usex doc html "")
+}
+
+src_install() {
+ use doc && HTML_DOCS=( "${BUILD_DIR}"/html/. )
+ autotools-utils_src_install
+}
diff --git a/sci-libs/bliss/files/bliss-0.72-autotools.patch b/sci-libs/bliss/files/bliss-0.72-autotools.patch
new file mode 100644
index 00000000000..d30c51622e2
--- /dev/null
+++ b/sci-libs/bliss/files/bliss-0.72-autotools.patch
@@ -0,0 +1,159 @@
+Replace simple Makefile by autotools
+- allow shared library
+- parallel build
+- added pkg-config support
+
+Author: Christoph Junghans <ottxor@gentoo.org>
+
+diff -Naur bliss-0.72-fedora/config/.dummy bliss-0.72/config/.dummy
+--- bliss-0.72-fedora/config/.dummy 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/config/.dummy 2013-04-28 14:43:06.143760368 -0600
+@@ -0,0 +1 @@
++Dummy file to make patch create config dir, which is needed for autotools
+diff -Naur bliss-0.72-fedora/configure.ac bliss-0.72/configure.ac
+--- bliss-0.72-fedora/configure.ac 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/configure.ac 2013-04-28 14:40:42.283242722 -0600
+@@ -0,0 +1,31 @@
++AC_PREREQ([2.65])
++AC_INIT([bliss], [0.72], [Tommi.Junttil@kk.fi])
++
++AC_CONFIG_AUX_DIR(config)
++AC_CONFIG_MACRO_DIR(config)
++
++AM_INIT_AUTOMAKE([1.8 foreign])
++
++SHARED_VERSION_INFO="1:0:0"
++AC_SUBST(SHARED_VERSION_INFO)
++
++# Checks for programs.
++AC_PROG_CXX
++
++LT_INIT
++# Checks for libraries.
++AC_ARG_WITH([gmp],
++ [AS_HELP_STRING([--with-gmp], [enable support for GNU Multiple Precision Arithmetic Library @<:@default=check@:>@])],
++ [], [with_readline=no])
++AS_IF([test "x$with_readline" != xno],
++ [AC_CHECK_HEADERS([gmp.h],,AC_MSG_ERROR([Cannot find gmp.h header]))
++ AC_CHECK_LIB([gmp],_init,,AC_MSG_ERROR([Cannot find gmp library]))
++ AC_SUBST([GMP],[-lgmp])
++ [CPPFLAGS="$CPPFLAGS -DBLISS_USE_GMP"]])
++
++AC_CHECK_PROG(DOXYGEN,doxygen,doxygen,no)
++AM_CONDITIONAL(HAVE_DOXYGEN,[test .$DOXYGEN != .no])
++
++AC_CONFIG_FILES([Makefile])
++AC_CONFIG_FILES([bliss.pc])
++AC_OUTPUT
+diff -Naur bliss-0.72-fedora/bliss.pc.in bliss-0.72/bliss.pc.in
+--- bliss-0.72-fedora/bliss.pc.in 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/bliss.pc.in 2013-04-28 14:40:54.223285686 -0600
+@@ -0,0 +1,13 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: bliss
++Description: Library for Computing Automorphism Groups and Canonical Labelings of Graphs
++URL: http://www.tcs.hut.fi/Software/bliss/index.shtml
++Version: @VERSION@
++Requires:
++Libs: -L${libdir} -lbliss @GMP@
++Libs.private: -lm
++Cflags: -I${includedir}
+diff -Naur bliss-0.72-fedora/Makefile bliss-0.72/Makefile
+--- bliss-0.72-fedora/Makefile 2013-04-28 14:40:10.543128514 -0600
++++ bliss-0.72/Makefile 1969-12-31 17:00:00.000000000 -0700
+@@ -1,57 +0,0 @@
+-CFLAGS = -I.
+-CFLAGS += -g
+-#CFLAGS += -pg
+-CFLAGS += -Wall
+-CFLAGS += --pedantic
+-CFLAGS += -O9
+-#CFLAGS += -DBLISS_DEBUG
+-CFLAGS += -fPIC
+-
+-SRCS = defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc
+-SRCS += timer.cc utils.cc bliss_C.cc
+-
+-OBJS = $(addsuffix .o, $(basename $(SRCS)))
+-
+-GMPOBJS = $(addsuffix g, $(OBJS))
+-
+-LIB =
+-#LIB += /usr/lib/ccmalloc.o -ldl
+-
+-CC = g++
+-RANLIB = ranlib
+-AR = ar
+-BLISSLIB = libbliss.a
+-
+-gmp: LIB += -lgmp
+-gmp: CFLAGS += -DBLISS_USE_GMP
+-
+-normal: bliss
+-gmp: bliss_gmp
+-
+-
+-all:: lib bliss
+-
+-%.o %.og: %.cc
+- $(CC) $(CFLAGS) -c -o $@ $<
+-
+-lib: $(OBJS)
+- rm -f $(BLISSLIB)
+- $(AR) cr $(BLISSLIB) $(OBJS)
+- $(RANLIB) $(BLISSLIB)
+-
+-lib_gmp: $(GMPOBJS)
+- rm -f $(BLISSLIB)
+- $(AR) cr $(BLISSLIB) $(GMPOBJS)
+- $(RANLIB) $(BLISSLIB)
+-
+-bliss: bliss.o lib $(OBJS)
+- $(CC) $(CFLAGS) -o bliss bliss.o $(OBJS) $(LIB)
+-
+-bliss_gmp: bliss.og lib_gmp $(GMPOBJS)
+- $(CC) $(CFLAGS) -o bliss bliss.og $(GMPOBJS) $(LIB)
+-
+-
+-clean:
+- rm -f bliss $(BLISSLIB) $(OBJS) bliss.o $(GMPOBJS) bliss.og
+-
+-# DO NOT DELETE
+diff -Naur bliss-0.72-fedora/Makefile.am bliss-0.72/Makefile.am
+--- bliss-0.72-fedora/Makefile.am 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/Makefile.am 2013-04-28 14:47:26.944698789 -0600
+@@ -0,0 +1,30 @@
++ACLOCAL_AMFLAGS = -I config
++
++lib_LTLIBRARIES = libbliss.la
++
++libbliss_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@
++libbliss_la_SOURCES = \
++ defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc \
++ timer.cc utils.cc bliss_C.cc
++
++pkginclude_HEADERS = \
++ bignum.hh bliss_C.h defs.hh graph.hh heap.hh kqueue.hh kstack.hh \
++ orbit.hh partition.hh timer.hh uintseqhash.hh utils.hh
++
++bin_PROGRAMS = bliss
++bliss_SOURCES = bliss.cc
++bliss_LDADD = libbliss.la
++dist_man1_MANS = bliss.1
++
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bliss.pc
++
++html-local: Doxyfile
++if HAVE_DOXYGEN
++ $(DOXYGEN) $(srcdir)/Doxyfile
++else
++ @echo "doxygen was not found, please re-run configure"
++endif
++
++clean-local:
++ -rm -rf html
diff --git a/sci-libs/bliss/files/bliss-0.72-fedora.patch b/sci-libs/bliss/files/bliss-0.72-fedora.patch
new file mode 100644
index 00000000000..e1f8b668510
--- /dev/null
+++ b/sci-libs/bliss/files/bliss-0.72-fedora.patch
@@ -0,0 +1,648 @@
+Pulled on 28-04-13 from
+http://pkgs.fedoraproject.org/cgit/bliss.git/tree/
+
+- Man page written by Jerry James using text borrowed from the sources.
+ The man page therefore has the same copyright and license as the sources.
+- Don't call exit() in library code.
+- Patch from Thomas Rehn, also sent upstream. Fix one bug and add one
+ performance enhancement.
+
+diff -Naur bliss-0.72.orig/bliss.1 bliss-0.72/bliss.1
+--- bliss-0.72.orig/bliss.1 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/bliss.1 2013-04-28 14:35:37.000000000 -0600
+@@ -0,0 +1,55 @@
++.TH "BLISS" "1" "@VERSION@" "Tommi Junttila & Petteri Kaski" "User Commands"
++.SH "NAME"
++bliss \- Compute automorphism groups and canonical labelings of graphs
++.SH "SYNOPSIS"
++.B bliss
++[\fIOPTIONS\fR] [<\fIGRAPH FILE\fR>]
++.SH "DESCRIPTION"
++.PP
++Bliss is an open source tool for computing automorphism groups and
++canonical forms of graphs. The graphs are specified in DIMACS format.
++.TP
++\fB\-directed\fR
++the input graph is directed
++.TP
++\fB\-can\fR
++compute canonical form
++.TP
++\fB\-ocan\fR=\fIf\fR
++compute canonical form and output it in file \fIf\fR
++.TP
++\fB\-v\fR=\fIN\fR
++set verbosity level to N [N >= 0, default: 1]
++.TP
++\fB\-sh\fR=\fIX\fR
++select splitting heuristics, where X is:
++.TS
++tab(;);
++R L.
++f;first non-singleton cell
++fl;first largest non-singleton cell
++fs;first smallest non-singleton cell
++fm;first maximally non-trivially connected non-singleton cell
++flm;first largest maximally non-trivially connected
++;non-singleton cell
++fsm;first smallest maximally non-trivially connected
++;non-singleton cell (default)
++.TE
++.TP
++\fB\-fr\fR=\fIX\fR
++use failure recording? [X=y/n, default: y]
++.TP
++\fB\-cr\fR=\fIX\fR
++use component recursion? [X=y/n, default: y]
++.TP
++\fB\-version\fR
++print the version number and exit
++.TP
++\fB\-help\fR
++print this help and exit
++.SH "AUTHORS"
++Bliss was written by Tommi Junttila <Tommi.Junttila@tkk.fi> and
++Petteri Kaski <petteri.kaski@aalto.fi>.
++.PP
++This man page was written by Jerry James <loganjerry@gmail.com>.
++It is distributed under the same terms as bliss.
+diff -Naur bliss-0.72.orig/bliss.cc bliss-0.72/bliss.cc
+--- bliss-0.72.orig/bliss.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/bliss.cc 2013-04-28 14:36:28.792330603 -0600
+@@ -276,13 +276,16 @@
+ if(opt_canonize == false)
+ {
+ /* No canonical labeling, only automorphism group */
+- g->find_automorphisms(stats, &report_aut, stdout);
++ if (!g->find_automorphisms(stats, &report_aut, stdout))
++ exit(1);
+ }
+ else
+ {
+ /* Canonical labeling and automorphism group */
+ const unsigned int* cl = g->canonical_form(stats, &report_aut, stdout);
+
++ if (!cl)
++ exit(1);
+ fprintf(stdout, "Canonical labeling: ");
+ bliss::print_permutation(stdout, g->get_nof_vertices(), cl, 1);
+ fprintf(stdout, "\n");
+@@ -290,6 +293,8 @@
+ if(opt_output_can_file)
+ {
+ bliss::AbstractGraph* cf = g->permute(cl);
++ if (!cf)
++ exit(1);
+ FILE* const fp = fopen(opt_output_can_file, "w");
+ if(!fp)
+ _fatal("Cannot open '%s' for outputting the canonical form, aborting", opt_output_can_file);
+diff -Naur bliss-0.72.orig/bliss_C.cc bliss-0.72/bliss_C.cc
+--- bliss-0.72.orig/bliss_C.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/bliss_C.cc 2013-04-28 14:36:28.792330603 -0600
+@@ -131,7 +131,7 @@
+ }
+
+ extern "C"
+-void
++int
+ bliss_find_automorphisms(BlissGraph *graph,
+ void (*hook)(void *user_param,
+ unsigned int n,
+@@ -142,7 +142,8 @@
+ bliss::Stats s;
+ assert(graph);
+ assert(graph->g);
+- graph->g->find_automorphisms(s, hook, hook_user_param);
++ if (!graph->g->find_automorphisms(s, hook, hook_user_param))
++ return 0;
+
+ if(stats)
+ {
+@@ -154,6 +155,7 @@
+ stats->nof_generators = s.get_nof_generators();
+ stats->max_level = s.get_max_level();
+ }
++ return 1;
+ }
+
+
+@@ -173,7 +175,7 @@
+
+ canonical_labeling = graph->g->canonical_form(s, hook, hook_user_param);
+
+- if(stats)
++ if(canonical_labeling && stats)
+ {
+ stats->group_size_approx = s.get_group_size_approx();
+ stats->nof_nodes = s.get_nof_nodes();
+diff -Naur bliss-0.72.orig/bliss_C.h bliss-0.72/bliss_C.h
+--- bliss-0.72.orig/bliss_C.h 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/bliss_C.h 2013-04-28 14:36:28.792330603 -0600
+@@ -156,6 +156,7 @@
+ * The argument \a perm should be an array of
+ * N=bliss::bliss_get_nof_vertices(\a graph) elements describing
+ * a bijection on {0,...,N-1}.
++ * Returns NULL if insufficient memory or internal error.
+ */
+ BlissGraph *bliss_permute(BlissGraph *graph, const unsigned int *perm);
+
+@@ -174,8 +175,9 @@
+ * if you want to use the automorphism later, you have to take a copy of it.
+ * Do not call bliss_* functions in the hook.
+ * If \a stats is non-null, then some search statistics are copied there.
++ * \return nonzero if successful, zero if insufficient memory or internal error
+ */
+-void
++int
+ bliss_find_automorphisms(BlissGraph *graph,
+ void (*hook)(void *user_param,
+ unsigned int N,
+@@ -194,6 +196,7 @@
+ * then bliss_permute() with the returned canonical labeling.
+ * Note that the computed canonical version may depend on the applied version
+ * of bliss.
++ * Returns NULL if insufficient memory or internal error.
+ */
+ const unsigned int *
+ bliss_find_canonical_labeling(BlissGraph *graph,
+diff -Naur bliss-0.72.orig/defs.cc bliss-0.72/defs.cc
+--- bliss-0.72.orig/defs.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/defs.cc 2013-04-28 14:36:28.792330603 -0600
+@@ -33,7 +33,6 @@
+ vfprintf(stderr, fmt, ap);
+ fprintf(stderr, "\nAborting!\n");
+ va_end(ap);
+- exit(1);
+ }
+
+ }
+diff -Naur bliss-0.72.orig/graph.cc bliss-0.72/graph.cc
+--- bliss-0.72.orig/graph.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/graph.cc 2013-04-28 14:37:16.162501050 -0600
+@@ -34,7 +34,10 @@
+ namespace bliss {
+
+ #define _INTERNAL_ERROR() fatal_error("%s:%d: internal error",__FILE__,__LINE__)
+-#define _OUT_OF_MEMORY() fatal_error("%s:%d: out of memory",__FILE__,__LINE__)
++#define _OUT_OF_MEMORY(label) do { \
++ fatal_error("%s:%d: out of memory",__FILE__,__LINE__); \
++ goto label; \
++ } while (0)
+
+ /*-------------------------------------------------------------------------
+ *
+@@ -279,20 +282,6 @@
+ *perm = i;
+ }
+
+-bool
+-AbstractGraph::is_automorphism(unsigned int* const perm)
+-{
+- _INTERNAL_ERROR();
+- return false;
+-}
+-
+-bool
+-AbstractGraph::is_automorphism(const std::vector<unsigned int>& perm) const
+-{
+- _INTERNAL_ERROR();
+- return false;
+-}
+-
+
+
+
+@@ -608,17 +597,7 @@
+ };
+
+
+-
+-
+-typedef struct {
+- unsigned int splitting_element;
+- unsigned int certificate_index;
+- unsigned int subcertificate_length;
+- UintSeqHash eqref_hash;
+-} PathInfo;
+-
+-
+-void
++bool
+ AbstractGraph::search(const bool canonical, Stats& stats)
+ {
+ const unsigned int N = get_nof_vertices();
+@@ -658,7 +637,7 @@
+ if(N == 0)
+ {
+ /* Nothing to do, return... */
+- return;
++ return true;
+ }
+
+ /* Initialize the partition ... */
+@@ -696,10 +675,10 @@
+ */
+ if(first_path_labeling) free(first_path_labeling);
+ first_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!first_path_labeling) _OUT_OF_MEMORY();
++ if(!first_path_labeling) _OUT_OF_MEMORY(oom1);
+ if(best_path_labeling) free(best_path_labeling);
+ best_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!best_path_labeling) _OUT_OF_MEMORY();
++ if(!best_path_labeling) _OUT_OF_MEMORY(oom2);
+
+ /*
+ * Is the initial partition discrete?
+@@ -710,7 +689,7 @@
+ update_labeling(best_path_labeling);
+ /* Update statistics */
+ stats.nof_leaf_nodes = 1;
+- return;
++ return true;
+ }
+
+ /*
+@@ -718,20 +697,39 @@
+ */
+ if(first_path_labeling_inv) free(first_path_labeling_inv);
+ first_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!first_path_labeling_inv) _OUT_OF_MEMORY();
++ if(!first_path_labeling_inv) _OUT_OF_MEMORY(oom3);
+ if(best_path_labeling_inv) free(best_path_labeling_inv);
+ best_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!best_path_labeling_inv) _OUT_OF_MEMORY();
++ if(!best_path_labeling_inv) _OUT_OF_MEMORY(oom4);
+
+ /*
+ * Allocate space for the automorphisms
+ */
+ if(first_path_automorphism) free(first_path_automorphism);
+ first_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int));
+- if(!first_path_automorphism) _OUT_OF_MEMORY();
++ if(!first_path_automorphism) _OUT_OF_MEMORY(oom5);
+ if(best_path_automorphism) free(best_path_automorphism);
+ best_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int));
+- if(!best_path_automorphism) _OUT_OF_MEMORY();
++ if(!best_path_automorphism) {
++ _OUT_OF_MEMORY(oom6);
++ oom6:
++ free(first_path_automorphism);
++ first_path_automorphism = NULL;
++ oom5:
++ free(best_path_labeling_inv);
++ best_path_labeling_inv = NULL;
++ oom4:
++ free(first_path_labeling_inv);
++ first_path_labeling_inv = NULL;
++ oom3:
++ free(best_path_labeling);
++ best_path_labeling = NULL;
++ oom2:
++ free(first_path_labeling);
++ first_path_labeling = NULL;
++ oom1:
++ return false;
++ }
+
+ /*
+ * Initialize orbit information so that all vertices are in their own orbits
+@@ -745,7 +743,6 @@
+ initialize_certificate();
+
+ std::vector<TreeNode> search_stack;
+- std::vector<PathInfo> first_path_info;
+ std::vector<PathInfo> best_path_info;
+
+ search_stack.clear();
+@@ -974,7 +971,6 @@
+ */
+ {
+ unsigned int next_split_element = UINT_MAX;
+- unsigned int* next_split_element_pos = 0;
+ unsigned int* ep = p.elements + cell->first;
+ if(current_node.fp_on)
+ {
+@@ -985,7 +981,6 @@
+ *ep < next_split_element and
+ first_path_orbits.is_minimal_representative(*ep)) {
+ next_split_element = *ep;
+- next_split_element_pos = ep;
+ }
+ }
+ }
+@@ -1001,7 +996,6 @@
+ current_node.long_prune_redundant.find(*ep) ==
+ current_node.long_prune_redundant.end())) {
+ next_split_element = *ep;
+- next_split_element_pos = ep;
+ }
+ }
+ }
+@@ -1015,7 +1009,6 @@
+ current_node.long_prune_redundant.find(*ep) ==
+ current_node.long_prune_redundant.end())) {
+ next_split_element = *ep;
+- next_split_element_pos = ep;
+ }
+ }
+ }
+@@ -1203,8 +1196,10 @@
+
+ #if defined(BLISS_VERIFY_EQUITABLEDNESS)
+ /* The new partition should be equitable */
+- if(!is_equitable())
++ if(!is_equitable()) {
+ fatal_error("consistency check failed - partition after refinement is not equitable");
++ return false;
++ }
+ #endif
+
+ /*
+@@ -1366,6 +1361,7 @@
+ goto handle_first_path_automorphism;
+ /* Should never get here because of CR:FP */
+ _INTERNAL_ERROR();
++ return false;
+ }
+ }
+
+@@ -1598,8 +1594,10 @@
+
+ #if defined(BLISS_VERIFY_AUTOMORPHISMS)
+ /* Verify that it really is an automorphism */
+- if(!is_automorphism(best_path_automorphism))
++ if(!is_automorphism(best_path_automorphism)) {
+ fatal_error("Best path automorhism validation check failed");
++ return false;
++ }
+ #endif
+
+ unsigned int gca_level_with_first = 0;
+@@ -1666,6 +1664,7 @@
+
+
+ _INTERNAL_ERROR();
++ return false;
+
+
+ handle_first_path_automorphism:
+@@ -1701,8 +1700,10 @@
+
+ #if defined(BLISS_VERIFY_AUTOMORPHISMS)
+ /* Verify that it really is an automorphism */
+- if(!is_automorphism(first_path_automorphism))
++ if(!is_automorphism(first_path_automorphism)) {
+ fatal_error("First path automorphism validation check failed");
++ return false;
++ }
+ #endif
+
+ if(opt_use_long_prune)
+@@ -1749,12 +1750,13 @@
+ /* Release component recursion data in partition */
+ if(opt_use_comprec)
+ p.cr_free();
++ return true;
+ }
+
+
+
+
+-void
++bool
+ AbstractGraph::find_automorphisms(Stats& stats,
+ void (*hook)(void *user_param,
+ unsigned int n,
+@@ -1764,7 +1766,8 @@
+ report_hook = hook;
+ report_user_param = user_param;
+
+- search(false, stats);
++ if (!search(false, stats))
++ return false;
+
+ if(first_path_labeling)
+ {
+@@ -1776,6 +1779,7 @@
+ free(best_path_labeling);
+ best_path_labeling = 0;
+ }
++ return true;
+ }
+
+
+@@ -1790,7 +1794,8 @@
+ report_hook = hook;
+ report_user_param = user_param;
+
+- search(true, stats);
++ if (!search(true, stats))
++ return NULL;
+
+ return best_path_labeling;
+ }
+@@ -3480,15 +3485,17 @@
+ * Check whether perm is an automorphism.
+ * Slow, mainly for debugging and validation purposes.
+ */
+-bool
++int
+ Digraph::is_automorphism(unsigned int* const perm)
+ {
+ std::set<unsigned int, std::less<unsigned int> > edges1;
+ std::set<unsigned int, std::less<unsigned int> > edges2;
+
+ #if defined(BLISS_CONSISTENCY_CHECKS)
+- if(!is_permutation(get_nof_vertices(), perm))
++ if(!is_permutation(get_nof_vertices(), perm)) {
+ _INTERNAL_ERROR();
++ return -1;
++ }
+ #endif
+
+ for(unsigned int i = 0; i < get_nof_vertices(); i++)
+@@ -3507,7 +3514,7 @@
+ ei++)
+ edges2.insert(*ei);
+ if(!(edges1 == edges2))
+- return false;
++ return 0;
+
+ edges1.clear();
+ for(std::vector<unsigned int>::iterator ei = v1.edges_out.begin();
+@@ -3520,10 +3527,10 @@
+ ei++)
+ edges2.insert(*ei);
+ if(!(edges1 == edges2))
+- return false;
++ return 0;
+ }
+
+- return true;
++ return 1;
+ }
+
+ bool
+@@ -4330,8 +4337,10 @@
+ Graph::permute(const unsigned int* perm) const
+ {
+ #if defined(BLISS_CONSISTENCY_CHECKS)
+- if(!is_permutation(get_nof_vertices(), perm))
++ if(!is_permutation(get_nof_vertices(), perm)) {
+ _INTERNAL_ERROR();
++ return NULL;
++ }
+ #endif
+
+ Graph* const g = new Graph(get_nof_vertices());
+@@ -5270,15 +5279,17 @@
+ *
+ *-------------------------------------------------------------------------*/
+
+-bool
++int
+ Graph::is_automorphism(unsigned int* const perm)
+ {
+ std::set<unsigned int, std::less<unsigned int> > edges1;
+ std::set<unsigned int, std::less<unsigned int> > edges2;
+
+ #if defined(BLISS_CONSISTENCY_CHECKS)
+- if(!is_permutation(get_nof_vertices(), perm))
++ if(!is_permutation(get_nof_vertices(), perm)) {
+ _INTERNAL_ERROR();
++ return -1;
++ }
+ #endif
+
+ for(unsigned int i = 0; i < get_nof_vertices(); i++)
+@@ -5298,10 +5309,10 @@
+ edges2.insert(*ei);
+
+ if(!(edges1 == edges2))
+- return false;
++ return 0;
+ }
+
+- return true;
++ return 1;
+ }
+
+
+@@ -5444,7 +5455,7 @@
+ component.clear();
+ component_elements = 0;
+ sh_return = 0;
+- unsigned int sh_first = 0;
++ unsigned int sh_first = 1 << 31;
+ unsigned int sh_size = 0;
+ unsigned int sh_nuconn = 0;
+
+diff -Naur bliss-0.72.orig/graph.hh bliss-0.72/graph.hh
+--- bliss-0.72.orig/graph.hh 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/graph.hh 2013-04-28 14:37:16.162501050 -0600
+@@ -109,9 +109,12 @@
+ unsigned long int get_max_level() const {return max_level;}
+ };
+
+-
+-
+-
++typedef struct {
++ unsigned int splitting_element;
++ unsigned int certificate_index;
++ unsigned int subcertificate_length;
++ UintSeqHash eqref_hash;
++} PathInfo;
+
+
+ /**
+@@ -270,7 +273,7 @@
+ void reset_permutation(unsigned int *perm);
+
+ /* Mainly for debugging purposes */
+- virtual bool is_automorphism(unsigned int* const perm);
++ virtual int is_automorphism(unsigned int* const perm) = 0;
+
+ std::vector<unsigned int> certificate_current_path;
+ std::vector<unsigned int> certificate_first_path;
+@@ -284,7 +287,11 @@
+ virtual Partition::Cell* find_next_cell_to_be_splitted(Partition::Cell *cell) = 0;
+
+
+- void search(const bool canonical, Stats &stats);
++ /**
++ * \return true if successful, false if insufficient memory to complete or
++ * other internal error
++ */
++ bool search(const bool canonical, Stats &stats);
+
+
+ void (*report_hook)(void *user_param,
+@@ -351,7 +358,7 @@
+ */
+ unsigned int cr_component_elements;
+
+-
++ std::vector<PathInfo> first_path_info;
+
+
+ public:
+@@ -362,7 +369,7 @@
+ * Check whether \a perm is an automorphism of this graph.
+ * Unoptimized, mainly for debugging purposes.
+ */
+- virtual bool is_automorphism(const std::vector<unsigned int>& perm) const;
++ virtual bool is_automorphism(const std::vector<unsigned int>& perm) const = 0;
+
+
+
+@@ -427,8 +434,10 @@
+ * if you want to use the automorphism later, you have to take a copy of it.
+ * Do not call any member functions in the hook.
+ * The search statistics are copied in \a stats.
++ * \return true if successful, false if insufficient memory to search or
++ * other internal error.
+ */
+- void find_automorphisms(Stats& stats,
++ bool find_automorphisms(Stats& stats,
+ void (*hook)(void* user_param,
+ unsigned int n,
+ const unsigned int* aut),
+@@ -448,6 +457,8 @@
+ * Note that the computed canonical version may depend on the applied version
+ * of bliss as well as on some other options (for instance, the splitting
+ * heuristic selected with bliss::Graph::set_splitting_heuristic()).
++ * This function returns NULL if there is insufficient memory, or another
++ * internal error occurs.
+ */
+ const unsigned int* canonical_form(Stats& stats,
+ void (*hook)(void* user_param,
+@@ -500,6 +511,10 @@
+ opt_use_long_prune = active;
+ }
+
++ /**
++ * Get an information vector about the first path.
++ */
++ std::vector<PathInfo> get_first_path_info() { return first_path_info; }
+ };
+
+
+@@ -615,7 +630,7 @@
+
+ void initialize_certificate();
+
+- bool is_automorphism(unsigned int* const perm);
++ int is_automorphism(unsigned int* const perm);
+
+
+ bool nucr_find_first_component(const unsigned int level);
+@@ -856,7 +871,7 @@
+
+ void initialize_certificate();
+
+- bool is_automorphism(unsigned int* const perm);
++ int is_automorphism(unsigned int* const perm);
+
+ void sort_edges();
+
diff --git a/sci-libs/bliss/metadata.xml b/sci-libs/bliss/metadata.xml
new file mode 100644
index 00000000000..64784b089c3
--- /dev/null
+++ b/sci-libs/bliss/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <maintainer>
+ <email>ottxor@gentoo.org</email>
+ <name>Christoph Junghans</name>
+ </maintainer>
+ <maintainer>
+ <email>tomka@gentoo.org</email>
+ <name>Thomas Kahle</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-libs/bmrblib/Manifest b/sci-libs/bmrblib/Manifest
new file mode 100644
index 00000000000..6b6dde85caf
--- /dev/null
+++ b/sci-libs/bmrblib/Manifest
@@ -0,0 +1 @@
+DIST bmrblib-1.0.3.tar.bz2 51246 SHA256 583e8d8f4ea2aaffec5eb30edfb4a840f1222512ad4f17c2d0d2c885a5afe3f6 SHA512 b03ad9e4ca035439165ebd1b7ba93ede427b2a233a4179be4e8089db988f1dcdce68b1e97348fe22fe7f2c3827ed003b654e0674a4d16a9e32a8a7c255c4b248 WHIRLPOOL 65b3a62142092af882be8d45fa84dd5b80e983c6bfb36d98b5ab444d6b0e4b0523ca64977a6643f27be9d64448a0c7e0ee2021bcbc306cbaa2101dcc3a1f6e1a
diff --git a/sci-libs/bmrblib/bmrblib-1.0.3.ebuild b/sci-libs/bmrblib/bmrblib-1.0.3.ebuild
new file mode 100644
index 00000000000..421a816c09a
--- /dev/null
+++ b/sci-libs/bmrblib/bmrblib-1.0.3.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} pypy )
+
+inherit distutils-r1
+
+DESCRIPTION="API abstracting the BioMagResBank (BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/)"
+HOMEPAGE="http://gna.org/projects/bmrblib/"
+SRC_URI="http://download.gna.org/${PN}/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
diff --git a/sci-libs/bmrblib/metadata.xml b/sci-libs/bmrblib/metadata.xml
new file mode 100644
index 00000000000..ce97f606bcd
--- /dev/null
+++ b/sci-libs/bmrblib/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
+ <longdescription>
+ Bmrblib is an API abstracting the BioMagResBank (BMRB) NMR-STAR format
+ (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files
+ for BMRB data deposition and the reading and easy extraction of data
+ from files residing in the BMRB data bank, all without knowledge of
+ the Self-Defining Text Archive and Retrieval (STAR) format. The API
+ has currently only python bindings.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/btf/Manifest b/sci-libs/btf/Manifest
new file mode 100644
index 00000000000..bc48bc451e8
--- /dev/null
+++ b/sci-libs/btf/Manifest
@@ -0,0 +1,2 @@
+DIST BTF-1.1.3.tar.gz 38276 SHA256 01032ba79baba9a90e3c03e9500c42cce9250c2ecab03c48323bc940f3a7cbfe SHA512 1e1b3e9bbed22ae417177f1bb960bd8097af05e7fede4b59df270020845e4bc9a77a16733af980d9b309503edc7ab6ffd852d28c6650e4e53b29125c5dc6364c WHIRLPOOL 319d1a512c42b3f6be294cd98020f9353d35456bd5136b76a98eb6fda77b5f0a6f924f1fc13c8aa29ddceb03602a3d0231d2283964f3a5041b3f4f9f28102bc3
+DIST btf-1.2.0.tar.bz2 290915 SHA256 9c26f0dc080891838421dd4d38bf1350d8f6fadb1e8a090c127e2667041191fb SHA512 4c2dcd5abf7a72485267a666e679545a5bfa8a20dfbf75a939c92547bdf960d40b6ae93cad23ac44f791e515a13f26c1dae446d3ba6e89b3d1f87d91d4dba50c WHIRLPOOL 0c40c7616b1fec6875ce4653e856f64056bd4eafe96c501cea5474d9ea7a1a75401a86db82f73b8f2f9c1244195746faca265abece3c7bfbf579f9bb2aaec37e
diff --git a/sci-libs/btf/btf-1.1.3.ebuild b/sci-libs/btf/btf-1.1.3.ebuild
new file mode 100644
index 00000000000..60a8f6dd54c
--- /dev/null
+++ b/sci-libs/btf/btf-1.1.3.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+AUTOTOOLS_AUTORECONF=yes
+inherit autotools-utils
+
+MY_PN=BTF
+
+DESCRIPTION="Algorithm for matrix permutation into block triangular form"
+HOMEPAGE="http://www.cise.ufl.edu/research/sparse/btf/"
+SRC_URI="http://www.cise.ufl.edu/research/sparse/${PN}/${MY_PN}-${PV}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="sci-libs/ufconfig"
+RDEPEND=""
+
+DOCS=( README.txt Doc/ChangeLog )
+PATCHES=( "${FILESDIR}"/${PN}-1.0.1-autotools.patch )
+
+S="${WORKDIR}/${MY_PN}"
diff --git a/sci-libs/btf/btf-1.2.0.ebuild b/sci-libs/btf/btf-1.2.0.ebuild
new file mode 100644
index 00000000000..a331bc8b1a9
--- /dev/null
+++ b/sci-libs/btf/btf-1.2.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils
+
+DESCRIPTION="Algorithm for matrix permutation into block triangular form"
+HOMEPAGE="http://www.cise.ufl.edu/research/sparse/btf/"
+SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+
+KEYWORDS=" ~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="static-libs"
+
+RDEPEND="sci-libs/suitesparseconfig"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
diff --git a/sci-libs/btf/files/btf-1.0.1-autotools.patch b/sci-libs/btf/files/btf-1.0.1-autotools.patch
new file mode 100644
index 00000000000..4156c2dfeb7
--- /dev/null
+++ b/sci-libs/btf/files/btf-1.0.1-autotools.patch
@@ -0,0 +1,34 @@
+--- configure.ac 1970-01-01 01:00:00.000000000 +0100
++++ configure.ac 2008-01-30 12:29:44.232979678 +0000
+@@ -0,0 +1,10 @@
++# -*- Autoconf -*-
++AC_PREREQ(2.59)
++AC_INIT(btf, 1.0.1, davis@cise.ufl.edu)
++AM_INIT_AUTOMAKE([foreign])
++AC_PROG_INSTALL
++AC_PROG_LIBTOOL
++AC_CHECK_LIB(m, sqrt)
++AC_CHECK_HEADERS(UFconfig.h)
++AC_CONFIG_FILES([Makefile Source/Makefile])
++AC_OUTPUT
+--- Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ Makefile.am 2008-01-30 12:30:12.862611188 +0000
+@@ -0,0 +1,3 @@
++SUBDIRS = Source
++EXTRA_DIST = README.txt
++include_HEADERS = Include/btf.h Include/btf_internal.h
+--- Source/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ Source/Makefile.am 2008-01-30 12:37:00.857861512 +0000
+@@ -0,0 +1,12 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include
++
++BTFSRC = btf_order.c btf_maxtrans.c btf_strongcomp.c
++
++lib_LTLIBRARIES = libbtf.la
++noinst_LTLIBRARIES = libbtfi.la libbtfl.la
++libbtfi_la_SOURCES = $(BTFSRC)
++libbtfi_la_CPPFLAGS = $(AM_CPPFLAGS)
++libbtfl_la_SOURCES = $(BTFSRC)
++libbtfl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
++libbtf_la_SOURCES =
++libbtf_la_LIBADD = libbtfl.la libbtfi.la
diff --git a/sci-libs/btf/metadata.xml b/sci-libs/btf/metadata.xml
new file mode 100644
index 00000000000..2c22e8591c5
--- /dev/null
+++ b/sci-libs/btf/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+ The Block Triangular Form is a library of routines offering
+ permutation of an unsymmetric matrix (square or rectangular) into
+ its block upper triangular form (more precisely, it computes a
+ Dulmage-Mendelsohn decomposition).
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/buddy/Manifest b/sci-libs/buddy/Manifest
new file mode 100644
index 00000000000..8c71890779b
--- /dev/null
+++ b/sci-libs/buddy/Manifest
@@ -0,0 +1,2 @@
+DIST buddy-2.4.tar.gz 766523 SHA256 d3df80a6a669d9ae408cb46012ff17bd33d855529d20f3a7e563d0d913358836 SHA512 43984969359ac363141ee8a67538ceeae1412efa172432a8355f6ce68ab5ffab12470ad7a2e0d7a6a557b8bf55e98b2f2dc5cc6710466403d45fab2195ba2e23 WHIRLPOOL 448c1eacc61a238083723693abca6f1600198e9ebd420a9b21179d82fd717c697bfe39758bffda1d96e3ace1a160da5cde91094bd67d9d288a632f1d03f2170a
+DIST buddy22.tar.gz 448103 SHA256 932be15566d95038239b76028bf8d371baadc421fe16c379d4b29d0b834530ca SHA512 edded743a9fdd762b2529408902069b559b24278c9ca8f10f8a72d486f0ea254f2b5d6fc414fb7599eb627841e4d8126198aebc96913c297cadd691485680df9 WHIRLPOOL cf0b668bfa50c0ae7f35f5936d8e9e5a83c70a8de0fadd0454a458cff7a0babef8f30829fe8414d0e012a6c7857f917f92a010c136e2689978779e99fffca971
diff --git a/sci-libs/buddy/buddy-2.2.ebuild b/sci-libs/buddy/buddy-2.2.ebuild
new file mode 100644
index 00000000000..f4cc8ccada2
--- /dev/null
+++ b/sci-libs/buddy/buddy-2.2.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Binary Decision Diagram Package"
+HOMEPAGE="http://www.itu.dk/research/buddy/"
+SRC_URI="http://www.itu.dk/research/buddy/buddy22.tar.gz"
+
+LICENSE="buddy"
+SLOT="0"
+KEYWORDS="x86 ~ppc"
+IUSE=""
+
+S=${WORKDIR}/buddy22
+
+src_compile() {
+ emake \
+ CFLAGS="${CFLAGS}" \
+ LIBDIR=usr/lib \
+ INCDIR=usr/include \
+ || die
+}
+
+src_install() {
+ dodir /usr/lib /usr/include
+ emake install \
+ LIBDIR="${D}"/usr/lib \
+ INCDIR="${D}"/usr/include || die
+ dodoc CHANGES README doc/*.txt
+ insinto /usr/share/doc/${P}/ps
+ doins doc/*.ps
+ insinto /usr/share/${PN}/examples
+ cd examples
+ for example in *; do
+ tar -czf ${example}.tar.gz ${example}
+ doins ${example}.tar.gz
+ done
+}
diff --git a/sci-libs/buddy/buddy-2.4.ebuild b/sci-libs/buddy/buddy-2.4.ebuild
new file mode 100644
index 00000000000..ecb37494e61
--- /dev/null
+++ b/sci-libs/buddy/buddy-2.4.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2
+
+DESCRIPTION="Binary Decision Diagram Package"
+HOMEPAGE="http://sourceforge.net/projects/buddy/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="buddy"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc examples static-libs"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-gcc43.patch \
+ "${FILESDIR}"/${P}-gold.patch
+}
+
+src_configure() {
+ econf $(use_enable static-libs static)
+}
+
+src_install() {
+ default
+
+ dodoc doc/*.txt
+
+ use doc && docinto /usr/share/doc/${PF}/ps && dodoc doc/*.ps
+
+ if use examples; then
+ insinto /usr/share/${PN}/
+ doins -r examples
+ fi
+}
diff --git a/sci-libs/buddy/files/buddy-2.4-gcc43.patch b/sci-libs/buddy/files/buddy-2.4-gcc43.patch
new file mode 100644
index 00000000000..c7b9f85688e
--- /dev/null
+++ b/sci-libs/buddy/files/buddy-2.4-gcc43.patch
@@ -0,0 +1,22 @@
+diff -Naurp buddy-2.4-orig/src/bddtest.cxx buddy-2.4/src/bddtest.cxx
+--- buddy-2.4-orig/src/bddtest.cxx 2004-06-25 07:22:26.000000000 -0600
++++ buddy-2.4/src/bddtest.cxx 2009-02-09 22:14:19.000000000 -0600
+@@ -28,6 +28,7 @@
+ ========================================================================*/
+
+ #include <string>
++#include <cstdlib>
+ #include "bdd.h"
+ #include "bvec.h"
+
+diff -Naurp buddy-2.4-orig/examples/bddcalc/parser_.h buddy-2.4/examples/bddcalc/parser_.h
+--- buddy-2.4-orig/examples/bddcalc/parser_.h 2004-06-25 07:21:43.000000000 -0600
++++ buddy-2.4/examples/bddcalc/parser_.h 2009-02-09 22:21:09.000000000 -0600
+@@ -9,6 +9,7 @@
+ #define _PARSER_H
+
+ #include <stdio.h>
++#include <stdlib.h>
+ #include "bdd.h"
+
+ #define MAXIDLEN 32 /* Max. number of allowed characters in an identifier */
diff --git a/sci-libs/buddy/files/buddy-2.4-gold.patch b/sci-libs/buddy/files/buddy-2.4-gold.patch
new file mode 100644
index 00000000000..dc30a642141
--- /dev/null
+++ b/sci-libs/buddy/files/buddy-2.4-gold.patch
@@ -0,0 +1,16 @@
+ examples/cmilner/Makefile.in | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/examples/cmilner/Makefile.in b/examples/cmilner/Makefile.in
+index 9b49e9d..f7a9b8a 100644
+--- a/examples/cmilner/Makefile.in
++++ b/examples/cmilner/Makefile.in
+@@ -217,7 +217,7 @@ clean-checkPROGRAMS:
+ done
+ cmilner$(EXEEXT): $(cmilner_OBJECTS) $(cmilner_DEPENDENCIES)
+ @rm -f cmilner$(EXEEXT)
+- $(LINK) $(cmilner_LDFLAGS) $(cmilner_OBJECTS) $(cmilner_LDADD) $(LIBS)
++ $(LINK) $(cmilner_LDFLAGS) $(cmilner_OBJECTS) $(cmilner_LDADD) $(LIBS) -lm
+
+ mostlyclean-compile:
+ -rm -f *.$(OBJEXT)
diff --git a/sci-libs/buddy/metadata.xml b/sci-libs/buddy/metadata.xml
new file mode 100644
index 00000000000..c09b86dde13
--- /dev/null
+++ b/sci-libs/buddy/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+ A Binary Decision Diagram library, with :many highly efficient
+ vectorized BDD operations,dynamic variable reordering,automated
+ garbage collection,a C++ interface with automatic reference
+ counting,and much more.
+</longdescription>
+ <upstream>
+ <remote-id type="sourceforge">buddy</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/camd/Manifest b/sci-libs/camd/Manifest
new file mode 100644
index 00000000000..87acde08cd6
--- /dev/null
+++ b/sci-libs/camd/Manifest
@@ -0,0 +1 @@
+DIST camd-2.3.1.tar.bz2 319766 SHA256 bb3fcb577307fa4a70281bea8db896b2300a484f27cb61b392be2c4cf7cd5a2e SHA512 13c5d687b9314f43a6c7237c7541e0c21cc544ffe52f8a984f64c5177a9f1f6b5ab07e9190388587f273424db8e6076ef050f836dbc9f33ca44e94d0034c8070 WHIRLPOOL a53b09c002b930a78055742f507b3ea7b14906378edb6808e65e4aac16dcad8178cc16de6373d633356b501fb8a5939737f8c4966d94c1162076be5b1b15c2ad
diff --git a/sci-libs/camd/camd-2.3.1.ebuild b/sci-libs/camd/camd-2.3.1.ebuild
new file mode 100644
index 00000000000..b085672fa7d
--- /dev/null
+++ b/sci-libs/camd/camd-2.3.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils
+
+DESCRIPTION="Library to order a sparse matrix prior to Cholesky factorization"
+HOMEPAGE="http://www.cise.ufl.edu/research/sparse/camd/"
+SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+
+KEYWORDS="amd64 ~arm hppa ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="doc static-libs"
+
+RDEPEND="sci-libs/suitesparseconfig"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig
+ doc? ( virtual/latex-base )"
+
+src_configure() {
+ local myeconfargs=(
+ $(use_with doc)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-libs/camd/files/camd-2.2.0-autotools.patch b/sci-libs/camd/files/camd-2.2.0-autotools.patch
new file mode 100644
index 00000000000..d112a5f1716
--- /dev/null
+++ b/sci-libs/camd/files/camd-2.2.0-autotools.patch
@@ -0,0 +1,71 @@
+--- configure.ac 1970-01-01 01:00:00.000000000 +0100
++++ configure.ac 2008-01-31 15:35:15.579030692 +0000
+@@ -0,0 +1,12 @@
++# -*- Autoconf -*-
++AC_PREREQ(2.59)
++AC_INIT(camd, 2.2.0, davis@cise.ufl.edu)
++AM_INIT_AUTOMAKE([foreign])
++AC_PROG_INSTALL
++AC_PROG_LIBTOOL
++AC_CHECK_LIB(m, sqrt)
++AC_CHECK_HEADERS(UFconfig.h)
++AC_CONFIG_FILES([Source/Makefile
++ Demo/Makefile
++ Makefile])
++AC_OUTPUT
+--- ./Demo/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ ./Demo/Makefile.am 2008-01-31 15:36:57.492838429 +0000
+@@ -0,0 +1,27 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include
++check_PROGRAMS = \
++ camd_demo \
++ camd_demo2 \
++ camd_simple
++# test is not robust
++# camd_l_demo
++
++LDADD = $(top_builddir)/Source/libcamd.la -lm
++
++camd_demo_SOURCES = camd_demo.c
++#camd_l_demo_SOURCES = camd_l_demo.c
++camd_demo2_SOURCES = camd_demo2.c
++camd_simple_SOURCES = camd_simple.c
++
++check-local: $(check_PROGRAMS)
++ @for i in $(check_PROGRAMS); do \
++ echo "Testing $$i"; \
++ ./$$i > my_$$i.out; \
++ if ! diff $(srcdir)/$$i.out my_$$i.out; then \
++ echo "Test $$i failed!"; \
++ exit 1; \
++ fi \
++ done;
++
++clean-local:
++ rm -f my*.out
+--- ./Source/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ ./Source/Makefile.am 2008-01-31 15:37:17.205961816 +0000
+@@ -0,0 +1,17 @@
++CAMDCSRC = \
++ camd_aat.c camd_1.c camd_2.c camd_dump.c camd_postorder.c \
++ camd_defaults.c camd_order.c camd_control.c camd_info.c \
++ camd_valid.c camd_preprocess.c
++
++lib_LTLIBRARIES = libcamd.la
++noinst_LTLIBRARIES = libcamdi.la libcamdl.la
++AM_CPPFLAGS = -I$(top_srcdir)/Include
++
++libcamdi_la_SOURCES = $(CAMDCSRC)
++libcamdi_la_CPPFLAGS = $(AM_CPPFLAGS) -DDINT
++libcamdl_la_SOURCES = $(CAMDCSRC)
++libcamdl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
++
++libcamd_la_SOURCES = camd_global.c
++libcamd_la_LIBADD = libcamdl.la libcamdi.la -lm
++
+--- ./Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ ./Makefile.am 2008-01-31 15:34:59.202097424 +0000
+@@ -0,0 +1,3 @@
++SUBDIRS = Demo Source
++EXTRA_DIST = README.txt
++include_HEADERS = Include/camd.h Include/camd_internal.h
diff --git a/sci-libs/camd/metadata.xml b/sci-libs/camd/metadata.xml
new file mode 100644
index 00000000000..9c4f1c34262
--- /dev/null
+++ b/sci-libs/camd/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+ Constrained Approximate Minimum Degree ordering is a set of routines
+ for ordering a sparse matrix prior to Cholesky factorization (or for
+ LU factorization with diagonal pivoting).
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/cbflib/Manifest b/sci-libs/cbflib/Manifest
new file mode 100644
index 00000000000..51d76249c0e
--- /dev/null
+++ b/sci-libs/cbflib/Manifest
@@ -0,0 +1,6 @@
+DIST CBFlib-0.9.2.10.tar.gz 4898574 SHA256 e98ed35e0659ca4ebc10cb035399e8a94f30c721be734ac2bac1933ae6a1bc6f SHA512 d0d9fa6f990f3fb03733887088f409bb348462ba4e8fa0a5431ae1c1087c54e8de969790f04d90e8f23e3eaf351f3253e3ae8791058b47a6cd230b04d9c51898 WHIRLPOOL d380f5144bd497fe4635c9a78579cab58c8fe6bfc14552eabd8da27d94654af1b0be024daff1cf4dbd769291e9011a708dbbab1c9e81c35e5eeb2588a3cca17a
+DIST CBFlib-0.9.2.2.tar.gz 4549837 SHA256 ce289756d643aa2ab79fd1614183ccee7ad06f128d1d8d59c97d7c107ce5f802 SHA512 756153ba81c17ea55d1397227273bc912a4fec7fd70d0b226b2519a5a14c92b612d6421f2748583aea5d0162b1defa51740200e936ce4f23b13b1506cfa5a043 WHIRLPOOL 4b690fa5698503eb424886391752fa2f4b5dad89b184cb4390506980032141ac5c147002b0261ec2769c9ea8aba696c629883b080bc504bc58d973367e399718
+DIST CBFlib-0.9.2.4.tar.gz 4564355 SHA256 c7d11a70e6454a6801e8f30d56db6639fa814aa25775bf54109325073c4a08c1 SHA512 e1ee1fe39b3d15e5d707d973c5666f198e3c9006b4c449fa56287032661a7ecfbeadad0fda528310f9cdd9f33856004333784a840d193a5c7db6c5c071fb07e5 WHIRLPOOL ded867cda1757196ad2188eda7a1a09999411a3d1a452172880fabdc5504aa346e44b2c8c25d921f674897ec7f8edf3da4de79d4843f68ecbb72634631ea43dd
+DIST CBFlib-0.9.3.3.tar.gz 5787633 SHA256 d6c3cc2c6c0aed2a3aa7c74dc645ad223470dc76bb2181242534d4c322bb00dc SHA512 e041c26770e12e09110d7c4f39737406c6ade6cae6fa941cd31dd3b90432a034426272b8daa851a8a23baceb7189479d2d8bde882b7cfdb8ae666fadc5be57ff WHIRLPOOL 8e9e0004cdd2411c9d37b588afa274e1c2b955fe361fc3df597acc30526958d5722993f36f33672769ef55eca51b87917f57ec56528a7711a934d9f8de2b8019
+DIST CBFlib_0.9.2_Data_Files_Input.tar.gz 17102003 SHA256 4414166a5a5b5ef6e4c460bb6941bd0aca53e7a41dbc9e5bdf0c6d44cf00d5ac SHA512 86689695155b822146e8cc1e310f4820292cde28c9cc240da34ef8259c429af7b182a055e1014078081528c505b0269367cd5e6e80278a53b448f0cc0dfcc3aa WHIRLPOOL a946dce8a6fa1a90a6fb3e7ec167a2ba41fdd5ef9435f4da083f9f9a7f5dfb94a2ebef1d1c36f5332fc486452b9b26c29161c7484ba337da83c24fbcd0334126
+DIST CBFlib_0.9.2_Data_Files_Output.tar.gz 36009958 SHA256 311cebff470b7d4f94b7888252cca879e6e0745f4e2eb6fa9e21cf84f984029b SHA512 fb08cbc5a68a73089c012c4c8da2a02ed7a216e02f23f2b24ba2e4dca7af834c7200868028921540e14326ea88e48028675e1be1f2c572eb3e962a79cf892002 WHIRLPOOL 386691e706dafacb9f5ee13f74fcf0f78c3a827d434ae18602fb2a8f805c178f9883e10658ed739a35bb7ceb58b628c1a9f1bbf89144efd793d13c7a62c3d05b
diff --git a/sci-libs/cbflib/cbflib-0.9.2.10-r1.ebuild b/sci-libs/cbflib/cbflib-0.9.2.10-r1.ebuild
new file mode 100644
index 00000000000..165e6324e88
--- /dev/null
+++ b/sci-libs/cbflib/cbflib-0.9.2.10-r1.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P1="CBFlib-${PV}"
+#MY_P2="CBFlib_${PV}"
+MY_P2="CBFlib_0.9.3"
+
+DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
+HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
+BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz"
+# test? (
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
+# )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+S=${WORKDIR}/${MY_P1}
+
+RDEPEND="sci-libs/hdf5:="
+DEPEND="${RDEPEND}"
+
+RESTRICT="test"
+
+src_prepare(){
+ rm -rf Py* drel* dRel* ply*
+ epatch "${FILESDIR}"/${PV}-Makefile.patch
+ cp Makefile_LINUX_gcc42 Makefile
+
+ append-fflags -fno-range-check
+ append-cflags -D_USE_XOPEN_EXTENDED -DCBF_DONT_USE_LONG_LONG
+
+ sed \
+ -e "s|^SOLDFLAGS.*$|SOLDFLAGS = -shared ${LDFLAGS}|g" \
+ -i Makefile || die
+ tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+ emake -j1 shared
+}
+
+src_test(){
+ emake -j1 basic
+}
+
+src_install() {
+ insinto /usr/include/${PN}
+ dosym ${PN} /usr/include/cbf
+ doins include/*.h
+
+ dolib.so solib/lib*
+
+ dodoc README
+ use doc && dohtml -r README.html html_graphics doc
+}
diff --git a/sci-libs/cbflib/cbflib-0.9.2.10.ebuild b/sci-libs/cbflib/cbflib-0.9.2.10.ebuild
new file mode 100644
index 00000000000..c84f4936d49
--- /dev/null
+++ b/sci-libs/cbflib/cbflib-0.9.2.10.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P1="CBFlib-${PV}"
+#MY_P2="CBFlib_${PV}"
+MY_P2="CBFlib_0.9.3"
+
+DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
+HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
+BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz"
+# test? (
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
+# )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+S=${WORKDIR}/${MY_P1}
+
+RDEPEND="sci-libs/hdf5:="
+DEPEND="${RDEPEND}"
+
+RESTRICT="test"
+
+src_prepare(){
+ rm -rf Py* drel* dRel* ply*
+ epatch "${FILESDIR}"/${PV}-Makefile.patch
+ cp Makefile_LINUX_gcc42 Makefile
+
+ append-fflags -fno-range-check
+ append-cflags -D_USE_XOPEN_EXTENDED -DCBF_DONT_USE_LONG_LONG
+
+ sed \
+ -e "s|^SOLDFLAGS.*$|SOLDFLAGS = -shared ${LDFLAGS}|g" \
+ -i Makefile || die
+ tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+ emake -j1 shared
+}
+
+src_test(){
+ emake -j1 basic
+}
+
+src_install() {
+ insinto /usr/include/${PN}
+ doins include/*.h
+
+ dolib.so solib/lib*
+
+ dodoc README
+ use doc && dohtml -r README.html html_graphics doc
+}
diff --git a/sci-libs/cbflib/cbflib-0.9.2.2.ebuild b/sci-libs/cbflib/cbflib-0.9.2.2.ebuild
new file mode 100644
index 00000000000..fe47e542220
--- /dev/null
+++ b/sci-libs/cbflib/cbflib-0.9.2.2.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P1="CBFlib-${PV}"
+#MY_P2="CBFlib_${PV}"
+MY_P2="CBFlib_0.9.2"
+
+DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
+HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz
+ test? (
+ mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
+ mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
+ )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+DEPEND="virtual/fortran"
+RDEPEND="${DEPEND}"
+#test? ( sys-process/time )"
+
+S=${WORKDIR}/${MY_P1}
+
+src_prepare(){
+ rm -rf Py* drel* dRel* ply*
+ epatch "${FILESDIR}"/${PV}-Makefile.patch
+ cp Makefile_LINUX_gcc42 Makefile
+
+ append-fflags -fno-range-check
+ append-cflags -D_USE_XOPEN_EXTENDED -DCBF_DONT_USE_LONG_LONG
+
+ sed \
+ -e "s|^CC.*$|CC = $(tc-getCC)|" \
+ -e "s|^C++.*$|C++ = $(tc-getCXX)|" \
+ -e "s|C++|CXX|g" \
+ -e "s|^CFLAGS.*$|CFLAGS = ${CFLAGS}|" \
+ -e "s|^F90C.*$|F90C = $(tc-getFC)|" \
+ -e "s|^F90FLAGS.*$|F90FLAGS = ${FFLAGS}|" \
+ -e "s|^SOLDFLAGS.*$|SOLDFLAGS = -shared ${LDFLAGS}|g" \
+ -e "s| /bin| ${EPREFIX}/bin|g" \
+ -e "s|/usr|${EPREFIX}/usr|g" \
+ -i Makefile || die
+}
+
+src_compile() {
+ emake -j1 shared
+}
+
+src_test(){
+ emake -j1 basic
+}
+
+src_install() {
+ insinto /usr/include/${PN}
+ doins include/*.h
+
+ dolib.so solib/lib*
+
+ dodoc README
+ if use doc; then
+ dohtml -r README.html html_graphics doc
+ fi
+}
diff --git a/sci-libs/cbflib/cbflib-0.9.2.4.ebuild b/sci-libs/cbflib/cbflib-0.9.2.4.ebuild
new file mode 100644
index 00000000000..374ab24a4ad
--- /dev/null
+++ b/sci-libs/cbflib/cbflib-0.9.2.4.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P1="CBFlib-${PV}"
+#MY_P2="CBFlib_${PV}"
+MY_P2="CBFlib_0.9.3"
+
+DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
+HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
+BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz"
+# test? (
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
+# )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+S=${WORKDIR}/${MY_P1}
+
+RESTRICT="test"
+
+src_prepare(){
+ rm -rf Py* drel* dRel* ply*
+ epatch "${FILESDIR}"/0.9.2.3-Makefile.patch
+ cp Makefile_LINUX_gcc42 Makefile
+
+ append-fflags -fno-range-check
+ append-cflags -D_USE_XOPEN_EXTENDED -DCBF_DONT_USE_LONG_LONG
+
+ sed \
+ -e "s|^CC.*$|CC = $(tc-getCC)|" \
+ -e "s|^C++.*$|C++ = $(tc-getCXX)|" \
+ -e "s|C++|CXX|g" \
+ -e "s|^CFLAGS.*$|CFLAGS = ${CFLAGS}|" \
+ -e "s|^F90C.*$|F90C = $(tc-getFC)|" \
+ -e "s|^F90FLAGS.*$|F90FLAGS = ${FFLAGS}|" \
+ -e "s|^SOLDFLAGS.*$|SOLDFLAGS = -shared ${LDFLAGS}|g" \
+ -e "s| /bin| ${EPREFIX}/bin|g" \
+ -e "s|/usr|${EPREFIX}/usr|g" \
+ -i Makefile || die
+}
+
+src_compile() {
+ emake -j1 shared
+}
+
+src_test(){
+ emake -j1 basic
+}
+
+src_install() {
+ insinto /usr/include/${PN}
+ doins include/*.h
+
+ dolib.so solib/lib*
+
+ dodoc README
+ use doc && dohtml -r README.html html_graphics doc
+}
diff --git a/sci-libs/cbflib/cbflib-0.9.3.3.ebuild b/sci-libs/cbflib/cbflib-0.9.3.3.ebuild
new file mode 100644
index 00000000000..2f3c1a86fd9
--- /dev/null
+++ b/sci-libs/cbflib/cbflib-0.9.3.3.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+CMAKE_MAKEFILE_GENERATOR=emake
+
+inherit cmake-utils eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P1="CBFlib-${PV}"
+#MY_P2="CBFlib_${PV}"
+MY_P2="CBFlib_0.9.3"
+
+DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
+HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
+BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz"
+# test? (
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
+# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
+# )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+S=${WORKDIR}/${MY_P1}
+
+RDEPEND="sci-libs/hdf5:="
+DEPEND="${RDEPEND}"
+
+RESTRICT="test"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-unbundle.patch
+)
+
+src_prepare(){
+ rm -rf Py* drel* dRel* ply* || die
+
+ append-fflags -fno-range-check
+
+ tc-export CC CXX AR RANLIB FC F77
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DUNPACKED_DIRECTORY="${S}"
+ )
+ cmake-utils_src_configure
+}
+
+src_install() {
+ cmake-utils_src_install
+ dosym ${PN} /usr/include/cbf
+}
diff --git a/sci-libs/cbflib/files/0.9.0-Makefile.patch b/sci-libs/cbflib/files/0.9.0-Makefile.patch
new file mode 100644
index 00000000000..914152c9e9e
--- /dev/null
+++ b/sci-libs/cbflib/files/0.9.0-Makefile.patch
@@ -0,0 +1,104 @@
+diff --git a/Makefile_LINUX_gcc42 b/Makefile_LINUX_gcc42
+index 52c5286..5c894a0 100644
+--- a/Makefile_LINUX_gcc42
++++ b/Makefile_LINUX_gcc42
+@@ -250,7 +250,10 @@
+
+
+ # Version string
+-VERSION = 0.9.0
++MAJOR = 0
++MINOR = 9
++MICRO = 0
++VERSION = ${MAJOR}.${MINOR}.${MICRO}
+
+
+ #
+@@ -282,7 +285,7 @@ SHAR = /usr/bin/shar
+ #
+ # Program to use to create archives
+ #
+-AR = /usr/bin/ar
++AR = ar
+
+ #
+ # Program to use to add an index to an archive
+@@ -292,13 +295,13 @@ RANLIB = /usr/bin/ranlib
+ #
+ # Program to use to decompress a data file
+ #
+-DECOMPRESS = /usr/bin/bunzip2
++DECOMPRESS = bunzip2
+
+
+ #
+ # Program to use to compress a data file
+ #
+-COMPRESS = /usr/bin/bzip2
++COMPRESS = bzip2
+
+ #
+ # Program to use to generate a signature
+@@ -486,9 +489,9 @@ F90SOURCE = $(SRC)/fcb_atol_wcnt.f90 \
+ $(SRC)/fcb_read_image.f90 \
+ $(SRC)/fcb_read_line.f90 \
+ $(SRC)/fcb_read_xds_i2.f90 \
+- $(SRC)/fcb_skip_whitespace.f90 \
+- $(EXAMPLES)/test_fcb_read_image.f90 \
+- $(EXAMPLES)/test_xds_binary.f90
++ $(SRC)/fcb_skip_whitespace.f90
++# $(EXAMPLES)/test_fcb_read_image.f90 \
++# $(EXAMPLES)/test_xds_binary.f90
+
+
+ #
+@@ -663,7 +666,7 @@ all:: $(BIN)/test_xds_binary \
+ $(BIN)/test_fcb_read_image
+ endif
+
+-shared: $(SOLIB)/libcbf.so $(SOLIB)/libfcb.so $(SOLIB)/libimg.so
++shared: $(SOLIB)/libcbf.so.${VERSION} $(SOLIB)/libfcb.so.${VERSION} $(SOLIB)/libimg.so.${VERSION}
+
+ javawrapper: shared $(JAVADIR) $(JAVADIR)/cbflib-$(VERSION).jar $(SOLIB)/libcbf_wrap.so
+
+@@ -846,10 +849,11 @@ ifneq ($(RANLIB),)
+ $(RANLIB) $@
+ endif
+
+-$(SOLIB)/libcbf.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++$(SOLIB)/libcbf.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+ $(CC) $(CFLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+ mv *.o $(SOLIB)
+- $(CC) -o $@ $(SOLIB)/*.o $(SOLDFLAGS) $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -Wl,-soname,libcbf.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ $(SOLIB)/*.o $(EXTRALIBS)
++ ln -sf libcbf.so.$(VERSION) $(SOLIB)/libcbf.so
+
+ #
+ # IMG library
+@@ -862,9 +866,10 @@ ifneq ($(RANLIB),)
+ endif
+ rm img.o
+
+-$(SOLIB)/libimg.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++$(SOLIB)/libimg.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+ $(CC) $(CFLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
+- $(CC) -o $@ img.o $(SOLDFLAGS)
++ $(CC) $(LDFLAGS) -Wl,-soname,libimg.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ img.o
++ ln -sf libimg.so.$(VERSION) $(SOLIB)/libimg.so
+ rm img.o
+
+ #
+@@ -888,10 +893,11 @@ else
+ echo "Define F90C to build $(LIB)/libfcb.a"
+ endif
+
+-$(SOLIB)/libfcb.so: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++$(SOLIB)/libfcb.so.${VERSION}: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+ ifneq ($(F90C),)
+ $(F90C) $(F90FLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
+- $(F90C) $(F90FLAGS) -o $@ *.o $(SOLDFLAGS)
++ $(F90C) $(LDFLAGS) -Wl,-soname,libfcb.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) $(F90FLAGS) -o $@ *.o
++ ln -sf libfcb.so.$(VERSION) $(SOLIB)/libfcb.so
+ rm *.o
+ else
+ echo "Define F90C to build $(SOLIB)/libfcb.so"
diff --git a/sci-libs/cbflib/files/0.9.0-python.patch b/sci-libs/cbflib/files/0.9.0-python.patch
new file mode 100644
index 00000000000..b18d019ff8e
--- /dev/null
+++ b/sci-libs/cbflib/files/0.9.0-python.patch
@@ -0,0 +1,16 @@
+diff --git a/pycbf/setup.py b/pycbf/setup.py
+index 0763f06..7fe9ccc 100644
+--- a/pycbf/setup.py
++++ b/pycbf/setup.py
+@@ -9,9 +9,9 @@ from distutils.core import setup, Extension
+ e = Extension('_pycbf',
+ sources = ["pycbf_wrap.c","../src/cbf_simple.c"],
+ extra_compile_args=["-g"],
+- library_dirs=["../lib/"],
++ library_dirs=["../solib/"],
+ libraries=["cbf"],
+ include_dirs = ["../include"] )
+
+ # Build it
+-setup(name="_pycbf",ext_modules=[e],)
++setup(name="_pycbf",ext_modules=[e],py_modules=["pycbf"],)
diff --git a/sci-libs/cbflib/files/0.9.2.10-Makefile.patch b/sci-libs/cbflib/files/0.9.2.10-Makefile.patch
new file mode 100644
index 00000000000..9c72300873f
--- /dev/null
+++ b/sci-libs/cbflib/files/0.9.2.10-Makefile.patch
@@ -0,0 +1,269 @@
+ Makefile_LINUX_gcc42 | 93 ++++++++++++++++++++++++++++------------------------
+ 1 file changed, 50 insertions(+), 43 deletions(-)
+
+diff --git a/Makefile_LINUX_gcc42 b/Makefile_LINUX_gcc42
+index 0aa639a..071863d 100644
+--- a/Makefile_LINUX_gcc42
++++ b/Makefile_LINUX_gcc42
+@@ -250,7 +250,11 @@
+
+
+ # Version string
+-VERSION = 0.9.2
++MAJOR = 0
++MINOR = 9
++MICRO = 3
++VERSION = ${MAJOR}.${MINOR}.${MICRO}
++
+
+
+ #
+@@ -297,12 +301,12 @@ SHAR = /usr/bin/shar
+ #
+ # Program to use to create archives
+ #
+-AR = /usr/bin/ar
++AR ?= ar
+
+ #
+ # Program to use to add an index to an archive
+ #
+-RANLIB = /usr/bin/ranlib
++RANLIB ?= ranlib
+
+ #
+ # Program to use to decompress a data file
+@@ -313,7 +317,7 @@ DECOMPRESS = bunzip2
+ #
+ # Program to use to compress a data file
+ #
+-COMPRESS = /usr/bin/bzip2
++COMPRESS = bzip2
+
+ #
+ # Program to use to generate a signature
+@@ -410,12 +414,12 @@ SETUP_PY = setup.py
+ # with gcc version 4.2
+ #
+ #########################################################
+-CC = gcc
+-C++ = g++
+-CFLAGS = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
+-F90C = gfortran
+-F90FLAGS = -g -fno-range-check
+-F90LDFLAGS =
++CC ?= gcc
++CXX ?= g++
++CFLAGS += -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
++FC ?= gfortran
++FCFLAGS += -g -fno-range-check
++LDFLAGS +=
+ SOCFLAGS = -fPIC
+ SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
+ JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
+@@ -425,7 +429,7 @@ M4FLAGS = -Dfcb_bytes_in_rec=131072
+ TIME = time
+
+ ifneq ($(NOFORTRAN),)
+-F90C =
++FC =
+ endif
+
+ #
+@@ -491,9 +495,9 @@ RTLPEXPORTS = export LD_LIBRARY_PATH=$(PWD)/solib:$(PWD)/lib;\
+ .m4.f90:
+ m4 -P $(M4FLAGS) $< > $@
+
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ .f90.o:
+- $(F90C) $(F90FLAGS) -c $< -o $@
++ $(FC) $(FCFLAGS) -c $< -o $@
+ endif
+
+
+@@ -701,7 +705,7 @@ default:
+ #
+ # Compile the library and examples
+ #
+-all:: $(BIN) $(SOURCE) $(F90SOURCE) $(HEADERS) $(HDF5)\
++all:: $(BIN) $(SOURCE) $(F90SOURCE) $(HEADERS) \
+ symlinksdone \
+ $(REGEXDEP) \
+ $(LIB)/libcbf.a \
+@@ -725,12 +729,12 @@ all:: $(BIN) $(SOURCE) $(F90SOURCE) $(HEADERS) $(HDF5)\
+ $(BIN)/tiff2cbf
+
+
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ all:: $(BIN)/test_xds_binary \
+ $(BIN)/test_fcb_read_image
+ endif
+
+-shared: $(SOLIB)/libcbf.so $(SOLIB)/libfcb.so $(SOLIB)/libimg.so
++shared: $(SOLIB)/libcbf.so.${VERSION} $(SOLIB)/libfcb.so.${VERSION} $(SOLIB)/libimg.so.${VERSION}
+
+ javawrapper: shared $(JCBF) $(JCBF)/cbflib-$(VERSION).jar $(SOLIB)/libcbf_wrap.so
+
+@@ -969,7 +973,7 @@ $(SRC)/cbf_stx.c: $(SRC)/cbf.stx.y
+ #
+ # CBF library
+ #
+-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) $(HDF5)
++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
+ $(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(PYCIFRWFLAG) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+ $(AR) cr $@ *.o
+ mv *.o $(LIB)
+@@ -977,10 +981,11 @@ ifneq ($(RANLIB),)
+ $(RANLIB) $@
+ endif
+
+-$(SOLIB)/libcbf.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB) $(HDF5)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(PYCIFRWFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+- $(CC) -o $@ *.o $(SOLDFLAGS) $(EXTRALIBS) $(HDF5SOLIBS)
+- rm *.o
++$(SOLIB)/libcbf.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ $(CC) $(CFLAGS) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
++ mv *.o $(SOLIB)
++ $(CC) $(LDFLAGS) -Wl,-soname,libcbf.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ $(SOLIB)/*.o $(EXTRALIBS) $(HDF5SOLIBS)
++ ln -sf libcbf.so.$(VERSION) $(SOLIB)/libcbf.so
+
+ #
+ # IMG library
+@@ -993,9 +998,10 @@ ifneq ($(RANLIB),)
+ endif
+ rm img.o
+
+-$(SOLIB)/libimg.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
+- $(CC) -o $@ img.o $(SOLDFLAGS)
++$(SOLIB)/libimg.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ $(CC) $(CFLAGS) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
++ $(CC) $(LDFLAGS) -Wl,-soname,libimg.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ img.o -lm
++ ln -sf libimg.so.$(VERSION) $(SOLIB)/libimg.so
+ rm img.o
+
+ #
+@@ -1007,25 +1013,26 @@ CBF_IMG_LIBS: $(LIB)/libcbf.a $(LIB)/libimg.a
+ #
+ # FCB library
+ #
+-$(LIB)/libfcb.a: $(F90SOURCE) $(COMMONDEP) $(LIB) $(HDF5)
+-ifneq ($(F90C),)
+- $(F90C) $(F90FLAGS) -c $(F90SOURCE)
++$(LIB)/libfcb.a: $(F90SOURCE) $(COMMONDEP) $(LIB)
++ifneq ($(FC),)
++ $(FC) $(FCFLAGS) -c $(F90SOURCE)
+ $(AR) cr $@ *.o
+ ifneq ($(RANLIB),)
+ $(RANLIB) $@
+ endif
+ rm *.o
+ else
+- echo "Define F90C to build $(LIB)/libfcb.a"
++ echo "Define FC to build $(LIB)/libfcb.a"
+ endif
+
+-$(SOLIB)/libfcb.so: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+-ifneq ($(F90C),)
+- $(F90C) $(F90FLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
+- $(F90C) $(F90FLAGS) -o $@ *.o $(SOLDFLAGS)
++$(SOLIB)/libfcb.so.${VERSION}: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ifneq ($(FC),)
++ $(FC) $(FCFLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
++ $(FC) $(LDFLAGS) -Wl,-soname,libfcb.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) $(FCFLAGS) -o $@ *.o
++ ln -sf libfcb.so.$(VERSION) $(SOLIB)/libfcb.so
+ rm *.o
+ else
+- echo "Define F90C to build $(SOLIB)/libfcb.so"
++ echo "Define FC to build $(SOLIB)/libfcb.so"
+ endif
+
+
+@@ -1183,7 +1190,7 @@ $(BIN)/cbf_template_t: $(DECTRIS_EXAMPLES)/cbf_template_t.c \
+ # testcell example program
+ #
+ $(BIN)/testcell: $(LIB)/libcbf.a $(EXAMPLES)/testcell.C
+- $(C++) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
++ $(CXX) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
+ $(EXAMPLES)/testcell.C -L$(LIB) \
+ -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+
+@@ -1191,7 +1198,7 @@ $(BIN)/testcell: $(LIB)/libcbf.a $(EXAMPLES)/testcell.C
+ # cif2c example program
+ #
+ $(BIN)/cif2c: $(LIB)/libcbf.a $(EXAMPLES)/cif2c.c
+- $(C++) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
++ $(CXX) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
+ $(EXAMPLES)/cif2c.c -L$(LIB) \
+ -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+
+@@ -1199,7 +1206,7 @@ $(BIN)/cif2c: $(LIB)/libcbf.a $(EXAMPLES)/cif2c.c
+ # sauter_test example program
+ #
+ $(BIN)/sauter_test: $(LIB)/libcbf.a $(EXAMPLES)/sauter_test.C
+- $(C++) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
++ $(CXX) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
+ $(EXAMPLES)/sauter_test.C -L$(LIB) \
+ -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+
+@@ -1253,19 +1260,19 @@ $(BIN)/testflatpacked: $(LIB)/libcbf.a $(EXAMPLES)/testflatpacked.c
+ $(EXAMPLES)/testflatpacked.c -L$(LIB) \
+ -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ #
+ # test_xds_binary example program
+ #
+ $(BIN)/test_xds_binary: $(LIB)/libfcb.a $(EXAMPLES)/test_xds_binary.f90
+- $(F90C) $(F90FLAGS) $(F90LDFLAGS) $(EXAMPLES)/test_xds_binary.f90 \
++ $(FC) $(FCFLAGS) $(LDFLAGS) $(EXAMPLES)/test_xds_binary.f90 \
+ -L$(LIB) -lfcb -o $@
+
+ #
+ # test_fcb_read_image example program
+ #
+ $(BIN)/test_fcb_read_image: $(LIB)/libfcb.a $(EXAMPLES)/test_fcb_read_image.f90
+- $(F90C) $(F90FLAGS) $(F90LDFLAGS) $(EXAMPLES)/test_fcb_read_image.f90 \
++ $(FC) $(FCFLAGS) $(LDFLAGS) $(EXAMPLES)/test_fcb_read_image.f90 \
+ -L$(LIB) -lfcb -o $@
+ endif
+
+@@ -1520,7 +1527,7 @@ basic: $(BIN)/makecbf $(BIN)/img2cif $(BIN)/cif2cbf $(TESTINPUT_BASIC)
+ #
+ # Extra Tests
+ #
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ extra: $(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
+ $(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
+ $(BIN)/test_xds_binary $(BIN)/test_fcb_read_image $(BIN)/convert_minicbf \
+@@ -1582,7 +1589,7 @@ endif
+ -cmp testflatin.cbf testflatout.cbf
+ $(TIME) $(BIN)/testflatpacked
+ -cmp testflatpackedin.cbf testflatpackedout.cbf
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ echo testflatout.cbf | $(TIME) $(BIN)/test_xds_binary > test_xds_bin_testflatout.out
+ -$(DIFF) test_xds_bin_testflatout.out test_xds_bin_testflatout_orig.out
+ echo testflatpackedout.cbf | $(TIME) $(BIN)/test_xds_binary > test_xds_bin_testflatpackedout.out
+@@ -1599,7 +1606,7 @@ endif
+ $(TIME) $(BIN)/cif2cbf -I 4 -C 100. -L 0. -e n -c b -i XRD1621.cbf -o XRD1621_I4encbC100.cbf
+ -$(DIFF) XRD1621_I4encbC100.cbf XRD1621_I4encbC100_orig.cbf
+
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ extra_sigs_only: $(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
+ $(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
+ $(BIN)/test_xds_binary $(BIN)/test_fcb_read_image $(BIN)/convert_minicbf \
+@@ -1650,7 +1657,7 @@ endif
+ -cmp testflatin.cbf testflatout.cbf
+ $(TIME) $(BIN)/testflatpacked
+ -cmp testflatpackedin.cbf testflatpackedout.cbf
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ echo testflatout.cbf | $(TIME) $(BIN)/test_xds_binary | \
+ $(SIGNATURE) | $(DIFF) - test_xds_bin_testflatout_orig.out$(SEXT)
+ echo testflatpackedout.cbf | $(TIME) $(BIN)/test_xds_binary | \
diff --git a/sci-libs/cbflib/files/0.9.2.2-Makefile.patch b/sci-libs/cbflib/files/0.9.2.2-Makefile.patch
new file mode 100644
index 00000000000..a2576030727
--- /dev/null
+++ b/sci-libs/cbflib/files/0.9.2.2-Makefile.patch
@@ -0,0 +1,150 @@
+From 44e303d998c72d5d502705895a536b3657a7c4c5 Mon Sep 17 00:00:00 2001
+Message-Id: <44e303d998c72d5d502705895a536b3657a7c4c5.1323790511.git.jlec@gentoo.org>
+From: Justin Lecher <jlec@gentoo.org>
+Date: Tue, 13 Dec 2011 16:10:43 +0100
+Subject: [PATCH] 0.9.0 Makefile.patch
+
+Conflicts:
+
+ Makefile_LINUX_gcc42
+---
+ Makefile_LINUX_gcc42 | 63 ++++++++++++++++++++++++++-----------------------
+ 1 files changed, 33 insertions(+), 30 deletions(-)
+
+diff --git a/Makefile_LINUX_gcc42 b/Makefile_LINUX_gcc42
+index a74be5f..1cfb066 100644
+--- a/Makefile_LINUX_gcc42
++++ b/Makefile_LINUX_gcc42
+@@ -250,7 +250,10 @@
+
+
+ # Version string
+-VERSION = 0.9.2
++MAJOR = 0
++MINOR = 9
++MICRO = 2
++VERSION = ${MAJOR}.${MINOR}.${MICRO}
+
+
+ #
+@@ -290,7 +293,7 @@ SHAR = /usr/bin/shar
+ #
+ # Program to use to create archives
+ #
+-AR = /usr/bin/ar
++AR = ar
+
+ #
+ # Program to use to add an index to an archive
+@@ -300,13 +303,13 @@ RANLIB = /usr/bin/ranlib
+ #
+ # Program to use to decompress a data file
+ #
+-DECOMPRESS = /usr/bin/bunzip2
++DECOMPRESS = bunzip2
+
+
+ #
+ # Program to use to compress a data file
+ #
+-COMPRESS = /usr/bin/bzip2
++COMPRESS = bzip2
+
+ #
+ # Program to use to generate a signature
+@@ -509,21 +512,18 @@ SOURCE = $(SRC)/cbf.c \
+
+
+ F90SOURCE = $(SRC)/fcb_atol_wcnt.f90 \
+- $(SRC)/fcb_ci_strncmparr.f90 \
+- $(SRC)/fcb_exit_binary.f90 \
+- $(SRC)/fcb_nblen_array.f90 \
+- $(SRC)/fcb_next_binary.f90 \
+- $(SRC)/fcb_open_cifin.f90 \
+- $(SRC)/fcb_packed.f90 \
+- $(SRC)/fcb_read_bits.f90 \
+- $(SRC)/fcb_read_byte.f90 \
+- $(SRC)/fcb_read_image.f90 \
+- $(SRC)/fcb_read_line.f90 \
+- $(SRC)/fcb_read_xds_i2.f90 \
+- $(SRC)/fcb_skip_whitespace.f90 \
+- $(EXAMPLES)/test_fcb_read_image.f90 \
+- $(EXAMPLES)/test_xds_binary.f90
+-
++ $(SRC)/fcb_ci_strncmparr.f90 \
++ $(SRC)/fcb_exit_binary.f90 \
++ $(SRC)/fcb_nblen_array.f90 \
++ $(SRC)/fcb_next_binary.f90 \
++ $(SRC)/fcb_open_cifin.f90 \
++ $(SRC)/fcb_packed.f90 \
++ $(SRC)/fcb_read_bits.f90 \
++ $(SRC)/fcb_read_byte.f90 \
++ $(SRC)/fcb_read_image.f90 \
++ $(SRC)/fcb_read_line.f90 \
++ $(SRC)/fcb_read_xds_i2.f90 \
++ $(SRC)/fcb_skip_whitespace.f90
+
+ #
+ # Header files
+@@ -701,7 +701,7 @@ all:: $(BIN)/test_xds_binary \
+ $(BIN)/test_fcb_read_image
+ endif
+
+-shared: $(SOLIB)/libcbf.so $(SOLIB)/libfcb.so $(SOLIB)/libimg.so
++shared: $(SOLIB)/libcbf.so.${VERSION} $(SOLIB)/libfcb.so.${VERSION} $(SOLIB)/libimg.so.${VERSION}
+
+ javawrapper: shared $(JCBF) $(JCBF)/cbflib-$(VERSION).jar $(SOLIB)/libcbf_wrap.so
+
+@@ -915,25 +915,27 @@ ifneq ($(RANLIB),)
+ $(RANLIB) $@
+ endif
+
+-$(SOLIB)/libcbf.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(PYCIFRWFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+- $(CC) -o $@ *.o $(SOLDFLAGS) $(EXTRALIBS)
+- rm *.o
++$(SOLIB)/libcbf.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ $(CC) $(CFLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
++ mv *.o $(SOLIB)
++ $(CC) $(LDFLAGS) -Wl,-soname,libcbf.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ $(SOLIB)/*.o $(EXTRALIBS)
++ ln -sf libcbf.so.$(VERSION) $(SOLIB)/libcbf.so
+
+ #
+ # IMG library
+ #
+ $(LIB)/libimg.a: $(EXAMPLES)/img.c $(HEADERS) $(COMMONDEP) $(LIB)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
++ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
+ $(AR) cr $@ img.o
+ ifneq ($(RANLIB),)
+ $(RANLIB) $@
+ endif
+ rm img.o
+
+-$(SOLIB)/libimg.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
+- $(CC) -o $@ img.o $(SOLDFLAGS)
++$(SOLIB)/libimg.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ $(CC) $(CFLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
++ $(CC) $(LDFLAGS) -Wl,-soname,libimg.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ img.o
++ ln -sf libimg.so.$(VERSION) $(SOLIB)/libimg.so
+ rm img.o
+
+ #
+@@ -957,10 +959,11 @@ else
+ echo "Define F90C to build $(LIB)/libfcb.a"
+ endif
+
+-$(SOLIB)/libfcb.so: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++$(SOLIB)/libfcb.so.${VERSION}: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+ ifneq ($(F90C),)
+ $(F90C) $(F90FLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
+- $(F90C) $(F90FLAGS) -o $@ *.o $(SOLDFLAGS)
++ $(F90C) $(LDFLAGS) -Wl,-soname,libfcb.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) $(F90FLAGS) -o $@ *.o
++ ln -sf libfcb.so.$(VERSION) $(SOLIB)/libfcb.so
+ rm *.o
+ else
+ echo "Define F90C to build $(SOLIB)/libfcb.so"
+--
+1.7.8
+
diff --git a/sci-libs/cbflib/files/0.9.2.3-Makefile.patch b/sci-libs/cbflib/files/0.9.2.3-Makefile.patch
new file mode 100644
index 00000000000..b7c50422521
--- /dev/null
+++ b/sci-libs/cbflib/files/0.9.2.3-Makefile.patch
@@ -0,0 +1,150 @@
+From 44e303d998c72d5d502705895a536b3657a7c4c5 Mon Sep 17 00:00:00 2001
+Message-Id: <44e303d998c72d5d502705895a536b3657a7c4c5.1323790511.git.jlec@gentoo.org>
+From: Justin Lecher <jlec@gentoo.org>
+Date: Tue, 13 Dec 2011 16:10:43 +0100
+Subject: [PATCH] 0.9.0 Makefile.patch
+
+Conflicts:
+
+ Makefile_LINUX_gcc42
+---
+ Makefile_LINUX_gcc42 | 63 ++++++++++++++++++++++++++-----------------------
+ 1 files changed, 33 insertions(+), 30 deletions(-)
+
+diff --git a/Makefile_LINUX_gcc42 b/Makefile_LINUX_gcc42
+index a74be5f..1cfb066 100644
+--- a/Makefile_LINUX_gcc42
++++ b/Makefile_LINUX_gcc42
+@@ -250,7 +250,10 @@
+
+
+ # Version string
+-VERSION = 0.9.2
++MAJOR = 0
++MINOR = 9
++MICRO = 3
++VERSION = ${MAJOR}.${MINOR}.${MICRO}
+
+
+ #
+@@ -290,7 +293,7 @@ SHAR = /usr/bin/shar
+ #
+ # Program to use to create archives
+ #
+-AR = /usr/bin/ar
++AR = ar
+
+ #
+ # Program to use to add an index to an archive
+@@ -300,13 +303,13 @@ RANLIB = /usr/bin/ranlib
+ #
+ # Program to use to decompress a data file
+ #
+-DECOMPRESS = /usr/bin/bunzip2
++DECOMPRESS = bunzip2
+
+
+ #
+ # Program to use to compress a data file
+ #
+-COMPRESS = /usr/bin/bzip2
++COMPRESS = bzip2
+
+ #
+ # Program to use to generate a signature
+@@ -509,21 +512,18 @@ SOURCE = $(SRC)/cbf.c \
+
+
+ F90SOURCE = $(SRC)/fcb_atol_wcnt.f90 \
+- $(SRC)/fcb_ci_strncmparr.f90 \
+- $(SRC)/fcb_exit_binary.f90 \
+- $(SRC)/fcb_nblen_array.f90 \
+- $(SRC)/fcb_next_binary.f90 \
+- $(SRC)/fcb_open_cifin.f90 \
+- $(SRC)/fcb_packed.f90 \
+- $(SRC)/fcb_read_bits.f90 \
+- $(SRC)/fcb_read_byte.f90 \
+- $(SRC)/fcb_read_image.f90 \
+- $(SRC)/fcb_read_line.f90 \
+- $(SRC)/fcb_read_xds_i2.f90 \
+- $(SRC)/fcb_skip_whitespace.f90 \
+- $(EXAMPLES)/test_fcb_read_image.f90 \
+- $(EXAMPLES)/test_xds_binary.f90
+-
++ $(SRC)/fcb_ci_strncmparr.f90 \
++ $(SRC)/fcb_exit_binary.f90 \
++ $(SRC)/fcb_nblen_array.f90 \
++ $(SRC)/fcb_next_binary.f90 \
++ $(SRC)/fcb_open_cifin.f90 \
++ $(SRC)/fcb_packed.f90 \
++ $(SRC)/fcb_read_bits.f90 \
++ $(SRC)/fcb_read_byte.f90 \
++ $(SRC)/fcb_read_image.f90 \
++ $(SRC)/fcb_read_line.f90 \
++ $(SRC)/fcb_read_xds_i2.f90 \
++ $(SRC)/fcb_skip_whitespace.f90
+
+ #
+ # Header files
+@@ -701,7 +701,7 @@ all:: $(BIN)/test_xds_binary \
+ $(BIN)/test_fcb_read_image
+ endif
+
+-shared: $(SOLIB)/libcbf.so $(SOLIB)/libfcb.so $(SOLIB)/libimg.so
++shared: $(SOLIB)/libcbf.so.${VERSION} $(SOLIB)/libfcb.so.${VERSION} $(SOLIB)/libimg.so.${VERSION}
+
+ javawrapper: shared $(JCBF) $(JCBF)/cbflib-$(VERSION).jar $(SOLIB)/libcbf_wrap.so
+
+@@ -915,25 +915,27 @@ ifneq ($(RANLIB),)
+ $(RANLIB) $@
+ endif
+
+-$(SOLIB)/libcbf.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(PYCIFRWFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+- $(CC) -o $@ *.o $(SOLDFLAGS) $(EXTRALIBS)
+- rm *.o
++$(SOLIB)/libcbf.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ $(CC) $(CFLAGS) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
++ mv *.o $(SOLIB)
++ $(CC) $(LDFLAGS) -Wl,-soname,libcbf.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ $(SOLIB)/*.o $(EXTRALIBS)
++ ln -sf libcbf.so.$(VERSION) $(SOLIB)/libcbf.so
+
+ #
+ # IMG library
+ #
+ $(LIB)/libimg.a: $(EXAMPLES)/img.c $(HEADERS) $(COMMONDEP) $(LIB)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
++ $(CC) $(CFLAGS) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
+ $(AR) cr $@ img.o
+ ifneq ($(RANLIB),)
+ $(RANLIB) $@
+ endif
+ rm img.o
+
+-$(SOLIB)/libimg.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+- $(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
+- $(CC) -o $@ img.o $(SOLDFLAGS)
++$(SOLIB)/libimg.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ $(CC) $(CFLAGS) $(SOCFLAGS) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
++ $(CC) $(LDFLAGS) -Wl,-soname,libimg.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ img.o -lm
++ ln -sf libimg.so.$(VERSION) $(SOLIB)/libimg.so
+ rm img.o
+
+ #
+@@ -957,10 +959,11 @@ else
+ echo "Define F90C to build $(LIB)/libfcb.a"
+ endif
+
+-$(SOLIB)/libfcb.so: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++$(SOLIB)/libfcb.so.${VERSION}: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+ ifneq ($(F90C),)
+ $(F90C) $(F90FLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
+- $(F90C) $(F90FLAGS) -o $@ *.o $(SOLDFLAGS)
++ $(F90C) $(LDFLAGS) -Wl,-soname,libfcb.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) $(F90FLAGS) -o $@ *.o
++ ln -sf libfcb.so.$(VERSION) $(SOLIB)/libfcb.so
+ rm *.o
+ else
+ echo "Define F90C to build $(SOLIB)/libfcb.so"
+--
+1.7.8
+
diff --git a/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch b/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch
new file mode 100644
index 00000000000..ef24c4b94b2
--- /dev/null
+++ b/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch
@@ -0,0 +1,181 @@
+ CMakeLists.txt | 118 +++------------------------------------------------------
+ 1 file changed, 6 insertions(+), 112 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 75054d6..15bab99 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -279,7 +279,7 @@ project (CBFlib C CXX Fortran)
+ enable_testing()
+ set (CBF_CMAKE_DEBUG "ON")
+
+-set(CMAKE_C_FLAGS "-Wall -fno-strict-aliasing")
++set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -fno-strict-aliasing")
+
+ #
+ # User setable parameters
+@@ -530,42 +530,6 @@ find_package(ZLIB)
+
+
+
+-#Load external packages in build directory at cmake time
+-add_subdirectory(${CBF__EXTERNAL_PACKAGES} "${CBF__EXT_PKG}")
+-
+-find_file(CBF_EXT_PKG_BLD_RUNNING cbf_ext_pkg_build_running "${CBF__EXT_PKG}")
+-if (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND")
+- file(WRITE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running" "cbf_ext_pkg_build_running")
+- CBF_DEBUG_MESSAGE("CMAKE_COMMAND: ${CMAKE_COMMAND}")
+- CBF_DEBUG_MESSAGE("CBFlib_SOURCE_DIR: ${CBFlib_SOURCE_DIR} ")
+- execute_process(
+- COMMAND ${CMAKE_COMMAND} ${CBFlib_SOURCE_DIR}
+- RESULT_VARIABLE CBF_BUILD_RESULT)
+- CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
+- execute_process(
+- COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target HDF5
+- RESULT_VARIABLE CBF_BUILD_RESULT)
+- CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
+- execute_process(
+- COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target TIFF
+- RESULT_VARIABLE CBF_BUILD_RESULT)
+- CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
+- file(REMOVE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running")
+-endif (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND")
+-
+-
+-file(GLOB CBF_HDF5_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*hdf5*")
+-CBF_DEBUG_MESSAGE( "CBF_HDF5_LIBRARY_PATH: ${CBF_HDF5_LIBRARY_PATH}")
+-file(GLOB CBF_TIFF_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*tif*")
+-CBF_DEBUG_MESSAGE( "CBF_TIFF_LIBRARY_PATH: ${CBF_TIFF_LIBRARY_PATH}")
+-
+-if ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||")
+- MESSAGE(STATUS "Must build external packages in ${CBF__EXT_PKG}")
+- MESSAGE(STATUS "Then rerun cmake")
+- MESSAGE(WARNING "Finishing run to make Makefiles")
+-endif ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||")
+-
+-
+ #
+ # Data Directories
+ #
+@@ -579,35 +543,6 @@ set(CBF_DATAURLBASE "http://downloads.sf.net/cbflib")
+ set(CBF_DATAURLI "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Input.tar.gz")
+ set(CBF_DATAURLO "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output.tar.gz")
+ set(CBF_DATAURLS "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output_Sigs_Only.tar.gz")
+-#
+-# Load and unpack the Data Files
+-#
+-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRI} ${CBF_DATAURLI})
+-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRO} ${CBF_DATAURLO})
+-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRS} ${CBF_DATAURLS})
+-#
+-# Verify the checksums
+-#
+-file(GLOB CBF_DATADIRI_FILES "${CBF_DATADIRI}/*")
+-file(GLOB CBF_DATADIRO_FILES "${CBF_DATADIRO}/*")
+-foreach(loop_file ${CBF_DATADIRI_FILES} )
+- if (NOT "${loop_file}" MATCHES "[*.]md5")
+- file(MD5 "${loop_file}" loop_file_md5)
+- file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1)
+- if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+- message(WARNINH "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|")
+- endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+- endif (NOT "${loop_file}" MATCHES "[*.]md5")
+-endforeach(loop_file)
+-foreach(loop_file ${CBF_DATADIRO_FILES} )
+- if (NOT "${loop_file}" MATCHES "[*.]md5")
+- file(MD5 "${loop_file}" loop_file_md5)
+- file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1)
+- if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+- message(WARNING "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|")
+- endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+- endif (NOT "${loop_file}" MATCHES "[*.]md5")
+-endforeach(loop_file)
+
+
+ #
+@@ -775,7 +710,7 @@ add_library(cbf_shared SHARED ${CBF_C_SOURCES})
+ set_target_properties(cbf_shared PROPERTIES OUTPUT_NAME "cbf")
+ set_target_properties(cbf_shared PROPERTIES LINKER_LANGUAGE C)
+ set_target_properties(cbf_shared PROPERTIES SOVERSION "${CBF_APIVERSION}")
+-target_link_libraries(cbf_shared ${CBF_HDF5_LIBRARY_PATH})
++target_link_libraries(cbf_shared hdf5)
+
+ #
+ # Build the static and shared IMG libraries
+@@ -791,7 +726,7 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CBFlib_BINARY_DIR}/solib")
+ add_library(img_shared SHARED ${CBF__EXAMPLES}/img.c)
+ set_target_properties(img_shared PROPERTIES OUTPUT_NAME "img")
+ set_target_properties(img_shared PROPERTIES LINKER_LANGUAGE C)
+-target_link_libraries(img_shared ${CBF_HDF5_LIBRARY_PATH})
++target_link_libraries(img_shared hdf5 m )
+
+
+ #
+@@ -829,26 +764,6 @@ target_link_libraries(fcb_shared ${CBF_HDF5_LIBRARY_PATH})
+ #
+ # C and C++ examples
+ #
+-CBF_ADD_C_EXAMPLE(convert_image "${CBF__EXAMPLES}" "" "img_static")
+-CBF_ADD_C_EXAMPLE(convert_minicbf "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(makecbf "${CBF__EXAMPLES}" "" "img_static")
+-CBF_ADD_C_EXAMPLE(adscimg2cbf "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/adscimg2cbf_sub.c" "")
+-CBF_ADD_C_EXAMPLE(cbf2adscimg "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/cbf2adscimg_sub.c" "")
+-CBF_ADD_C_EXAMPLE(cbf_tail "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(changtestcompression "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(img2cif "${CBF__EXAMPLES}" "" "img_static")
+-CBF_ADD_C_EXAMPLE(cif2cbf "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(cbf2nexus "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(minicbf2nexus "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(cbf_template_t "${CBF__DECTRIS_EXAMPLES}" "" "")
+-CBF_ADD_CXX_EXAMPLE(testcell "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_CXX_EXAMPLE(sauter_test "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(sequence_match "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(tiff2cbf "${CBF__EXAMPLES}" "${CBF__EXT_PKG}/${CBF_TIFF}/libtiff/tif_sprint.c" "${CBF_TIFF_LIBRARY_PATH}")
+-CBF_ADD_C_EXAMPLE(testulp "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(testhdf5 "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(testtree "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(testalloc "${CBF__EXAMPLES}" "" "")
+
+
+
+@@ -876,26 +791,9 @@ target_link_libraries(test_xds_binary fcb_static)
+ #
+ # install
+ #
+-install (TARGETS makecbf DESTINATION bin)
+-install (TARGETS img2cif DESTINATION bin)
+-install (TARGETS cif2cbf DESTINATION bin)
+-install (TARGETS adscimg2cbf DESTINATION bin)
+-install (TARGETS cbf2adscimg DESTINATION bin)
+-install (TARGETS changtestcompression DESTINATION bin)
+-install (TARGETS convert_image DESTINATION bin)
+-install (TARGETS convert_minicbf DESTINATION bin)
+-install (TARGETS minicbf2nexus DESTINATION bin)
+-install (TARGETS cbf_template_t DESTINATION bin)
+-install (TARGETS testcell DESTINATION bin)
+-install (TARGETS sauter_test DESTINATION bin)
+-install (TARGETS sequence_match DESTINATION bin)
+-install (TARGETS tiff2cbf DESTINATION bin)
+-install (TARGETS cbf_static DESTINATION lib)
+-install (TARGETS cbf_shared DESTINATION lib)
+-install (TARGETS fcb_static DESTINATION lib)
+-install (TARGETS fcb_shared DESTINATION lib)
+-install (TARGETS img_static DESTINATION lib)
+-install (TARGETS img_shared DESTINATION lib)
++install (TARGETS cbf_shared DESTINATION lib${LIB_SUFFIX})
++install (TARGETS fcb_shared DESTINATION lib${LIB_SUFFIX})
++install (TARGETS img_shared DESTINATION lib${LIB_SUFFIX})
+ install (DIRECTORY ${CBF__INCLUDE}/ DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h")
+ install (DIRECTORY ${CBF__BIN_INCLUDE}/* DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h")
+
+@@ -914,10 +812,6 @@ endif ()
+ #
+ # tests -- to be extended
+ #
+-add_test(NAME cbftest_makecbf
+- COMMAND ${CMAKE_COMMAND}
+- -DCMD1=$<TARGET_FILE:makecbf> -DARG11=${CBF_DATADIRI}/example.mar2300 -DARG12=makecbf.cbf
+- -P ${CMAKE_CURRENT_SOURCE_DIR}/runcommands.cmake)
+ add_test(cbftest_testalloc ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testalloc)
+ add_test(cbftest_testhdf5 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testhdf5)
+ add_test(cbftest_testtree ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testtree)
diff --git a/sci-libs/cbflib/metadata.xml b/sci-libs/cbflib/metadata.xml
new file mode 100644
index 00000000000..7371ec6ccff
--- /dev/null
+++ b/sci-libs/cbflib/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription>
+CBFLIB is a library of ANSI-C functions providing a simple mechanism
+for accessing Crystallographic Binary Files (CBF files) and Image-supporting
+CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for
+mmCIF files. Starting with this release, CBFLIB performs validation checks
+on reading of a CBF. If a dictionary is provided, values will be validated
+against dictionary ranges and enumerations. Tags missing under parent-child
+relationships or category key requirements will be reported. CBFlib provides
+functions to create, read, modify and write CBF binary data files and imgCIF
+ASCII data files.
+</longdescription>
+ <upstream>
+ <remote-id type="sourceforge">cbflib</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/cblas-reference/Manifest b/sci-libs/cblas-reference/Manifest
new file mode 100644
index 00000000000..1e8316091c8
--- /dev/null
+++ b/sci-libs/cblas-reference/Manifest
@@ -0,0 +1 @@
+DIST cblas.tgz 197694 SHA256 9b49d7177fda62b6141bf2ca29e475e86f0b12d8f72e0b944058d02b439dd52a SHA512 8edc4f939d36e6bb9bcbc4ffe414b6c991192ef2e76ec4eda16d3578591185d31e46be5e747d74c740411db6bd2c2d414a18f73193d4a288e8c7e4b83cb0895d WHIRLPOOL e3f9f2b6a58f000ac2dc02326cd5a41f8a5cc1437035e710c49eb2ff8b366906c099285c982394e69082d861be16cacd8bef2c3191d84dcace120b5d73623915
diff --git a/sci-libs/cblas-reference/cblas-reference-20030223-r4.ebuild b/sci-libs/cblas-reference/cblas-reference-20030223-r4.ebuild
new file mode 100644
index 00000000000..72164d89c97
--- /dev/null
+++ b/sci-libs/cblas-reference/cblas-reference-20030223-r4.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit autotools eutils fortran-2 multilib toolchain-funcs
+
+MyPN="${PN/-reference/}"
+
+DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation"
+HOMEPAGE="http://www.netlib.org/blas/"
+SRC_URI="http://www.netlib.org/blas/blast-forum/${MyPN}.tgz"
+
+SLOT="0"
+LICENSE="public-domain"
+IUSE=""
+KEYWORDS="alpha amd64 hppa ppc ppc64 s390 sparc x86 ~x86-fbsd"
+
+RDEPEND="
+ virtual/blas
+ app-eselect/eselect-cblas"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+ESELECT_PROF=reference
+S="${WORKDIR}/CBLAS"
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-autotool.patch
+ eautoreconf
+}
+
+src_compile() {
+ econf \
+ --libdir=/usr/$(get_libdir)/blas/reference \
+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+ emake || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc README || die "failed to install docs"
+ insinto /usr/share/doc/${PF}
+ doins cblas_example*c || die "install examples failed"
+ eselect cblas add $(get_libdir) "${FILESDIR}"/eselect.cblas.reference ${ESELECT_PROF}
+}
+
+pkg_postinst() {
+ local p=cblas
+ local current_lib=$(eselect ${p} show | cut -d' ' -f2)
+ if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then
+ # work around eselect bug #189942
+ local configfile="${ROOT}"/etc/env.d/${p}/$(get_libdir)/config
+ [[ -e ${configfile} ]] && rm -f ${configfile}
+ eselect ${p} set ${ESELECT_PROF}
+ elog "${p} has been eselected to ${ESELECT_PROF}"
+ else
+ elog "Current eselected ${p} is ${current_lib}"
+ elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):"
+ elog "\t eselect ${p} set ${ESELECT_PROF}"
+ fi
+}
diff --git a/sci-libs/cblas-reference/cblas-reference-20030223-r5.ebuild b/sci-libs/cblas-reference/cblas-reference-20030223-r5.ebuild
new file mode 100644
index 00000000000..6d0264b4438
--- /dev/null
+++ b/sci-libs/cblas-reference/cblas-reference-20030223-r5.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit autotools eutils fortran-2 multilib toolchain-funcs
+
+MyPN="${PN/-reference/}"
+
+DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation"
+HOMEPAGE="http://www.netlib.org/blas/"
+SRC_URI="http://www.netlib.org/blas/blast-forum/${MyPN}.tgz"
+
+SLOT="0"
+LICENSE="public-domain"
+IUSE=""
+KEYWORDS="~alpha ~amd64 ~hppa ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+ virtual/blas
+ app-eselect/eselect-cblas"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+ESELECT_PROF=reference
+S="${WORKDIR}/CBLAS"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-autotool.patch
+ eautoreconf
+
+ cp "${FILESDIR}"/eselect.cblas.reference "${T}"/
+ sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.reference || die
+ if [[ ${CHOST} == *-darwin* ]] ; then
+ sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \
+ "${T}"/eselect.cblas.reference || die
+ fi
+}
+
+src_configure() {
+ econf \
+ --libdir="${EPREFIX}"/usr/$(get_libdir)/blas/reference \
+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+ dodoc README || die "failed to install docs"
+ insinto /usr/share/doc/${PF}
+ doins cblas_example*c || die "install examples failed"
+ eselect cblas add $(get_libdir) "${T}"/eselect.cblas.reference ${ESELECT_PROF}
+}
+
+pkg_postinst() {
+ local p=cblas
+ local current_lib=$(eselect ${p} show | cut -d' ' -f2)
+ if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then
+ # work around eselect bug #189942
+ local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config
+ [[ -e ${configfile} ]] && rm -f ${configfile}
+ eselect ${p} set ${ESELECT_PROF}
+ elog "${p} has been eselected to ${ESELECT_PROF}"
+ else
+ elog "Current eselected ${p} is ${current_lib}"
+ elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):"
+ elog "\t eselect ${p} set ${ESELECT_PROF}"
+ fi
+}
diff --git a/sci-libs/cblas-reference/files/cblas-reference-20030223-autotool.patch b/sci-libs/cblas-reference/files/cblas-reference-20030223-autotool.patch
new file mode 100644
index 00000000000..0dd595bf4a2
--- /dev/null
+++ b/sci-libs/cblas-reference/files/cblas-reference-20030223-autotool.patch
@@ -0,0 +1,567 @@
+--- configure.ac 1970-01-01 01:00:00.000000000 +0100
++++ configure.ac 2007-11-09 17:59:16.000000000 +0000
+@@ -0,0 +1,24 @@
++AC_PREREQ(2.59)
++AC_INIT(cblas, 20030223, lapack@cs.utk.edu)
++AC_CONFIG_SRCDIR([cblas_example2.c])
++AC_CONFIG_HEADER([config.h])
++AM_INIT_AUTOMAKE([foreign])
++
++AC_LANG(C)
++AC_PROG_CC
++AC_PROG_F77
++AC_F77_LIBRARY_LDFLAGS
++AC_PROG_LIBTOOL
++
++sinclude(acx_blas.m4)
++ACX_BLAS
++if test x"$BLAS_LIBS" = x; then
++ AC_MSG_ERROR([Cannot find blas libraries])
++fi
++
++
++AC_CONFIG_FILES([Makefile
++ src/Makefile
++ testing/Makefile
++ cblas.pc])
++AC_OUTPUT
+--- Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ Makefile.am 2007-11-09 16:20:41.000000000 +0000
+@@ -0,0 +1,8 @@
++SUBDIRS = src testing
++
++pkgconfigdir = $(libdir)
++pkgconfig_DATA = cblas.pc
++
++EXTRA = cblas.pc
++
++
+--- cblas.pc.in 1970-01-01 01:00:00.000000000 +0100
++++ cblas.pc.in 2007-11-09 16:20:41.000000000 +0000
+@@ -0,0 +1,13 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: @PACKAGE_NAME@
++Description: Basic Linear Algebra Subprograms C reference wrapper
++Version: @PACKAGE_VERSION@
++Requires: blas
++URL: http://www.netlib.org/blas/
++Libs: -lcblas
++Libs.private: @FLIBS@
++Cflags: -I${includedir}
+--- acx_blas.m4 1970-01-01 01:00:00.000000000 +0100
++++ acx_blas.m4 2007-08-04 22:50:48.000000000 +0100
+@@ -0,0 +1,191 @@
++##### http://autoconf-archive.cryp.to/acx_blas.html
++#
++# SYNOPSIS
++#
++# ACX_BLAS([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
++#
++# DESCRIPTION
++#
++# This macro looks for a library that implements the BLAS
++# linear-algebra interface (see http://www.netlib.org/blas/). On
++# success, it sets the BLAS_LIBS output variable to hold the
++# requisite library linkages.
++#
++# To link with BLAS, you should link with:
++#
++# $BLAS_LIBS $LIBS $FLIBS
++#
++# in that order. FLIBS is the output variable of the
++# AC_F77_LIBRARY_LDFLAGS macro (called if necessary by ACX_BLAS), and
++# is sometimes necessary in order to link with F77 libraries. Users
++# will also need to use AC_F77_DUMMY_MAIN (see the autoconf manual),
++# for the same reason.
++#
++# Many libraries are searched for, from ATLAS to CXML to ESSL. The
++# user may also use --with-blas=<lib> in order to use some specific
++# BLAS library <lib>. In order to link successfully, however, be
++# aware that you will probably need to use the same Fortran compiler
++# (which can be set via the F77 env. var.) as was used to compile the
++# BLAS library.
++#
++# ACTION-IF-FOUND is a list of shell commands to run if a BLAS
++# library is found, and ACTION-IF-NOT-FOUND is a list of commands to
++# run it if it is not found. If ACTION-IF-FOUND is not specified, the
++# default action will define HAVE_BLAS.
++#
++# This macro requires autoconf 2.50 or later.
++#
++# LAST MODIFICATION
++#
++# 2007-07-29
++#
++# COPYLEFT
++#
++# Copyright (c) 2007 Steven G. Johnson <stevenj@alum.mit.edu>
++#
++# This program is free software: you can redistribute it and/or
++# modify it under the terms of the GNU General Public License as
++# published by the Free Software Foundation, either version 3 of the
++# License, or (at your option) any later version.
++#
++# This program is distributed in the hope that it will be useful, but
++# WITHOUT ANY WARRANTY; without even the implied warranty of
++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
++# General Public License for more details.
++#
++# You should have received a copy of the GNU General Public License
++# along with this program. If not, see
++# <http://www.gnu.org/licenses/>.
++#
++# As a special exception, the respective Autoconf Macro's copyright
++# owner gives unlimited permission to copy, distribute and modify the
++# configure scripts that are the output of Autoconf when processing
++# the Macro. You need not follow the terms of the GNU General Public
++# License when using or distributing such scripts, even though
++# portions of the text of the Macro appear in them. The GNU General
++# Public License (GPL) does govern all other use of the material that
++# constitutes the Autoconf Macro.
++#
++# This special exception to the GPL applies to versions of the
++# Autoconf Macro released by the Autoconf Macro Archive. When you
++# make and distribute a modified version of the Autoconf Macro, you
++# may extend this special exception to the GPL to apply to your
++# modified version as well.
++
++AC_DEFUN([ACX_BLAS], [
++AC_PREREQ(2.50)
++AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS])
++acx_blas_ok=no
++
++AC_ARG_WITH(blas,
++ [AC_HELP_STRING([--with-blas=<lib>], [use BLAS library <lib>])])
++case $with_blas in
++ yes | "") ;;
++ no) acx_blas_ok=disable ;;
++ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;;
++ *) BLAS_LIBS="-l$with_blas" ;;
++esac
++
++# Get fortran linker names of BLAS functions to check for.
++AC_F77_FUNC(sgemm)
++AC_F77_FUNC(dgemm)
++
++acx_blas_save_LIBS="$LIBS"
++LIBS="$LIBS $FLIBS"
++
++# First, check BLAS_LIBS environment variable
++if test $acx_blas_ok = no; then
++if test "x$BLAS_LIBS" != x; then
++ save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS"
++ AC_MSG_CHECKING([for $sgemm in $BLAS_LIBS])
++ AC_TRY_LINK_FUNC($sgemm, [acx_blas_ok=yes], [BLAS_LIBS=""])
++ AC_MSG_RESULT($acx_blas_ok)
++ LIBS="$save_LIBS"
++fi
++fi
++
++# BLAS linked to by default? (happens on some supercomputers)
++if test $acx_blas_ok = no; then
++ save_LIBS="$LIBS"; LIBS="$LIBS"
++ AC_CHECK_FUNC($sgemm, [acx_blas_ok=yes])
++ LIBS="$save_LIBS"
++fi
++
++# BLAS in ATLAS library? (http://math-atlas.sourceforge.net/)
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(atlas, ATL_xerbla,
++ [AC_CHECK_LIB(f77blas, $sgemm,
++ [AC_CHECK_LIB(cblas, cblas_dgemm,
++ [acx_blas_ok=yes
++ BLAS_LIBS="-lcblas -lf77blas -latlas"],
++ [], [-lf77blas -latlas])],
++ [], [-latlas])])
++fi
++
++# BLAS in PhiPACK libraries? (requires generic BLAS lib, too)
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(blas, $sgemm,
++ [AC_CHECK_LIB(dgemm, $dgemm,
++ [AC_CHECK_LIB(sgemm, $sgemm,
++ [acx_blas_ok=yes; BLAS_LIBS="-lsgemm -ldgemm -lblas"],
++ [], [-lblas])],
++ [], [-lblas])])
++fi
++
++# BLAS in Alpha CXML library?
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(cxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-lcxml"])
++fi
++
++# BLAS in Alpha DXML library? (now called CXML, see above)
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(dxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-ldxml"])
++fi
++
++# BLAS in Sun Performance library?
++if test $acx_blas_ok = no; then
++ if test "x$GCC" != xyes; then # only works with Sun CC
++ AC_CHECK_LIB(sunmath, acosp,
++ [AC_CHECK_LIB(sunperf, $sgemm,
++ [BLAS_LIBS="-xlic_lib=sunperf -lsunmath"
++ acx_blas_ok=yes],[],[-lsunmath])])
++ fi
++fi
++
++# BLAS in SCSL library? (SGI/Cray Scientific Library)
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(scs, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lscs"])
++fi
++
++# BLAS in SGIMATH library?
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(complib.sgimath, $sgemm,
++ [acx_blas_ok=yes; BLAS_LIBS="-lcomplib.sgimath"])
++fi
++
++# BLAS in IBM ESSL library? (requires generic BLAS lib, too)
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(blas, $sgemm,
++ [AC_CHECK_LIB(essl, $sgemm,
++ [acx_blas_ok=yes; BLAS_LIBS="-lessl -lblas"],
++ [], [-lblas $FLIBS])])
++fi
++
++# Generic BLAS library?
++if test $acx_blas_ok = no; then
++ AC_CHECK_LIB(blas, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lblas"])
++fi
++
++AC_SUBST(BLAS_LIBS)
++
++LIBS="$acx_blas_save_LIBS"
++
++# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
++if test x"$acx_blas_ok" = xyes; then
++ ifelse([$1],,AC_DEFINE(HAVE_BLAS,1,[Define if you have a BLAS library.]),[$1])
++ :
++else
++ acx_blas_ok=no
++ $2
++fi
++])dnl ACX_BLAS
+--- src/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ src/Makefile.am 2007-11-09 16:20:41.000000000 +0000
+@@ -0,0 +1,232 @@
++lib_LTLIBRARIES = libcblas.la
++
++pkgincludedir = $(includedir)/cblas
++pkginclude_HEADERS = cblas.h
++
++AM_CPPFLAGS = -DADD_
++
++ERRHAND_SOURCES = \
++ cblas_globals.c \
++ cblas_xerbla.c \
++ xerbla.c
++
++SINGLE_SOURCES = \
++ cblas_scasum.c \
++ cblas_scnrm2.c \
++ scasumsub.f \
++ scnrm2sub.f
++
++SLEV_SOURCES = \
++ isamaxsub.f \
++ sdotsub.f \
++ sdsdotsub.f \
++ snrm2sub.f \
++ sasumsub.f
++
++SLEV1_SOURCES = \
++ cblas_srotg.c \
++ cblas_srotmg.c \
++ cblas_srot.c \
++ cblas_srotm.c \
++ cblas_sswap.c \
++ cblas_sscal.c \
++ cblas_scopy.c \
++ cblas_saxpy.c \
++ cblas_sdot.c \
++ cblas_sdsdot.c \
++ cblas_snrm2.c \
++ cblas_sasum.c \
++ cblas_isamax.c
++
++SLEV2_SOURCES = \
++ cblas_sgemv.c \
++ cblas_sgbmv.c \
++ cblas_sger.c \
++ cblas_ssbmv.c \
++ cblas_sspmv.c \
++ cblas_sspr.c \
++ cblas_sspr2.c \
++ cblas_ssymv.c \
++ cblas_ssyr.c \
++ cblas_ssyr2.c \
++ cblas_stbmv.c \
++ cblas_stbsv.c \
++ cblas_stpmv.c \
++ cblas_stpsv.c \
++ cblas_strmv.c \
++ cblas_strsv.c
++
++SLEV3_SOURCES = \
++ cblas_sgemm.c \
++ cblas_ssymm.c \
++ cblas_ssyrk.c \
++ cblas_ssyr2k.c \
++ cblas_strmm.c \
++ cblas_strsm.c
++
++DLEV_SOURCES = \
++ ddotsub.f \
++ dsdotsub.f \
++ dnrm2sub.f \
++ dasumsub.f \
++ idamaxsub.f
++
++DLEV1_SOURCES = \
++ cblas_drotg.c \
++ cblas_drotmg.c \
++ cblas_drot.c \
++ cblas_drotm.c \
++ cblas_dswap.c \
++ cblas_dscal.c \
++ cblas_dcopy.c \
++ cblas_daxpy.c \
++ cblas_ddot.c \
++ cblas_dsdot.c \
++ cblas_dnrm2.c \
++ cblas_dasum.c \
++ cblas_idamax.c
++
++DLEV2_SOURCES = \
++ cblas_dgemv.c \
++ cblas_dgbmv.c \
++ cblas_dger.c \
++ cblas_dsbmv.c \
++ cblas_dspmv.c \
++ cblas_dspr.c \
++ cblas_dspr2.c \
++ cblas_dsymv.c \
++ cblas_dsyr.c \
++ cblas_dsyr2.c \
++ cblas_dtbmv.c \
++ cblas_dtbsv.c \
++ cblas_dtpmv.c \
++ cblas_dtpsv.c \
++ cblas_dtrmv.c \
++ cblas_dtrsv.c
++
++DLEV3_SOURCES = \
++ cblas_dgemm.c \
++ cblas_dsymm.c \
++ cblas_dsyrk.c \
++ cblas_dsyr2k.c \
++ cblas_dtrmm.c \
++ cblas_dtrsm.c
++
++CLEV_SOURCES = \
++ cdotcsub.f \
++ cdotusub.f \
++ icamaxsub.f
++
++CLEV1_SOURCES = \
++ cblas_cswap.c \
++ cblas_cscal.c \
++ cblas_csscal.c \
++ cblas_ccopy.c \
++ cblas_caxpy.c \
++ cblas_cdotu_sub.c \
++ cblas_cdotc_sub.c \
++ cblas_icamax.c
++
++CLEV2_SOURCES = \
++ cblas_cgemv.c \
++ cblas_cgbmv.c \
++ cblas_chemv.c \
++ cblas_chbmv.c \
++ cblas_chpmv.c \
++ cblas_ctrmv.c \
++ cblas_ctbmv.c \
++ cblas_ctpmv.c \
++ cblas_ctrsv.c \
++ cblas_ctbsv.c \
++ cblas_ctpsv.c \
++ cblas_cgeru.c \
++ cblas_cgerc.c \
++ cblas_cher.c \
++ cblas_cher2.c \
++ cblas_chpr.c \
++ cblas_chpr2.c
++
++CLEV3_SOURCES = \
++ cblas_cgemm.c \
++ cblas_csymm.c \
++ cblas_chemm.c \
++ cblas_cherk.c \
++ cblas_cher2k.c \
++ cblas_ctrmm.c \
++ cblas_ctrsm.c \
++ cblas_csyrk.c \
++ cblas_csyr2k.c
++
++ZLEV_SOURCES = \
++ zdotcsub.f \
++ zdotusub.f \
++ dzasumsub.f \
++ dznrm2sub.f \
++ izamaxsub.f
++
++ZLEV1_SOURCES = \
++ cblas_zswap.c \
++ cblas_zscal.c \
++ cblas_zdscal.c \
++ cblas_zcopy.c \
++ cblas_zaxpy.c \
++ cblas_zdotu_sub.c \
++ cblas_zdotc_sub.c \
++ cblas_dznrm2.c \
++ cblas_dzasum.c \
++ cblas_izamax.c
++
++ZLEV2_SOURCES = \
++ cblas_zgemv.c \
++ cblas_zgbmv.c \
++ cblas_zhemv.c \
++ cblas_zhbmv.c \
++ cblas_zhpmv.c \
++ cblas_ztrmv.c \
++ cblas_ztbmv.c \
++ cblas_ztpmv.c \
++ cblas_ztrsv.c \
++ cblas_ztbsv.c \
++ cblas_ztpsv.c \
++ cblas_zgeru.c \
++ cblas_zgerc.c \
++ cblas_zher.c \
++ cblas_zher2.c \
++ cblas_zhpr.c \
++ cblas_zhpr2.c
++
++ZLEV3_SOURCES = \
++ cblas_zgemm.c \
++ cblas_zsymm.c \
++ cblas_zhemm.c \
++ cblas_zherk.c \
++ cblas_zher2k.c \
++ cblas_ztrmm.c \
++ cblas_ztrsm.c \
++ cblas_zsyrk.c \
++ cblas_zsyr2k.c
++
++libcblas_la_SOURCES = \
++ cblas_f77.h \
++ cblas.h \
++ $(ERRHAND_SOURCES) \
++ $(SINGLE_SOURCES) \
++ $(SLEV_SOURCES) \
++ $(DLEV_SOURCES) \
++ $(CLEV_SOURCES) \
++ $(ZLEV_SOURCES) \
++ $(SLEV1_SOURCES) \
++ $(DLEV1_SOURCES) \
++ $(CLEV1_SOURCES) \
++ $(ZLEV1_SOURCES) \
++ $(SLEV2_SOURCES) \
++ $(DLEV2_SOURCES) \
++ $(CLEV2_SOURCES) \
++ $(ZLEV2_SOURCES) \
++ $(SLEV3_SOURCES) \
++ $(DLEV3_SOURCES) \
++ $(CLEV3_SOURCES) \
++ $(ZLEV3_SOURCES)
++
++libcblas_la_LIBADD = @BLAS_LIBS@
++
+--- testing/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ testing/Makefile.am 2007-11-09 17:20:37.000000000 +0000
+@@ -0,0 +1,70 @@
++TESTS = cblas_tests
++
++cblas_tests:
++ @install -m0755 cblas_tests.sh cblas_tests
++
++check_PROGRAMS = \
++ xscblat1 xdcblat1 xccblat1 xzcblat1 \
++ xscblat2 xdcblat2 xccblat2 xzcblat2 \
++ xscblat3 xdcblat3 xccblat3 xzcblat3
++
++LDADD = $(top_builddir)/src/libcblas.la @BLAS_LIBS@
++
++AM_CPPFLAGS = -I$(top_srcdir)/src -DADD_
++
++AUX_SOURCES = \
++ auxiliary.c \
++ c_xerbla.c
++
++xscblat1_SOURCES = \
++ c_sblas1.c \
++ c_sblat1.f
++xscblat2_SOURCES = \
++ c_sblas2.c \
++ c_s2chke.c \
++ c_sblat2.f \
++ $(AUX_SOURCES)
++xscblat3_SOURCES = \
++ c_sblas3.c \
++ c_s3chke.c \
++ c_sblat3.f \
++ $(AUX_SOURCES)
++xdcblat1_SOURCES = \
++ c_dblas1.c \
++ c_dblat1.f
++xdcblat2_SOURCES = \
++ c_dblas2.c \
++ c_d2chke.c \
++ c_dblat2.f \
++ $(AUX_SOURCES)
++xdcblat3_SOURCES = \
++ c_dblas3.c \
++ c_d3chke.c \
++ c_dblat3.f \
++ $(AUX_SOURCES)
++xccblat1_SOURCES = \
++ c_cblas1.c \
++ c_cblat1.f
++xccblat2_SOURCES = \
++ c_cblas2.c \
++ c_c2chke.c \
++ c_cblat2.f \
++ $(AUX_SOURCES)
++xccblat3_SOURCES = \
++ c_cblas3.c \
++ c_c3chke.c \
++ c_cblat3.f \
++ $(AUX_SOURCES)
++xzcblat1_SOURCES = \
++ c_zblas1.c \
++ c_zblat1.f
++xzcblat2_SOURCES = \
++ c_zblas2.c \
++ c_z2chke.c \
++ c_zblat2.f \
++ $(AUX_SOURCES)
++xzcblat3_SOURCES = \
++ c_zblas3.c \
++ c_z3chke.c \
++ c_zblat3.f \
++ $(AUX_SOURCES)
+--- testing/cblas_tests.sh 1970-01-01 01:00:00.000000000 +0100
++++ testing/cblas_tests.sh 2007-11-09 16:20:41.000000000 +0000
+@@ -0,0 +1,8 @@
++#!/bin/sh
++
++for t in x*blat1; do
++ ./${t}
++done
++for t in x*blat{2,3}; do
++ ./${t} < ${t:1:1}in${t:7:1}
++done
diff --git a/sci-libs/cblas-reference/files/eselect.cblas.reference b/sci-libs/cblas-reference/files/eselect.cblas.reference
new file mode 100644
index 00000000000..62b581860fc
--- /dev/null
+++ b/sci-libs/cblas-reference/files/eselect.cblas.reference
@@ -0,0 +1,5 @@
+blas/reference/libcblas.so /usr/@LIBDIR@/libcblas.so
+blas/reference/libcblas.so.0 /usr/@LIBDIR@/libcblas.so.0
+blas/reference/libcblas.a /usr/@LIBDIR@/libcblas.a
+../blas/reference/cblas.pc /usr/@LIBDIR@/pkgconfig/cblas.pc
+cblas/cblas.h /usr/include/cblas.h
diff --git a/sci-libs/cblas-reference/metadata.xml b/sci-libs/cblas-reference/metadata.xml
new file mode 100644
index 00000000000..f08baae0892
--- /dev/null
+++ b/sci-libs/cblas-reference/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+The BLAS (Basic Linear Algebra Subprograms) are high quality "building
+block" routines for performing basic vector and matrix operations. Level 1
+BLAS do vector-vector operations, Level 2 BLAS do matrix-vector operations,
+and Level 3 BLAS do matrix-matrix operations. Because the BLAS are
+efficient, portable, and widely available, they're commonly used in the
+development of high quality linear algebra software, LAPACK for
+example. This packages implements the reference C library as a wrapper
+to the FORTRAN 77 BLAS library.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/ccfits/Manifest b/sci-libs/ccfits/Manifest
new file mode 100644
index 00000000000..13e11de1231
--- /dev/null
+++ b/sci-libs/ccfits/Manifest
@@ -0,0 +1 @@
+DIST CCfits-2.4.tar.gz 1792643 SHA256 ba6c5012b260adf7633f92581279ea582e331343d8c973981aa7de07242bd7f8 SHA512 b12d455bb6dd631056e02a12e996d3bf0b6169f8922011e4b64f979b08d2ab8f405e14947c6f5d26ad18bf2f5764854a84987ae105944515f533fe6b0b4ef7be WHIRLPOOL 7f0ca6f0e684f7d66d7272a89dbeb8fa95e3907f358ec624f5f817311288fdfb6467ec915d0ab9f2eee753fcaee3f4b68f497c2dffcf7a38bdce9a7f97681e2a
diff --git a/sci-libs/ccfits/ccfits-2.4.ebuild b/sci-libs/ccfits/ccfits-2.4.ebuild
new file mode 100644
index 00000000000..f309dc2c30d
--- /dev/null
+++ b/sci-libs/ccfits/ccfits-2.4.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+inherit eutils autotools
+
+MYPN=CCfits
+MYP=${MYPN}-${PV}
+
+DESCRIPTION="C++ interface for cfitsio"
+HOMEPAGE="http://heasarc.gsfc.nasa.gov/fitsio/CCfits/"
+SRC_URI="${HOMEPAGE}/${MYP}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc static-libs"
+
+RDEPEND=">=sci-libs/cfitsio-3.080"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MYPN}"
+
+src_prepare() {
+ # avoid building cookbook by default and no rpath
+ epatch "${FILESDIR}"/${PN}-2.2-makefile.patch
+ AT_M4DIR=config/m4 eautoreconf
+}
+
+src_configure() {
+ econf $(use_enable static-libs static)
+}
+
+src_install () {
+ default
+ use doc && dodoc *.pdf && dohtml -r html/*
+}
diff --git a/sci-libs/ccfits/files/ccfits-2.2-makefile.patch b/sci-libs/ccfits/files/ccfits-2.2-makefile.patch
new file mode 100644
index 00000000000..e92d9306900
--- /dev/null
+++ b/sci-libs/ccfits/files/ccfits-2.2-makefile.patch
@@ -0,0 +1,26 @@
+--- Makefile.am.orig 2010-01-20 02:52:22.000000000 +0000
++++ Makefile.am 2010-01-20 02:50:34.000000000 +0000
+@@ -26,12 +26,11 @@
+ EXTRA_DIST = config CHANGES README.INSTALL License.txt file1.pha $(MSVC_FILES)
+
+
+-bin_PROGRAMS = cookbook
++check_PROGRAMS = cookbook
+
+ cookbook_SOURCES = cookbook.cxx
+
+ cookbook_LDADD = libCCfits.la
+-cookbook_LDFLAGS = -R $(R_LIB_PATH) -R $(CXX_LIB_PATH)
+
+ pkgconfigdir = $(libdir)/pkgconfig
+ pkgconfig_DATA = CCfits.pc
+@@ -64,8 +63,7 @@
+
+ # This will tell shared library which STD C++ library to use without
+ # needing the user to use LD_LIBRARY_PATH environment variable
+-libCCfits_la_LIBADD = $(LIBSTDCPP)
+-libCCfits_la_LDFLAGS = -R $(R_LIB_PATH) -R $(CXX_LIB_PATH)
++#libCCfits_la_LIBADD = $(LIBSTDCPP)
+
+ libCCfits_ladir = $(pkgincludedir)
+
diff --git a/sci-libs/ccfits/metadata.xml b/sci-libs/ccfits/metadata.xml
new file mode 100644
index 00000000000..b4532406f70
--- /dev/null
+++ b/sci-libs/ccfits/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+ CCfits is an object oriented interface to the cfitsio library. It is
+ designed to make the capabilities of cfitsio available to
+ programmers working in C++. It is written in ANSI C++ and
+ implemented using the C++ Standard Library with namespaces,
+ exception handling, and member template functions.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/ccolamd/Manifest b/sci-libs/ccolamd/Manifest
new file mode 100644
index 00000000000..1f5e80f44d1
--- /dev/null
+++ b/sci-libs/ccolamd/Manifest
@@ -0,0 +1 @@
+DIST ccolamd-2.8.0.tar.bz2 309907 SHA256 0e3d0d147f22ef6d3e6eedc7540be6135303a064dae9f10ff443ade1196d12eb SHA512 6a515a8250ed98d52aa932a6f93170174ff32f76c1ecedcedeb1540a471416d0cd40b5613a839b96fbc79c66b3cb5106c6a340a33fafdd695c83b7d949756e77 WHIRLPOOL f999836681321d0f1ee0ccaae8cbc86b934220eb4151792b5163a7a1f115319442a9a3db8cb707b7e42cd50fa092765a0fc49c8e60daf756aaff56fa8eb93169
diff --git a/sci-libs/ccolamd/ccolamd-2.8.0.ebuild b/sci-libs/ccolamd/ccolamd-2.8.0.ebuild
new file mode 100644
index 00000000000..5f19e42750f
--- /dev/null
+++ b/sci-libs/ccolamd/ccolamd-2.8.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils
+
+DESCRIPTION="Constrained Column approximate minimum degree ordering algorithm"
+HOMEPAGE="http://www.cise.ufl.edu/research/sparse/ccolamd/"
+SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+
+KEYWORDS="amd64 ~arm hppa ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="static-libs"
+
+RDEPEND="sci-libs/suitesparseconfig"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
diff --git a/sci-libs/ccolamd/files/ccolamd-2.7.1-autotools.patch b/sci-libs/ccolamd/files/ccolamd-2.7.1-autotools.patch
new file mode 100644
index 00000000000..8386325da74
--- /dev/null
+++ b/sci-libs/ccolamd/files/ccolamd-2.7.1-autotools.patch
@@ -0,0 +1,60 @@
+--- Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ Makefile.am 2008-01-29 18:53:56.000000000 +0000
+@@ -0,0 +1,3 @@
++SUBDIRS = Demo Source
++EXTRA_DIST = Doc/ChangeLog README.txt
++include_HEADERS = Include/ccolamd.h
+--- configure.ac 1970-01-01 01:00:00.000000000 +0100
++++ configure.ac 2008-01-29 18:54:17.000000000 +0000
+@@ -0,0 +1,13 @@
++# -*- Autoconf -*-
++AC_PREREQ(2.59)
++AC_INIT(ccolamd, 2.7.1, davis@cise.ufl.edu)
++AM_INIT_AUTOMAKE([foreign])
++AC_PROG_INSTALL
++AC_PROG_LIBTOOL
++AC_CHECK_LIB(m, sqrt)
++AC_CHECK_HEADERS(UFconfig.h)
++AC_CONFIG_FILES([
++ Source/Makefile
++ Demo/Makefile
++ Makefile])
++AC_OUTPUT
+--- Source/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ Source/Makefile.am 2008-01-29 18:53:56.000000000 +0000
+@@ -0,0 +1,10 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include
++lib_LTLIBRARIES = libccolamd.la
++noinst_LTLIBRARIES = libccolamdl.la libccolamdi.la
++
++libccolamdl_la_SOURCES = ccolamd.c
++libccolamdl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
++libccolamdi_la_SOURCES = ccolamd.c
++
++libccolamd_la_SOURCES = ccolamd_global.c
++libccolamd_la_LIBADD = libccolamdl.la libccolamdi.la
+--- Demo/Makefile.am 1970-01-01 01:00:00.000000000 +0100
++++ Demo/Makefile.am 2008-01-29 18:55:44.000000000 +0000
+@@ -0,0 +1,22 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include
++
++check_PROGRAMS = \
++ ccolamd_example \
++ ccolamd_l_example
++
++LDADD = $(top_builddir)/Source/libccolamd.la -lm
++ccolamd_example_SOURCES = ccolamd_example.c
++ccolamd_l_example_SOURCES = ccolamd_l_example.c
++
++check-local: $(check_PROGRAMS)
++ @for i in $(check_PROGRAMS); do \
++ echo "Testing $$i"; \
++ ./$$i > my_$$i.out; \
++ if ! diff $(srcdir)/$$i.out my_$$i.out; then \
++ echo "Test $$i failed!"; \
++ exit 1; \
++ fi \
++ done;
++
++clean-local:
++ rm -f my*.out
diff --git a/sci-libs/ccolamd/metadata.xml b/sci-libs/ccolamd/metadata.xml
new file mode 100644
index 00000000000..2451169809d
--- /dev/null
+++ b/sci-libs/ccolamd/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <longdescription lang="en">
+ Constrained COLAMD computes an column approximate minimum degree ordering
+ algorithm, (like COLAMD), but it can also be given a set of ordering
+ constraints.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
new file mode 100644
index 00000000000..9d3fe280636
--- /dev/null
+++ b/sci-libs/ccp4-libs/Manifest
@@ -0,0 +1 @@
+DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild
new file mode 100644
index 00000000000..ffa5a866a2f
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild
@@ -0,0 +1,359 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+MY_P="${P/-libs}"
+
+PATCH_TOT="0"
+
+DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
+# patch tarball from upstream
+ [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# patches created by us
+ [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+
+for i in $(seq $PATCH_TOT); do
+ NAME="PATCH${i}[1]"
+ SRC_URI="${SRC_URI}
+ ${SRC}/${PV}/patches/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE="minimal"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+ ${PYTHON_DEPS}
+ !<sci-chemistry/ccp4-6.1.3
+ !<sci-chemistry/ccp4-apps-${PV}-r10
+ app-shells/tcsh
+ dev-lang/tcl:0
+ >=sci-libs/cbflib-0.9.2.2
+ sci-libs/fftw:2.1
+ sci-libs/mmdb:0
+ sci-libs/monomer-db
+ sci-libs/ssm
+ virtual/jpeg:0=
+ virtual/lapack
+ virtual/blas"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+MAKEOPTS+=" -j1"
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ tc-export PKG_CONFIG RANLIB AR
+
+ sed \
+ -e "/^AR/s:ar:$(tc-getAR):g" \
+ -i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
+
+ einfo "Applying upstream patches ..."
+ for patch in $(seq $PATCH_TOT); do
+ base="PATCH${patch}"
+ dir=$(eval echo \${${base}[0]})
+ p=$(eval echo \${${base}[1]})
+ pushd "${dir}" >& /dev/null
+ ccp_patch "${DISTDIR}/${p}"
+ popd >& /dev/null
+ done
+ einfo "Done."
+ echo
+
+ [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+ einfo "Applying Gentoo patches ..."
+ # fix buffer overflows wrt bug 339706
+ ccp_patch "${FILESDIR}"/${PV}-overflows.patch
+
+ # it tries to create libdir, bindir etc on live system in configure
+ ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
+
+ # gerror_ gets defined twice on ppc if you're using gfortran/g95
+ ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
+
+ # make creation of libccif.so smooth
+ ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
+
+ # lets try to build libmmdb seperatly
+ ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
+
+ # unbundle libjpeg and cbflib
+ ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
+
+ # Fix missing DESTIDR
+ # not installing during build
+ ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
+ sed \
+ -e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
+ -i configure || die
+
+ # Fix upstreams code
+ ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
+
+ # use pkg-config to detect BLAS/LAPACK
+ ccp_patch "${FILESDIR}"/${PV}-lapack.patch
+
+ # proto type changing in version 0.9.2.2
+ ccp_patch "${FILESDIR}"/${PV}-cbf.patch
+
+ # proto type changing in version 0.9.2.2
+ ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
+
+ ccp_patch "${FILESDIR}"/${P}-force.patch
+
+ ccp_patch "${FILESDIR}"/${P}-format-security.patch
+
+ einfo "Done." # done applying Gentoo patches
+ echo
+
+ # not needed, we have it extra
+ rm -rf src/rapper/{libxml2,gc7.0} || die
+
+ sed \
+ -e "s:/usr:${EPREFIX}/usr:g" \
+ -e 's:-Wl,-rpath,$CLIB::g' \
+ -e 's: -rpath $CLIB::g' \
+ -e 's: -I${srcdir}/include/cpp_c_headers::g' \
+ -e 's:sleep 1:sleep .2:g' \
+ -i configure || die
+
+ gnuconfig_update
+
+ for i in lib/DiffractionImage src/rapper src/pisa; do
+ pushd ${i} > /dev/null
+ sed 's:-g::g' -i configure* || die
+ [[ -f configure.in ]] && mv configure.{in,ac}
+ eautoreconf
+ popd > /dev/null
+ done
+
+ ## unbundle libssm
+ sed -e '/libdir/s:ssm::g' -i Makefile.in || die
+ find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
+}
+
+src_configure() {
+ rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
+
+ # Build system is broken if we set LDFLAGS
+ userldflags="${LDFLAGS}"
+ export SHARED_LIB_FLAGS="${LDFLAGS}"
+ unset LDFLAGS
+
+ # GENTOO_OSNAME can be one of:
+ # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+ # linux_compaq_compilers linux_intel_compilers generic Darwin
+ # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+ if [[ "$(tc-getFC)" = "ifort" ]]; then
+ if use ia64; then
+ GENTOO_OSNAME="ia64_linux_intel"
+ else
+ # Should be valid for x86, maybe amd64
+ GENTOO_OSNAME="linux_intel_compilers"
+ fi
+ else
+ # Should be valid for x86 and amd64, at least
+ GENTOO_OSNAME="linux"
+ fi
+
+ # Sets up env
+ ln -s \
+ ccp4.setup-bash \
+ "${S}"/include/ccp4.setup || die
+
+ # We agree to the license by emerging this, set in LICENSE
+ sed -i \
+ -e "s~^\(^agreed=\).*~\1yes~g" \
+ "${S}"/configure || die
+
+ # Fix up variables -- need to reset CCP4_MASTER at install-time
+ sed -i \
+ -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+ -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+ -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+ "${S}"/include/ccp4.setup* || die
+
+ # Set up variables for build
+ source "${S}"/include/ccp4.setup-sh
+
+ export CC=$(tc-getCC)
+ export CXX=$(tc-getCXX)
+ export COPTIM=${CFLAGS}
+ export CXXOPTIM=${CXXFLAGS}
+ # Default to -O2 if FFLAGS is unset
+ export FC=$(tc-getFC)
+ export FOPTIM=${FFLAGS:- -O2}
+
+ export SHARE_LIB="\
+ $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
+ $(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
+
+ # Can't use econf, configure rejects unknown options like --prefix
+ ./configure \
+ --onlylibs \
+ --with-shared-libs \
+ --with-fftw="${EPREFIX}/usr" \
+ --with-warnings \
+ --disable-cctbx \
+ --disable-clipper \
+ --disable-ssm \
+ --tmpdir="${TMPDIR}" \
+ --bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
+ --libdir="${EPREFIX}/usr/$(get_libdir)" \
+ ${GENTOO_OSNAME} || die "configure failed"
+}
+
+src_compile() {
+ emake DESTDIR="${D}" onlylib
+}
+
+src_install() {
+ # Set up variables for build
+ source "${S}"/include/ccp4.setup-sh
+
+ emake \
+ DESTDIR="${D}" \
+ includedir="${EPREFIX}/usr/include" \
+ library_includedir="${EPREFIX}/usr/include" \
+ install
+
+ sed \
+ -e "330,1000d" \
+ -i "${S}"/include/ccp4.setup-sh || die
+
+ sed \
+ -e "378,1000d" \
+ -i "${S}"/include/ccp4.setup-csh || die
+
+ sed \
+ -e "s:-${PV/-r*/}::g" \
+ -e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
+ -e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
+ -e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
+ -e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
+ -e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
+ -e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
+ -e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
+ -e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
+ -e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
+ -e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
+ -e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
+ -e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
+ -e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
+ -e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
+ -e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+ -e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+ -e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+ -e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+ -e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+ -e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+ -e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
+ -e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
+ -e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+ -e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+ -e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
+ -e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
+ -e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
+ -e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
+ -e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
+ -e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
+ -e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+ -e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+ -e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
+ -e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
+ -e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
+ -e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
+ -e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
+ -e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
+ -e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \
+ -e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \
+ -e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
+ -e '/CLIB=/d' \
+ -e '/CLIB /d' \
+ -e '/CLIBS=/d' \
+ -e '/CLIBS /d' \
+ -e "/alias/d" \
+ -e "/CCP4_HELPDIR/d" \
+ -e "/IMOSFLM_VERSION/d" \
+ -i "${S}"/include/ccp4.setup* || die
+
+ # Don't check for updates on every sourcing of /etc/profile
+ sed -i \
+ -e "s:\(eval python.*\):#\1:g" \
+ "${S}"/include/ccp4.setup* || die
+
+ # Libs
+ for file in "${S}"/lib/*; do
+ if [[ -d ${file} ]]; then
+ continue
+ elif [[ -x ${file} ]]; then
+ dolib.so ${file}
+ else
+ insinto /usr/$(get_libdir)
+ doins ${file}
+ fi
+ done
+
+ prune_libtool_files
+
+ sed \
+ -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
+ -i "${S}"/include/ccp4.setup-sh || die
+
+ if ! use minimal; then
+ # Setup scripts
+ insinto /etc/profile.d
+ newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
+ newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
+
+ # Data
+ insinto /usr/share/ccp4/data/
+ doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
+
+ # Environment files, setup scripts, etc.
+ rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
+ insinto /usr/share/ccp4/
+ doins -r "${S}"/include
+ fi
+
+ rm -f "${S}"/include/ccp4.setup* || die
+
+ dodoc "${S}"/lib/data/*.doc
+ newdoc "${S}"/lib/data/README DATA-README
+}
+
+pkg_postinst() {
+ einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
+ einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+ EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
new file mode 100644
index 00000000000..a77d9494a05
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
@@ -0,0 +1,11 @@
+--- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700
++++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700
+@@ -716,7 +716,7 @@
+
+ #endif /* end of apple xlf support */
+
+-#if ( defined (__linux__) && defined (_CALL_SYSV) )
++#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
+ /* linuxppc xlf support */
+ void gerror_ (str, Lstr)
+ char *str;
diff --git a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
new file mode 100644
index 00000000000..6930fcad766
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
@@ -0,0 +1,16 @@
+ lib/DiffractionImage/DiffractionImageCBF.cpp | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
+index 69b32b0..3ffee26 100755
+--- a/lib/DiffractionImage/DiffractionImageCBF.cpp
++++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
+@@ -62,7 +62,7 @@ namespace DI
+ int* tmpimg;
+ tmpimg=new int[height*width];
+ test= cbf_decompress_byte_offset ((void *)tmpimg,sizeof(int),sign,
+- nelements,&nread,0,32,sign,ccbbff,0,
++ nelements,&nread,0,0,32,sign,ccbbff,0,
+ byte_ord.c_str(),2,(size_t) width,
+ (size_t) height,1,(size_t) padding);
+ for(int i=0;i<height*width;i++)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
new file mode 100644
index 00000000000..ca18d75bc84
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
@@ -0,0 +1,33 @@
+--- configure 2009-08-04 22:35:34.000000000 +0200
++++ configure.new 2009-08-04 22:54:32.000000000 +0200
+@@ -3136,8 +3136,8 @@
+ fi
+ ( touch /tmp/$$.cache_file 2>/dev/null && \
+ cat /dev/null > /tmp/$$.cache_file && \
+- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \
+- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
++ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \
++ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib
+ rm -f /tmp/$$.cache_file
+ if [ "X$LIBFOPTIM" != "X" ]; then
+ FOPTIM=$FOPTIM_save
+--- lib/ccif/configure 2009-08-04 22:35:37.000000000 +0200
++++ lib/ccif/configure.new 2009-08-04 23:05:44.000000000 +0200
+@@ -5568,7 +5568,7 @@
+ enable_shared_lib=no
+ ;;
+
+- i?86-unknown-linux | i?86-pc-linux-gnu )
++ i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu)
+ if test $enable_shared_lib = yes ; then
+
+ SO_LOC_VAR='LD_LIBRARY_PATH'
+@@ -5585,7 +5585,7 @@
+ else
+ SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
+ fi
+- SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
++ SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
+ # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
+ SHARED_LIB_EXPORTS_CMD=''
+ fi
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
new file mode 100644
index 00000000000..b3147ad81bb
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
@@ -0,0 +1,24 @@
+diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
+index c23f488..b32dd1e 100755
+--- a/lib/src/Makefile.in
++++ b/lib/src/Makefile.in
+@@ -176,7 +176,7 @@ $(mmdbsrcdir)/mmdb_sbase0.h $(mmdbsrcdir)/hybrid_36.h
+
+ ##### Makefile targets ######
+
+-all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
++all: fsplit $(LC) $(LF) $(SCRIPT_MODULES)
+ # maybe create shared library
+ $(SHARE_LIB)
+
+@@ -717,10 +717,8 @@ uninstall-mmdbHEADERS:
+ done
+
+ install : all install-ccp4HEADERS install-mmdbHEADERS
+- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
+ $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
+ $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
+- $(RANLIB) $(libdir)/$(LMMDB)
+ $(RANLIB) $(libdir)/$(LC)
+ $(RANLIB) $(libdir)/$(LF)
+ $(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
new file mode 100644
index 00000000000..583697cea0a
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
@@ -0,0 +1,87 @@
+--- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700
++++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700
+@@ -643,45 +643,45 @@
+ # echo "! Beware -- the $system installation isn't properly tested." ; }
+ syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
+
+-if test -z "$onlylibs" ; then
+- for i in CCP4_SCR BINSORT_SCR; do
+- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
+- else
+- eval echo "! No directory \$$i and can\'t create it."
+- echo " Check the value of $i."
+- badvar=1
+- fi
+- done
+-
+- for i in libdir bindir includedir; do
+- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
+- else
+- eval echo "! No directory \$$i and can\'t create it."
+- echo " Check the argument of --$i."
+- badvar=1
+- fi
+- done
+-
+- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
+- if test -d $i || mkdir $i; then :
+- else
+- eval echo "! No directory $i and can\'t create it."
+- badvar=1
+- fi
+- done
+-else
+- # Kludge to fool the "Makefile" target in the top-level CCP4
+- # Makefile into not trying to remake src/Makefile.in
+- for i in $srcdir/src $srcdir/lib/src ; do
+- if test -d $i || mkdir $i; then
+- if ! test -f $i/Makefile.in ; then
+- echo
+- echo "onlylibs: making dummy file $i/Makefile.in"
+- touch $i/Makefile.in
+- fi
+- fi
+- done
+-fi
++#if test -z "$onlylibs" ; then
++# for i in CCP4_SCR BINSORT_SCR; do
++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
++# else
++# eval echo "! No directory \$$i and can\'t create it."
++# echo " Check the value of $i."
++# badvar=1
++# fi
++# done
++#
++# for i in libdir bindir includedir; do
++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
++# else
++# eval echo "! No directory \$$i and can\'t create it."
++# echo " Check the argument of --$i."
++# badvar=1
++# fi
++# done
++#
++# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
++# if test -d $i || mkdir $i; then :
++# else
++# eval echo "! No directory $i and can\'t create it."
++# badvar=1
++# fi
++# done
++#else
++# # Kludge to fool the "Makefile" target in the top-level CCP4
++# # Makefile into not trying to remake src/Makefile.in
++# for i in $srcdir/src $srcdir/lib/src ; do
++# if test -d $i || mkdir $i; then
++# if ! test -f $i/Makefile.in ; then
++# echo
++# echo "onlylibs: making dummy file $i/Makefile.in"
++# touch $i/Makefile.in
++# fi
++# fi
++# done
++#fi
+
+ ### sanity checks
+
diff --git a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
new file mode 100644
index 00000000000..6e399764795
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
@@ -0,0 +1,22 @@
+--- lib/ccif/configure.in 2009-06-10 13:52:59.000000000 +0200
++++ lib/ccif/configure.in.new 2009-06-10 14:04:31.000000000 +0200
+@@ -363,7 +363,7 @@
+ fi
+ SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
+ --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
+- $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
++ $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
+ SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
+ fi
+ ;;
+--- lib/ccif/configure 2009-06-10 14:26:58.000000000 +0200
++++ lib/ccif/configure.new 2009-06-10 14:43:31.000000000 +0200
+@@ -1807,7 +1807,7 @@
+ SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
+ $(SHARED_LIB_NAME) \\\
+ --whole-archive $L \\\
+- -o $(SHARED_LIB_NAME)'
++ -o $(SHARED_LIB_NAME) -lm'
+ SHARED_LIB_EXPORTS_CMD=''
+ fi
+ ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch b/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch
new file mode 100644
index 00000000000..8bfa7db8cbf
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch
@@ -0,0 +1,140 @@
+diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c
+index bfda882..f821e04 100755
+--- a/lib/DiffractionImage/Bruker/FRM_LIB.c
++++ b/lib/DiffractionImage/Bruker/FRM_LIB.c
+@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files.
+ #include "sys/types.h" /* _open, etc. */
+ #include "sys/stat.h" /* _open, etc. */
+
++#include <unistd.h>
++
+ #ifndef _MSC_VER
+ int min(int a, int b)
+ {
+diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c
+index 1a933de..1c40c32 100755
+--- a/lib/DiffractionImage/MAR/mar300_header.c
++++ b/lib/DiffractionImage/MAR/mar300_header.c
+@@ -23,6 +23,9 @@
+ */
+ #include "mar300_header.h"
+
++#include <sys/types.h>
++#include <unistd.h>
++
+ /*
+ * Local functions
+ */
+diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c
+index a8351ea..16d0f7b 100755
+--- a/lib/DiffractionImage/MAR/mar345_header.c
++++ b/lib/DiffractionImage/MAR/mar345_header.c
+@@ -32,6 +32,9 @@
+ */
+ #include "mar345_header.h"
+
++#include <sys/types.h>
++#include <unistd.h>
++
+ /*
+ * Definitions
+ */
+diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c
+index 07f2741..6364ca4 100755
+--- a/lib/DiffractionImage/MAR/nb_header.c
++++ b/lib/DiffractionImage/MAR/nb_header.c
+@@ -20,6 +20,8 @@
+ #include <io.h>
+ #endif
+
++#include <sys/types.h>
++#include <unistd.h>
+ /*
+ * mar software include files
+ */
+diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c
+index 443bb8c..0d96b3f 100755
+--- a/lib/DiffractionImage/MAR/swap.c
++++ b/lib/DiffractionImage/MAR/swap.c
+@@ -10,6 +10,9 @@
+ *
+ **********************************************************************/
+
++#define _XOPEN_SOURCE
++#include <unistd.h>
++
+ void swaplong();
+ void swapshort();
+
+diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c
+index 0f6a6b7..a09dc48 100755
+--- a/lib/ccif/f_interface.c
++++ b/lib/ccif/f_interface.c
+@@ -25,6 +25,7 @@
+ ********************************************************************/
+
+ #include "stdpccts.h"
++#include <sys/mman.h>
+
+ /* This file is terribly organised, and badly needs re-doing. There is probably
+ * scope for splitting this into three modules:
+diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c
+index 8b5d04f..74ee3f7 100755
+--- a/lib/src/ccp4_general_f.c
++++ b/lib/src/ccp4_general_f.c
+@@ -26,6 +26,7 @@
+ #include <string.h>
+ #include <stdlib.h>
+ #include <math.h>
++#include <time.h>
+ #include "ccp4_errno.h"
+ #include "ccp4_fortran.h"
+ #include "ccp4_parser.h"
+diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c
+index 3e83d4d..bb3e975 100755
+--- a/lib/src/ccp4_program.c
++++ b/lib/src/ccp4_program.c
+@@ -25,6 +25,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
++#include <time.h>
+ #include "ccp4_program.h"
+ #include "ccp4_parser.h"
+ #include "ccp4_utils.h"
+diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c
+index ee8af24..c6fb3cd 100755
+--- a/lib/src/fsplit.c
++++ b/lib/src/fsplit.c
+@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91";
+ #include <string.h>
+ #include <sys/types.h>
+ #include <sys/stat.h>
++#include <unistd.h>
+
+ /*
+ * usage: fsplit [-e efile] ... [file]
+diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c
+index ea52e96..30dbd56 100755
+--- a/src/clipper_progs/src/pirate/compress42.c
++++ b/src/clipper_progs/src/pirate/compress42.c
+@@ -142,6 +142,7 @@
+ #include <sys/types.h>
+ #include <sys/stat.h>
+ #include <errno.h>
++#include <unistd.h>
+
+ #ifdef DIRENT
+ # include <dirent.h>
+diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c
+index e224430..c7b82f4 100755
+--- a/src/mtz2cif_/mtz2cif.c
++++ b/src/mtz2cif_/mtz2cif.c
+@@ -28,6 +28,7 @@
+ #include "cmtzlib.h"
+ #include "ccp4_parser.h"
+ #include "ccp4_general.h"
++#include "ccp4_program.h"
+ #include "csymlib.h"
+ #include "mtz2cif_lib.h"
+
diff --git a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch b/sci-libs/ccp4-libs/files/6.1.3-lapack.patch
new file mode 100644
index 00000000000..0463b371952
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-lapack.patch
@@ -0,0 +1,597 @@
+diff --git a/configure b/configure
+index 833f483..bcfa62d 100755
+--- a/configure
++++ b/configure
+@@ -3226,574 +3226,14 @@ else
+ echo
+ echo "Warning: this option has not been extensively tested!"
+ echo "Please report problems to ccp4@ccp4.ac.uk"
+- # Search for vendor LAPACK/BLAS first
+- if test ! "$with_netlib_lapack" ; then
+- # Initialise variables to blank
+- lapackdir=
+- XLAPACK_LIB=
+- # Possible directories to check for vendor or pre-existing LAPACK or
+- # BLAS - add to these if you want to test others
+- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib"
+- # Possible library names
+- # These are the names like xxxx where the library will be libxxxx.a
+- # or libxxxx.so
+- echo
+- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries"
+- echo "on this system"
+- case $system in
+- linux | linux64 | linux32 )
+- # linux users will usually have them in /usr/lib but don't call it
+- trylapack="lapack"
+- tryblas="blas"
+- # if code is non_shared then this can lead to problems. both blas and lapack
+- # need to be resolved even if they are not called!
+- if test "$non_shared" = yes; then
+- echo "You are compiling linux non_shared. This sometimes causes problems "
+- echo " so checking for requirements."
+- echo "Checking: try to link library against test program"
+- if test -f testlink.f || test -f testlink ; then
+- rm -f testlink*
+- fi
+- cat > testlink.f <<EOF
+- PROGRAM TESTLINK
+-C A bit of scala code to test the linking
+- real bf(3), bnorm
+-c
+- integer maxbmt
+- parameter (maxbmt = 2)
+- double precision B(maxbmt,maxbmt), eigval(maxbmt),
+- $ eigvec(maxbmt,maxbmt), w(5*maxbmt)
+- integer m, ia, ix, istat
+-c
+- B(1,1) = 1.00
+- B(1,2) = 1.00
+- B(2,1) = 1.00
+- B(2,2) = 1.00
+-c
+- m = maxbmt
+- ia = maxbmt
+- ix = maxbmt
+- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat)
+- end
+-EOF
+- #firstly test without -lblas
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
+- echo $test_compile
+- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
+- # Compilation was okay
+- echo "... only -llapack needed"
+- XLAPACK_LIB="-llapack"
+- # Set the next two variables so that configure
+- # doesn't try to build netlib libraries
+- LAPACKLIB="lapack"
+- noblas=yes
+- trylapack=
+- tryblas=
+- else
+- echo "more than just -llapack needed...."
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
+- echo $test_compile
+- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+- # Compilation was okay
+- echo "...-llapack and -lblas were needed"
+- XLAPACK_LIB="-llapack -lblas"
+- # Set the next two variables so that configure
+- # doesn't try to build netlib libraries
+- LAPACKLIB="lapack blas"
+- noblas=no
+- trylapack=
+- tryblas=
+- else
+- echo "....could not find either lapack or blas."
+- fi
+- fi
+- fi
+- # add 64 bit libs
+- case $system in
+- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;;
+- esac
+-
+- ;;
+- osf1)
+- # OSF1 has dxml (old version) and cxml
+- # which should have both lapack and blas
+- trylapack="dxml cxml"
+- tryblas=
+- trydirs="${trydirs} /usr/shlib"
+- ;;
+- irix)
+- # Additional search paths for IRIX
+- trydirs="${trydirs} /usr/lib32"
+- # SCSL should have both LAPACK and BLAS
+- trylapack="scs"
+- tryblas="blas"
+- ;;
+- irix64)
+- # Additional search paths for IRIX64
+- trydirs="${trydirs} /usr/lib64"
+- # SCSL should have both LAPACK and BLAS
+- trylapack="scs"
+- tryblas="blas"
+- # Extra compiler flags?
+- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON"
+- ;;
+- aix)
+- # Additional search paths for AIX
+- trydirs="${trydirs}"
+- # AIX might have ESSL library - blas only I think
+- trylapack=
+- tryblas="essl"
+- ;;
+- hpux)
+- # Additional search paths for HPUX
+- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0"
+- # HPUX should have both LAPACK (part of mlib) and BLAS
+- trylapack="lapack"
+- tryblas="blas"
+- # Extra compiler flags?
+- # +U77 required for ETIME function - this is already in XFFLAGS
+- #XLAPACKFLAGS="+U77"
+- ;;
+-
+- sunos | sunos64)
+- # Sun has libraries with BLAS and LAPACK invoked using
+- # -xlic_lib=sunperf
+- trylapack=
+- tryblas=
+- echo "SunOs can use the Sun Performance Library (if installed)"
+- echo "which has both BLAS and LAPACK 3.0"
+- echo
+- echo "Looking for a valid library to use..."
+- echo
+- # Loop over the possible library names
+- try_libs="sunperf"
+- for testlib in $try_libs
+- do
+- if test ! "$XLAPACK_LIB" ; then
+- # Try running a test compile to see if this a valid library
+- if test -f testlink.f || test -f testlink ; then
+- rm -f testlink*
+- fi
+- cat > testlink.f <<EOF
+-c Test fortran program to link against library
+- PROGRAM TESTLINK
+- IMPLICIT NONE
+- INTEGER A
+- A = 1
+- STOP
+- END
+-EOF
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib"
+- echo $test_compile
+- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+- # Compilation was okay
+- echo "... -xlic_lib=$testlib is okay"
+- XLAPACK_LIB="-dalign -xlic_lib=$testlib"
+- # Set the next two variables so that configure
+- # doesn't try to build netlib libraries
+- LAPACKLIB="$testlib"
+- noblas=yes
+- else
+- # Compilation failed
+- echo "... cannot use -xlic_lib=$testlib"
+- fi
+- # End of test for testlib
+- fi
+- # End of loop over possible lib names
+- done
+- # Report if no suitable library was found
+- if test ! "$XLAPACK_LIB" ; then
+- echo
+- echo "No suitable LAPACK library was found."
+- echo "This may be because the Sun Performance Library is not"
+- echo "installed on your system"
+- echo "Contact your system administrator or Sun vendor"
+- fi
+- ;;
+- Darwin | Darwin32 | Darwin64 )
+- # Darwin has libraries with BLAS and LAPACK invoked using
+- # -framework vecLib
+- echo "Darwin can use the vecLib Library (if installed)"
+- echo "which has both BLAS and LAPACK 3.0"
+- echo
+- # This is a special case so try running a test compile
+- echo "Checking: try to link library against test program"
+- if test -f testlink.f || test -f testlink ; then
+- rm -f testlink*
+- fi
+- cat > testlink.f <<EOF
+-c Test fortran program to link against library
+- PROGRAM TESTLINK
+- IMPLICIT NONE
+- INTEGER A
+- A = 1
+- STOP
+- END
+-EOF
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib"
+- echo $test_compile
+- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+- # Compilation was okay
+- echo "... -framework vecLib is okay"
+- XLAPACK_LIB="-framework vecLib"
+- # Set the next two variables so that configure
+- # doesn't try to build netlib libraries
+- LAPACKLIB="vecLib"
+- noblas=yes
+- else
+-#alternative linking for vecLib libraries
+- case `uname -sr` in
+- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;;
+- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;;
+- esac
+-
+- echo $test_compile
+- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+- # Compilation was okay
+- echo "... -framework vecLib is okay"
+- XLAPACK_LIB="-Wl,-framework -Wl,vecLib"
+- # Set the next two variables so that configure
+- # doesn't try to build netlib libraries
+- LAPACKLIB="-Wl,-framework -Wl,vecLib"
+- noblas=yes
+- else
+- # Compilation failed
+- echo "... cannot use -framework vecLib"
+- echo
+- fi
+- fi
+- trylapack=
+- tryblas=
+-# try the fink installation
+- trydirs="${trydirs} /sw"
+- ;;
+- Darwin_ibm_compilers )
+- # Darwin has libraries with BLAS and LAPACK invoked using
+- # -framework vecLib
+- echo "Darwin can use the vecLib Library (if installed)"
+- echo "which has both BLAS and LAPACK 3.0"
+- echo
+- # This is a special case so try running a test compile
+- echo "Checking: try to link library against test program"
+- if test -f testlink.f || test -f testlink ; then
+- rm -f testlink*
+- fi
+- cat > testlink.f <<EOF
+-c Test fortran program to link against library
+- PROGRAM TESTLINK
+- IMPLICIT NONE
+- INTEGER A
+- A = 1
+- STOP
+- END
+-EOF
+- case `uname -sr` in
+- Darwin\ 8* )
+- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
+- ;;
+- Darwin\ 7* )
+- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB"
+- ;;
+- *)
+- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib"
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
+- esac
+- echo $test_compile
+- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+- # Compilation was okay
+- echo "... -framework vecLib is okay"
+- # Set the next two variables so that configure
+- # doesn't try to build netlib libraries
+- LAPACKLIB="vecLib"
+- noblas=yes
+- else
+- # Compilation failed
+- XLAPACK_LIB=""
+- echo "... cannot use -framework vecLib"
+- echo
+- fi
+- trylapack=
+- tryblas=
+-# try the fink installation
+- trydirs="${trydirs} /sw"
+- ;;
+-
+- Darwin_intel_compilers)
+- # Darwin has libraries with BLAS and LAPACK invoked using
+- # -F vecLib
+- echo "Darwin can use the vecLib Library (if installed)"
+- echo "which has both BLAS and LAPACK 3.0"
+- echo
+- # This is a special case so try running a test compile
+- echo "Checking: try to link library against test program"
+- if test -f testlink.f || test -f testlink ; then
+- rm -f testlink*
+- fi
+- cat > testlink.f <<EOF
+-c Test fortran program to link against library
+- PROGRAM TESTLINK
+- IMPLICIT NONE
+- INTEGER A
+- A = 1
+- STOP
+- END
+-EOF
+- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib"
+- echo $test_compile