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-rw-r--r--dev-libs/libconfig/ChangeLog7
-rw-r--r--dev-libs/libconfig/libconfig-9999.ebuild61
-rw-r--r--dev-libs/libconfig/metadata.xml12
-rw-r--r--licenses/CeCILL-B515
-rw-r--r--licenses/Mendeley-terms220
-rw-r--r--sci-biology/gfftools/ChangeLog9
-rw-r--r--sci-biology/gfftools/Manifest2
-rw-r--r--sci-biology/gfftools/gfftools-0.98d.ebuild26
-rw-r--r--sci-biology/gfftools/metadata.xml9
-rw-r--r--sci-biology/quicktree/quicktree-1.1-r1.ebuild4
-rw-r--r--sci-libs/armadillo/ChangeLog8
-rw-r--r--sci-libs/armadillo/Manifest1
-rw-r--r--sci-libs/armadillo/armadillo-4.600.2.ebuild112
-rw-r--r--sci-libs/arrayfire/ChangeLog8
l---------sci-libs/arrayfire/arrayfire-0.9999.ebuild1
-rw-r--r--sci-libs/arrayfire/arrayfire-9999.ebuild10
-rw-r--r--sci-libs/givaro/ChangeLog12
-rw-r--r--sci-libs/givaro/Manifest5
-rw-r--r--sci-libs/givaro/givaro-3.2.13.ebuild13
-rw-r--r--sci-libs/givaro/givaro-3.3.0.ebuild20
-rw-r--r--sci-libs/givaro/givaro-3.8.0.ebuild21
-rw-r--r--sci-misc/mendeleydesktop/ChangeLog8
-rw-r--r--sci-misc/mendeleydesktop/Manifest2
-rw-r--r--sci-misc/mendeleydesktop/mendeleydesktop-1.13.ebuild114
-rw-r--r--sci-misc/mendeleydesktop/metadata.xml9
-rw-r--r--sci-physics/geant-vmc/ChangeLog6
-rw-r--r--sci-physics/geant-vmc/geant-vmc-9999.ebuild4
-rw-r--r--sci-physics/qcl/ChangeLog6
-rw-r--r--sci-physics/qcl/qcl-0.6.3-r1.ebuild19
-rw-r--r--sci-physics/qcl/qcl-0.6.4.ebuild12
30 files changed, 1204 insertions, 52 deletions
diff --git a/dev-libs/libconfig/ChangeLog b/dev-libs/libconfig/ChangeLog
new file mode 100644
index 000000000..81bc2ab99
--- /dev/null
+++ b/dev-libs/libconfig/ChangeLog
@@ -0,0 +1,7 @@
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 11 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
+ +libconfig-9999.ebuild:
+ Add ebuild based on libconfig-1.4.9-r1 to the overlay
+
diff --git a/dev-libs/libconfig/libconfig-9999.ebuild b/dev-libs/libconfig/libconfig-9999.ebuild
new file mode 100644
index 000000000..e56d00d59
--- /dev/null
+++ b/dev-libs/libconfig/libconfig-9999.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF="1"
+inherit eutils autotools-multilib
+
+DESCRIPTION="Libconfig is a simple library for manipulating structured configuration files"
+HOMEPAGE="http://www.hyperrealm.com/libconfig/libconfig.html"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+if [[ ${PV} == "9999" ]] ; then
+ EGIT_REPO_URI="https://github.com/hyperrealm/libconfig.git git://github.com/hyperrealm/libconfig.git"
+ inherit git-r3
+ KEYWORDS=""
+else
+ SRC_URI="http://www.hyperrealm.com/${PN}/${P}.tar.gz"
+ KEYWORDS="amd64 ~arm ~mips ppc ppc64 sparc x86 ~x86-linux"
+ PATCHES=( "${FILESDIR}/${P}-out-of-source-build.patch" )
+fi
+
+IUSE="+cxx examples static-libs"
+
+DEPEND="
+ sys-devel/libtool
+ virtual/yacc"
+
+src_prepare() {
+ sed -i configure.ac -e 's|AM_CONFIG_HEADER|AC_CONFIG_HEADERS|g' || die
+ autotools-multilib_src_prepare
+}
+
+multilib_src_configure() {
+ local myeconfargs=(
+ $(use_enable cxx)
+ --disable-examples
+ )
+ autotools-utils_src_configure
+}
+
+multilib_src_test() {
+ # It responds to check but that does not work as intended
+ emake test
+}
+
+multilib_src_install_all() {
+ einstalldocs
+ prune_libtool_files
+
+ if use examples; then
+ find examples/ -name "Makefile.*" -delete || die
+ local dir
+ for dir in examples/c examples/c++; do
+ insinto /usr/share/doc/${PF}/${dir}
+ doins ${dir}/*
+ done
+ fi
+}
diff --git a/dev-libs/libconfig/metadata.xml b/dev-libs/libconfig/metadata.xml
new file mode 100644
index 000000000..b76530ac9
--- /dev/null
+++ b/dev-libs/libconfig/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">
+ Libconfig is a simple library for processing structured configuration files.
+ Libconfig is very compact — a fraction of the size of the expat XML parser library.
+ This makes it well-suited for memory-constrained systems like handheld devices.
+ The library includes bindings for both the C and C++ languages.
+ It works on POSIX-compliant UNIX systems (GNU/Linux, Mac OS X, Solaris, FreeBSD).
+ </longdescription>
+</pkgmetadata>
diff --git a/licenses/CeCILL-B b/licenses/CeCILL-B
new file mode 100644
index 000000000..3ad4deaa3
--- /dev/null
+++ b/licenses/CeCILL-B
@@ -0,0 +1,515 @@
+
+CeCILL-B FREE SOFTWARE LICENSE AGREEMENT
+
+
+ Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+
+The authors of the CeCILL-B (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat ŕ l'Energie Atomique - CEA, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - CNRS, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+INRIA, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, Rocquencourt, BP
+105, 78153 Le Chesnay cedex, France.
+
+
+ Preamble
+
+This Agreement is an open source software license intended to give users
+significant freedom to modify and redistribute the software licensed
+hereunder.
+
+The exercising of this freedom is conditional upon a strong obligation
+of giving credits for everybody that distributes a software
+incorporating a software ruled by the current license so as all
+contributions to be properly identified and acknowledged.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+
+ Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+Agreement: means this license agreement, and its possible subsequent
+versions and annexes.
+
+Software: means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+Initial Software: means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+Modified Software: means the Software modified by at least one
+Contribution.
+
+Source Code: means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+Object Code: means the binary files originating from the compilation of
+the Source Code.
+
+Holder: means the holder(s) of the economic rights over the Initial
+Software.
+
+Licensee: means the Software user(s) having accepted the Agreement.
+
+Contributor: means a Licensee having made at least one Contribution.
+
+Licensor: means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+Contribution: means any or all modifications, corrections, translations,
+adaptations and/or new functions integrated into the Software by any or
+all Contributors, as well as any or all Internal Modules.
+
+Module: means a set of sources files including their documentation that
+enables supplementary functions or services in addition to those offered
+by the Software.
+
+External Module: means any or all Modules, not derived from the
+Software, so that this Module and the Software run in separate address
+spaces, with one calling the other when they are run.
+
+Internal Module: means any or all Module, connected to the Software so
+that they both execute in the same address space.
+
+Parties: mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+ Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software.
+
+
+ Article 3 - ACCEPTANCE
+
+3.1 The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+ * (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+
+3.2 One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+
+ Article 4 - EFFECTIVE DATE AND TERM
+
+
+ 4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1.
+
+
+ 4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+ Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+ 5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+
+
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation thereof.
+
+
+ 5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows effective access to the full Source
+Code of the Software at a minimum during the entire period of its
+distribution of the Software, it being understood that the additional
+cost of acquiring the Source Code shall not exceed the cost of
+transferring the data.
+
+
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+If the Licensee makes any Contribution to the Software, the resulting
+Modified Software may be distributed under a license agreement other
+than this Agreement subject to compliance with the provisions of Article
+5.3.4.
+
+
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+
+ 5.3.4 CREDITS
+
+Any Licensee who may distribute a Modified Software hereby expressly
+agrees to:
+
+ 1. indicate in the related documentation that it is based on the
+ Software licensed hereunder, and reproduce the intellectual
+ property notice for the Software,
+
+ 2. ensure that written indications of the Software intended use,
+ intellectual property notice and license hereunder are included in
+ easily accessible format from the Modified Software interface,
+
+ 3. mention, on a freely accessible website describing the Modified
+ Software, at least throughout the distribution term thereof, that
+ it is based on the Software licensed hereunder, and reproduce the
+ Software intellectual property notice,
+
+ 4. where it is distributed to a third party that may distribute a
+ Modified Software without having to make its source code
+ available, make its best efforts to ensure that said third party
+ agrees to comply with the obligations set forth in this Article .
+
+If the Software, whether or not modified, is distributed with an
+External Module designed for use in connection with the Software, the
+Licensee shall submit said External Module to the foregoing obligations.
+
+
+ 5.3.5 COMPATIBILITY WITH THE CeCILL AND CeCILL-C LICENSES
+
+Where a Modified Software contains a Contribution subject to the CeCILL
+license, the provisions set forth in Article 5.3.4 shall be optional.
+
+A Modified Software may be distributed under the CeCILL-C license. In
+such a case the provisions set forth in Article 5.3.4 shall be optional.
+
+
+ Article 6 - INTELLECTUAL PROPERTY
+
+
+ 6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+
+ 6.2 OVER THE CONTRIBUTIONS
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+ 6.3 OVER THE EXTERNAL MODULES
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+
+ 6.4 JOINT PROVISIONS
+
+The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis-ŕ-vis its staff, any and all
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+
+ Article 7 - RELATED SERVICES
+
+7.1 Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+
+ Article 8 - LIABILITY
+
+8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2 The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+
+ Article 9 - WARRANTY
+
+9.1 The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2 The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+9.3 The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any warranty
+as to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4 The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+
+ Article 10 - TERMINATION
+
+10.1 In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2 A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+
+ Article 11 - MISCELLANEOUS
+
+
+ 11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2 Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3 The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4 In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+
+ 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2 So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3 Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version.
+
+
+ Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2 Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
+
+Version 1.0 dated 2006-09-05.
diff --git a/licenses/Mendeley-terms b/licenses/Mendeley-terms
new file mode 100644
index 000000000..e4e3e32c4
--- /dev/null
+++ b/licenses/Mendeley-terms
@@ -0,0 +1,220 @@
+TERMS OF USE
+
+These terms (“Terms of Use”) apply to the use of our website at http://www.mendeley.com (the "Site"), and our software (the "Software") downloaded from the Site (collectively, the “Services”). Please read these Terms of Use carefully before you start to use the Services. These Terms of Use include the Site’s privacy policy, Copyright and Intellectual Property Policy and any additional terms or product requirements applicable to the Services you use. By using our Services, you are agreeing to these Terms of Use.
+
+We may revise these Terms of Use at any time by amending this page. You are expected to check this page from time to time to take notice of any changes we make, as they are binding on you.
+
+
+1. INFORMATION ABOUT US
+
+1.1. The Services are provided by Mendeley Limited ("we", "us" and "our"). We are registered in England and Wales under company number 6419015 and have our registered office at White Bear Yard, 144a Clerkenwell Road, London, EC1R 5DF, United Kingdom. Our VAT number is 494 6272 12.
+
+
+2. PURPOSE
+
+2.1. The principal purposes of the Services are to:
+
+2.1.1. assist you in the cataloguing and managing of your academic papers and articles ("Academic Papers");
+
+2.1.2. share your academic and scientific knowledge with selected colleagues;
+
+2.1.3. discover academic knowledge and enable detailed search of academic papers;
+
+2.1.4. put you in touch with like-minded people and facilitate research projects;
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+2.1.5. provide data and analytics to help monitor, guide and facilitate the research being undertaken across your institution.
+
+
+3. ACCESSING OUR SITE
+
+3.1. We restrict access to certain parts of our Site to users who have registered with us. If you register with us, you must provide true and accurate information about yourself. Should the registration information provided prove false or misleading (including your personal details), we may suspend or terminate your account.
+
+3.2. We restrict access to the Mendeley Institutional Edition portion of our Site to users who are covered by their institution’s license agreement granting such access, if any. If you are covered by such license agreement, additional terms detailed therein govern your use of the Services.
+
+3.3. If you choose a password or any other piece of information as part of our security procedures, you must take reasonable steps to keep such information confidential and secure, and you must not disclose it to any third party. We have the right to disable any account or password, if in our reasonable opinion, your account information has been compromised. You must tell us immediately if you become aware of or suspect any unauthorised use of your account or access to your password.
+
+
+4. OUR SOFTWARE
+
+4.1. We hereby grant to you a non-exclusive, personal, non-transferable license, in accordance with these Terms of Use, to:
+
+4.1.1. download, install and use the Software for the purposes of cataloguing and managing your Academic Papers, including making a back-up copy of your Academic Papers;
+
+4.1.2. distribute the Software so that other users may install and use the Software for the purposes of cataloguing and managing their Academic Papers; and
+
+4.1.3. make a copy of the Software for back-up purposes.
+
+4.2. When you download our Software and connect it to a Mendeley web account by entering your account details, our Software collects (even while you are offline) certain data which is uploaded to our servers when you synchronize your Software and Mendeley web account, specifically, data relating to:
+
+4.2.1. Academic Papers such as the author name, title and keywords for the purpose of assisting in the:
+
+
+ cataloguing of your and other user's Academic Papers;
+ indexing of academic articles and materials;
+ searching of the indexed academic articles and materials;
+ improving the document recognition process for all users;
+
+4.2.2. reading, cataloguing and accessing your Academic Papers for the purpose of:
+
+
+ generating recommendations for you including articles that you may be interested in reading and these recommendations are displayed in your private account;
+ preparing individualized statistical information which will only be made available to you via your account; and
+ generating anonymous aggregate statistical information regarding the interests, habits and reading patterns of all users and/or certain sub-groups of our users such as all users at your institution.
+
+4.3. Except as we permit in these Terms of Use or as permitted by any local law, you undertake:
+
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+
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+
+4.3.4. not to remove or alter our (or our licensors’) copyright or other proprietary notice on our Software.
+
+4.4. Save for the Content (as defined below), you acknowledge that we are the owner of or the licensee of all intellectual property rights in our Site and in the material published on it, including the Software, and that you have no rights in or to our Software other than the right to use the Software in accordance with these Terms of Use.
+
+
+5. INTERACTIVE AND SOCIAL NETWORKING SERVICES
+
+5.1. We may from time to time provide interactive services on our Site, including, without limitation:
+
+5.1.1. forums for discussion of issues of interest to users and members of our Site;
+
+5.1.2. wikis for users and members to share and collaborate on knowledge relating to issues of mutual interest;
+
+5.1.3. social networking services where registered members can: (i) create online personal profiles; and (ii) interact with other members;
+
+5.1.4. facilities for the uploading and sharing of users' and members' Academic Papers with other users or private user groups you have created;
+
+5.1.5. generation of statistics and recommendations.
+
+5.2. We do not oversee, monitor or moderate the content that you upload to our Site using our interactive services and neither do we vet or screen users of our Site.
+
+
+6. ACCEPTABLE USE
+
+6.1. You may use our Services only for lawful purposes. Accordingly, you may only post versions of Academic Papers or other Content (as defined below) on the Site if you have the right to do so. By way of example, while many journal publishers permit posting of some versions of Academic Papers, most journals restrict the sharing of final versions. To be sure you have the right to upload such content, you should review your publishing agreement, the publisher’s copyright policies, and/or any other applicable information prior to posting any version of an Academic Paper.
+
+6.2. "Content" shall mean any material you post on or through the Site, including, without limitation, Academic Papers and any comments on forums, wikis, personal profiles and communications with members. By using the Site and posting any Content, you permit us to extract metadata and convert to PDF form, for indexing and improved searchability purposes only, any such Content that you post or upload to the Site. We do not claim any ownership rights in your or any other user’s Content. After posting or uploading your Content to the Site, except for the permissions granted to us hereunder, you continue to retain all your rights in such Content.
+
+6.3. By posting your Content you represent and warrant that: (i) your Content is original to you and/or is licensed and fully cleared to permit us to use such Content as contemplated herein; (ii) your Content was produced in compliance with all applicable laws and regulations; (iii) your Content does and will not, in any way, violate or breach any of these Terms of Use; (iv) your Content does not contain libelous, tortious, or otherwise unlawful information, infringe or violate any copyright or other right, or contain any matter the publication or sale of which will violate any federal or state statute or regulation; (v) your Content is not obscene or in any other manner unlawful; (vi) your Content shall not be injurious to the health of any user; and (vii) we shall not be required to pay or incur any sums to any person or entity as a result of our use or exploitation of your Content.
+
+6.4. You may not use our Services:
+
+6.4.1. to send, knowingly receive, upload, download, use or re-use any Academic Papers without authorization. You may perform these actions only if you are the copyright owner, have the copyright owner’s permission, are permitted to do so under your publishing agreement or your institution’s license agreement or under license from an Open Access database or under a Creative Commons license.
+
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+
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+
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+
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+
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+6.4.8. to impersonate any person, or to misrepresent your identity or affiliation with any person;
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+
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+
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+
+6.6. You also agree:
+
+6.6.1. not to access without authority, interfere with, damage or disrupt:
+
+
+ any part of our Site;
+ any equipment or network on which our Site is stored;
+ our Software or any software used in the provision of our Site; or
+ any equipment or network or software owned or used by any third party.
+
+6.6.2. to use our Services only for research related activity (e.g, not to store your personal collection of movies, music and other large file types unrelated to your research activities).
+
+6.7. You may form more than one private group as part of a Mendeley for Teams package only if you intend to be active in all such groups; you may not form more than one private group to act solely as an administrator.
+
+
+7. FAILURE TO COMPLY WITH THESE TERMS OF USE
+
+7.1. To raise complaints regarding alleged copyright or other intellectual property infringement, you must follow the instructions set forth on the Copyright and Intellectual Property Policy page. For all other complaints about the use of our Site or Content (as defined below) posted to our Site, please contact us at complaints [at] mendeley [dot] com. We request that you provide a sufficiently detailed description of the basis of your complaint and your contact information in case additional information is necessary. We will then review your complaint and decide whether there has been a failure to comply with our Terms of Use. If not, we will deal with the matter as described below. We will inform you of the outcome of our review within a reasonable time of receiving your complaint.
+
+7.2. If we determine, in our sole discretion and judgment, that you have failed to comply with these Terms of Use we reserve the right at any time to take all or any of the following actions (and any other action we reasonably deem appropriate):
+
+7.2.1. temporary or permanent withdrawal of your right to use our Site and/or closure of your account;
+
+7.2.2. temporary or permanent removal of any posting or material uploaded by you to our Site;
+
+7.2.3. issue of a warning to you;
+
+7.2.4. legal action against you including proceedings for reimbursement of all costs on an indemnity basis (including, but not limited to, reasonable administrative and legal costs) resulting from the breach;
+
+7.2.5. disclosure of such information to law enforcement authorities or third party complainants as we reasonably feel is necessary or required;
+
+7.2.6. disclosure of your identity to any third party who is claiming that any material posted or uploaded by you to our Site constitutes a violation of their intellectual property rights, right to privacy or other legal rights;
+
+7.2.7. use any technological, legal, operational or other means available to us to enforce the provisions of these Terms of Use.
+
+7.3. You hereby hold harmless and indemnify us and our affiliates, officers, agents and employees from and against any claim, suit or action made by any third party arising from or related to your use of the Services or violation of these Terms of Use, including any liability or expense arising from losses, damages, claims, costs and reasonable attorneys’ fees.
+
+
+8. DELETION OF CONTENT
+
+8.1. Except as set out in 8.2, you may delete your Content at any time using the automated account deactivation tool. When you delete your Content, our right to use it shall cease save that we may retain a copy in backup for a reasonable period of time and as necessary to comply with our legal obligations. However, the deleted Content will not be generally available to other users or registered members.
+
+8.2. Where you make use of the interactive features of our Services to share Content with others, you may not be able to delete such shared Content.
+
+
+9. OUR SITE CHANGES REGULARLY
+
+9.1. We aim to update our Site regularly. If the need arises such as an operational issue, we may suspend access to our Site, or close it indefinitely. Any of the material on our Site may be out of date at any given time, and we are under no obligation to update such material.
+
+9.2. Although we aim to keep the Services available at all reasonable times, we may withdraw, suspend or amend the Services in whole or in part without notice including, for example, in the event of technical failures, upgrades, routine or emergency repair work or some reason outside our control. We will not be liable if for any reason our Services are unavailable at any time or for any period.
+
+
+10. LIMITATION OF LIABILITY
+
+THE SERVICES AND ALL CONTENT ARE MADE AVAILABLE ON AN "AS IS" AND "AS AVAILABLE" BASIS, WITHOUT ANY REPRESENTATION OR WARRANTY OF ANY KIND, EXPRESS OR IMPLIED (INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF TITLE AND NONINFRINGEMENT AND THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE), OR ANY GUARANTY OR ASSURANCE THE SERVICES WILL BE AVAILABLE FOR USE, OR THAT ALL FEATURES, FUNCTIONS OR OPERATIONS WILL BE AVAILABLE OR PERFORM AS DESCRIBED, OR THAT THE SERVICES WILL BE FREE OF VIRUSES OR OTHER HARMFUL COMPONENTS. Without limiting the foregoing, we are not responsible or liable for any malicious code, delays, inaccuracies, errors, or omissions arising out of your use of the Services.
+
+You understand, acknowledge and agree that you are assuming the entire risk as to your use of the Services and the Content, including without limitation the quality, accuracy, performance, timeliness, adequacy, completeness, correctness, authenticity, non-infringement, security and validity of any and all features and functions of the Services, your Content and materials associated with your use of the Services.
+
+YOU UNDERSTAND AND AGREE THAT, TO THE FULLEST EXTENT PERMISSIBLE BY LAW, WE, ANY OF OUR AFFILIATES, OR OUR RESPECTIVE SUCCESSORS AND ASSIGNS, OR ANY OF OUR RESPECTIVE OFFICERS, DIRECTORS, EMPLOYEES, AGENTS, REPRESENTATIVES, LICENSORS, PARTNERS, OPERATIONAL SERVICE PROVIDERS, ADVERTISERS, OR SUPPLIERS, SHALL NOT BE LIABLE FOR ANY LOSS OR DAMAGE, OF ANY KIND, DIRECT OR INDIRECT, IN CONNECTION WITH OR ARISING FROM USE OF THE SERVICES, INCLUDING, WITHOUT LIMITATION, COMPENSATORY, CONSEQUENTIAL, INCIDENTAL, INDIRECT, SPECIAL OR PUNITIVE DAMAGES.
+
+We do not claim ownership, endorse or take responsibility for any third-party product, information, guidelines, materials or services that may be offered, advertised, provided or displayed on the Site or incorporated in the Content, products or services contained on, accessible from or distributed through the Site.
+
+Some jurisdictions do not allow for the exclusion of certain warranties or certain limitations on damages and remedies, accordingly some of the exclusions and limitations described in these Terms of Use may not apply to you.
+
+
+11. RELIANCE ON SITE INFORMATION
+
+11.1. We do not claim that the information on any specific subject contained on our Site is accurate, comprehensive, verified, complete or error free. Commentary and other materials posted on our Site are not intended to amount to advice on which reliance should be placed. You should seek appropriate professional advice.
+
+
+12. UNITED STATES OF AMERICA FEDERAL AGENCIES
+
+12.1. Use by U.S.A. federal agencies will follow the amended terms found here.
+
+
+13. LINKS FROM OUR SITE
+
+13.1. Where our Site contains links to other sites and resources provided by third parties, these links are provided for your information only. We have no control over the contents of those sites or resources, and accept no responsibility for them or for any loss or damage that may arise from your use of them.
+
+
+14. JURISDICTION AND APPLICABLE LAW
+
+14.1. The English courts will have non-exclusive jurisdiction over any claim arising from, or related to, our Services although we retain the right to bring proceedings against you for breach of these conditions in your country of residence or any other relevant country. These terms of use are governed by English law.
+
+
+15. YOUR CONCERNS
+
+15.1. If you have any comments on our Site or our Software, please contact us.
+
+Thank you for visiting our Site and using our Software.
+
+
+These Terms of Use were last updated on February 6, 2014.
+
+Copyright © 2013 Mendeley Ltd. – All Rights Reserved.
diff --git a/sci-biology/gfftools/ChangeLog b/sci-biology/gfftools/ChangeLog
new file mode 100644
index 000000000..cedf1d50c
--- /dev/null
+++ b/sci-biology/gfftools/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/gfftools
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*gfftools-0.98d (12 Jan 2015)
+
+ 12 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +gfftools-0.98d.ebuild, +metadata.xml:
+ sci-biology/gfftools: new package
diff --git a/sci-biology/gfftools/Manifest b/sci-biology/gfftools/Manifest
new file mode 100644
index 000000000..6b0030795
--- /dev/null
+++ b/sci-biology/gfftools/Manifest
@@ -0,0 +1,2 @@
+DIST MANUAL_GFF2PS_v0.96.ps.gz 139407 SHA256 eac552a4acc18a9c91d02233921ba0128d7a123c421909e02ab7be2bf716cb56 SHA512 3f11586b481b90f874898f5f18e6220a2cf7e6a9917455a3b5d6db3601e52604e139e5abdf2c7e9e14a87ae79cd47b81b7e46b42805a017b8586b280777b84bb WHIRLPOOL c45ad22c51c9df0732f039209dbcf3c0e41820526087a11dfe32810888846d4b0c0784a0d87b5aeb1cce10afd21ae6aca120da1eb8e88f40373735136392872b
+DIST gff2ps_v0.98d.gz 45329 SHA256 7d250141b79403fa2f632ae62273352edb6b2f73fd7db3c7fc9510404dc4fdab SHA512 a1c219ac14afb94c6da331179e306197805b2930e5291b20509ea1a979c4c645af8aade4a030f2ce364cba561e90fb5161bfb3ac3259503dc07937ce924033d4 WHIRLPOOL a65e70e45f9dc35237d0d10314b85f7cc18bdad8316232efc4b54187412da828bf4c58afc1c7ac296fbfac0d34e4afc4020df08da8cef7b77cb5a6cf0fc8e915
diff --git a/sci-biology/gfftools/gfftools-0.98d.ebuild b/sci-biology/gfftools/gfftools-0.98d.ebuild
new file mode 100644
index 000000000..6cd5cd1d0
--- /dev/null
+++ b/sci-biology/gfftools/gfftools-0.98d.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="gff2ps can render features annotated in GFF file format into PostScript figures"
+HOMEPAGE="http://genome.crg.es/software/gfftools/GFF2PS.html"
+SRC_URI="ftp://genome.imim.es/pub/gff_tools/gff2ps/gff2ps_v0.98d.gz
+ http://genome.imim.es/software/gfftools/gff2ps_docs/manual/MANUAL_GFF2PS_v0.96.ps.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_install(){
+ mv gff2ps_v0.98d gff2ps
+ dobin gff2ps
+ dodoc MANUAL_GFF2PS_v0.96.ps
+}
diff --git a/sci-biology/gfftools/metadata.xml b/sci-biology/gfftools/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/gfftools/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/quicktree/quicktree-1.1-r1.ebuild b/sci-biology/quicktree/quicktree-1.1-r1.ebuild
index a0d00fd56..5262e73f7 100644
--- a/sci-biology/quicktree/quicktree-1.1-r1.ebuild
+++ b/sci-biology/quicktree/quicktree-1.1-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=2
+EAPI=5
inherit toolchain-funcs
diff --git a/sci-libs/armadillo/ChangeLog b/sci-libs/armadillo/ChangeLog
index ce386e2b2..92146ca41 100644
--- a/sci-libs/armadillo/ChangeLog
+++ b/sci-libs/armadillo/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-libs/armadillo
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*armadillo-4.600.2 (11 Jan 2015)
+
+ 11 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
+ +armadillo-4.600.2.ebuild:
+ Version bump, fix examples install location
+
*armadillo-4.300.9 (28 Jun 2014)
28 Jun 2014; Jauhien Piatlicki <jauhien@gentoo.org>
diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest
index f380fb985..355b29400 100644
--- a/sci-libs/armadillo/Manifest
+++ b/sci-libs/armadillo/Manifest
@@ -1,3 +1,4 @@
DIST armadillo-4.200.0.tar.gz 5479492 SHA256 77d4c64346da9fb90d1150c290919e49530cef45713e830375e04566218335ff SHA512 83afccbf0ed4b8a7873b5fc5d47975600a71d7130e59716d9f044a2cd58343e4d0f5c0037abd1e6d110413d0192c5f0f87a2f3af8183189bd82032414237244d WHIRLPOOL c785cc5b89a542c276ec3cddd56ee40a766960353d7174356c0e891dd8744d08bff350405c3b629a7a4b66a4a8b7564697faa7e9600e57065a3f1cd5e1180bd9
DIST armadillo-4.300.8.tar.gz 5484286 SHA256 1d1a77ad7a74e8b4a74d7b71c5e3fe488e26283907b316618de0a8558c60173a SHA512 3b5d6c9bcefb427e1dc15c259bd24154b6d2138a75be49275e2be5a456f4e2357852c7520b171109ee2b6a716c8ef2a19dea8c2a9b908b13fc2a1624500d54f3 WHIRLPOOL 90789113a10ca0e0264af3212f2c59f6f0b68cf726c22935433bc5d396c763143e6bd1b9d961ee6e5fd78adad3ee58bf1b532931761d9fbe51e99179beebf789
DIST armadillo-4.300.9.tar.gz 5484297 SHA256 1cc96e7eb1cd3872c193f3954561e6d8539d2a4120235213c42c6db44b650d27 SHA512 5129c9ac8e76b6d367691380315d3f4e80e643349a9013238c0672b4d93aabc395d20b9fd95678dcc9172baa793eba5b54011bbf35f69913a7381ca2f62638d0 WHIRLPOOL a3c6c24cbbf85a585bb20c0773800f24065cf57976759543653bddbee0e09559cfad7de30829bc1b5db5583fe1d8c17112b5a463924deaaad5bebf41ec525f7f
+DIST armadillo-4.600.2.tar.gz 5347346 SHA256 d5f85cac54db16d3cf25af54460eb5fde190c81ddbb8690a6c453012934891bf SHA512 b077ad19b7a3e996e9edeceaf980bea53ecaccb012dd2438a70bfc863bd8113e8308325ca91ce033c152bc757a0ac847d81ba99d87b5e4af28ae44dc71ed595b WHIRLPOOL 1d41ab103a7b89e2c11fc4b5b0a9649a690d704dcdd073bcc2de4ddb996a560e6e397309987c848443f294e83af2ae3e269c323ff68c1c8d512ad698861fa35a
diff --git a/sci-libs/armadillo/armadillo-4.600.2.ebuild b/sci-libs/armadillo/armadillo-4.600.2.ebuild
new file mode 100644
index 000000000..35856d707
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-4.600.2.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0/4"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack atlas blas debug doc examples hdf5 lapack mkl tbb test"
+REQUIRED_USE="test? ( lapack )"
+
+RDEPEND="
+ dev-libs/boost
+ arpack? ( sci-libs/arpack )
+ atlas? ( sci-libs/atlas[lapack] )
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+ arpack? ( virtual/pkgconfig )
+ atlas? ( 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/arrayfire/ChangeLog b/sci-libs/arrayfire/ChangeLog
index c21468ac0..37799ee6d 100644
--- a/sci-libs/arrayfire/ChangeLog
+++ b/sci-libs/arrayfire/ChangeLog
@@ -1,7 +1,13 @@
-# ChangeLog for sys-cluster/mpe2
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*arrayfire-0.9999 (12 Jan 2015)
+
+ 12 jan 2015; Marius Brehler <marbre@linux.sungazer.de>
+ +arrayfire-0.9999.ebuild:
+ Symlink to arrayfire-9999, pulls the master branch;
+ default HEAD points to devel
+
*arrayfire-9999 (10 Jan 2015)
10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml,
diff --git a/sci-libs/arrayfire/arrayfire-0.9999.ebuild b/sci-libs/arrayfire/arrayfire-0.9999.ebuild
new file mode 120000
index 000000000..71d00d46a
--- /dev/null
+++ b/sci-libs/arrayfire/arrayfire-0.9999.ebuild
@@ -0,0 +1 @@
+arrayfire-9999.ebuild \ No newline at end of file
diff --git a/sci-libs/arrayfire/arrayfire-9999.ebuild b/sci-libs/arrayfire/arrayfire-9999.ebuild
index 107af240e..352a81483 100644
--- a/sci-libs/arrayfire/arrayfire-9999.ebuild
+++ b/sci-libs/arrayfire/arrayfire-9999.ebuild
@@ -10,9 +10,13 @@ GTEST_PV="1.7.0"
DESCRIPTION="A general purpose GPU library."
HOMEPAGE="http://www.arrayfire.com/"
-EGIT_REPO_URI="https://github.com/arrayfire/arrayfire.git"
+EGIT_REPO_URI="https://github.com/arrayfire/arrayfire.git git://github.com/arrayfire/arrayfire.git"
SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )"
-KEYWORDS="~amd64"
+KEYWORDS=""
+if [[ ${PV} == "0.9999" ]] ; then
+ # the remote HEAD points to devel, but we want to pull the master instead
+ EGIT_BRANCH="master"
+fi
LICENSE="BSD"
SLOT="0"
@@ -78,5 +82,5 @@ src_configure() {
src_install() {
cmake-utils_src_install
- dobin "bin2cpp"
+ dobin "${BUILD_DIR}/bin2cpp"
}
diff --git a/sci-libs/givaro/ChangeLog b/sci-libs/givaro/ChangeLog
index 1df7d4e4e..eb8991107 100644
--- a/sci-libs/givaro/ChangeLog
+++ b/sci-libs/givaro/ChangeLog
@@ -1,7 +1,16 @@
# ChangeLog for sci-libs/givaro
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*givaro-3.8.0 (11 Jan 2015)
+
+ 11 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> +givaro-3.8.0.ebuild:
+ Version bump
+
+ 11 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
+ givaro-3.3.0, givaro-3.2.13:
+ Move to EAPI=5; Cleanup ebuilds, Fix SRC_URI for 3.3.0
+
*givaro-3.3.0 (09 Nov 2009)
*givaro-3.2.13 (09 Nov 2009)
@@ -12,4 +21,3 @@
18 Jul 2008; Francois Bissey <f.r.bissey@massey.ac.nz> ChangeLog:
Initial import, see bug #227803
-
diff --git a/sci-libs/givaro/Manifest b/sci-libs/givaro/Manifest
index 1ea550033..4100d6544 100644
--- a/sci-libs/givaro/Manifest
+++ b/sci-libs/givaro/Manifest
@@ -1,2 +1,3 @@
-DIST givaro-3.2.13.tar.gz 601026 SHA256 cef5972a79038c7fdbbcc80c90917ed0b339614723e9cd12436b55358ef34eb0
-DIST givaro-3.3.tar.gz 643288 SHA256 90677ee9af4a33f827dfce48359c2c419302dfb46227fb8cc16de23f18ac757e
+DIST givaro-3.2.13.tar.gz 601026 SHA256 cef5972a79038c7fdbbcc80c90917ed0b339614723e9cd12436b55358ef34eb0 SHA512 ba792f00003940aedadbea388ff652bc7df3472a9451a950c0818d5424e2656d479ee32a4cf40c2e91f3437c13882a0067040585f9744f309b77067360a267d7 WHIRLPOOL 6840ee4a39f3b2b1f464dd864128825cbfc6adc6b71bf62a81bb8fccc55ec21cfafee971e59be1e5026d22749f813547f73a412190fb5b68e8bd44533f9a1375
+DIST givaro-3.3.0.tar.gz 643288 SHA256 90677ee9af4a33f827dfce48359c2c419302dfb46227fb8cc16de23f18ac757e SHA512 0121917855989b31ce888280229e022fafcdb4f1da4411328d79accac3ce1f057805d4efa23798e3c888b3ddcdcbde8d6e841d415c6509ed4a299287482f5032 WHIRLPOOL ced6bc6ce47e767087feb993922f53e1e160bfa328f9ea12a5b715937bf6aa06ee876abf891f9055da434566642aabb5cd2317dcf302651ec239f65e2f170d53
+DIST givaro-3.8.0.tar.gz 823507 SHA256 d89728d6ae527e80e9cd48fb40daf9b8a16907ed1b7cb621416a1483b69e42a0 SHA512 067a89093501bb4a9627b2141653b4f0636dd2e9323503e6b9c9e6d25e50240d30a6fc9971415ef5c0f227449493a585e4408ebbc4da6f5ee7363faee78f88fb WHIRLPOOL 67ca6f54aa59cab0bae78959ee01bc53486e5b18d6be0649b2447ec30ff588d9026d812757ad85f174d2076caeef64afb6a58c040324f08871e8e991fb61c88f
diff --git a/sci-libs/givaro/givaro-3.2.13.ebuild b/sci-libs/givaro/givaro-3.2.13.ebuild
index ad54cbee8..c6ffca68e 100644
--- a/sci-libs/givaro/givaro-3.2.13.ebuild
+++ b/sci-libs/givaro/givaro-3.2.13.ebuild
@@ -1,16 +1,13 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=2
+EAPI=5
DESCRIPTION="C++ library for arithmetic and algebraic computations"
HOMEPAGE="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/"
SRC_URI="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/Downloads/${P}.tar.gz"
-#### Remove the following line when moving this ebuild to the main tree!
-RESTRICT="mirror"
-
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86 ~ppc64"
@@ -20,11 +17,7 @@ RDEPEND=">=dev-libs/gmp-4.1-r1"
DEPEND="${RDEPEND}"
src_configure(){
- econf "--enable-shared" || die "Configure failed!"
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "Install failed"
+ econf "--enable-shared"
}
pkg_postinst() {
diff --git a/sci-libs/givaro/givaro-3.3.0.ebuild b/sci-libs/givaro/givaro-3.3.0.ebuild
index fb965a0ec..02a9f2745 100644
--- a/sci-libs/givaro/givaro-3.3.0.ebuild
+++ b/sci-libs/givaro/givaro-3.3.0.ebuild
@@ -1,20 +1,14 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=2
-
-inherit versionator
+EAPI=5
DESCRIPTION="C++ library for arithmetic and algebraic computations"
HOMEPAGE="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/"
-MY_P=${PN}-$(get_version_component_range 1-2)
-SRC_URI="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/Downloads/${MY_P}.tar.gz"
-
-#### Remove the following line when moving this ebuild to the main tree!
-RESTRICT="mirror"
+SRC_URI="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/Downloads/${P}.tar.gz"
-LICENSE="GPL-2"
+LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86 ~ppc64"
IUSE=""
@@ -23,11 +17,7 @@ RDEPEND=">=dev-libs/gmp-4.1-r1"
DEPEND="${RDEPEND}"
src_configure(){
- econf "--enable-shared" || die "Configure failed!"
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "Install failed"
+ econf "--enable-shared"
}
pkg_postinst() {
diff --git a/sci-libs/givaro/givaro-3.8.0.ebuild b/sci-libs/givaro/givaro-3.8.0.ebuild
new file mode 100644
index 000000000..79f1db0b5
--- /dev/null
+++ b/sci-libs/givaro/givaro-3.8.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="C++ library for arithmetic and algebraic computations"
+HOMEPAGE="http://ljk.imag.fr/CASYS/LOGICIELS/givaro/"
+SRC_URI="https://forge.imag.fr/frs/download.php/592/${P}.tar.gz"
+
+LICENSE="CeCILL-B"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~ppc64"
+IUSE=""
+
+RDEPEND=">=dev-libs/gmp-4.1-r1"
+DEPEND="${RDEPEND}"
+
+src_configure(){
+ econf "--enable-shared"
+}
diff --git a/sci-misc/mendeleydesktop/ChangeLog b/sci-misc/mendeleydesktop/ChangeLog
new file mode 100644
index 000000000..032fcadaf
--- /dev/null
+++ b/sci-misc/mendeleydesktop/ChangeLog
@@ -0,0 +1,8 @@
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mendeleydesktop-1.13 (08 Jan 2015)
+
+ 13 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>,
+ +mendeleydesktop-1.13.ebuild, metadata.xml:
+ Add version bumped ebuild
diff --git a/sci-misc/mendeleydesktop/Manifest b/sci-misc/mendeleydesktop/Manifest
new file mode 100644
index 000000000..06202a7ca
--- /dev/null
+++ b/sci-misc/mendeleydesktop/Manifest
@@ -0,0 +1,2 @@
+DIST mendeleydesktop-1.13-linux-i486.tar.bz2 32921317 SHA256 d2809a954b24d3ac2b00f7f7858557bd911b79951a212d070bbaacdece627254 SHA512 de46280ba715fb5efd97682c237395e51640ea7d77c766834f4f61535942d76651164bae13536a1dcfc55061c3bab4ebea52e1cebf3dd9bf2625547fd59db0b0 WHIRLPOOL df8214cb24d387358d8c0fe051c3c5817e283d2dc3bc6687fdeaed93566d183775e5ce6cfafa54b110a671a4a12a7d7c25e4569dd74656e2f8cad5126ffd0a89
+DIST mendeleydesktop-1.13-linux-x86_64.tar.bz2 32701145 SHA256 eb2beb599b06938f6b12009ac58382936e6e2594a5202fb2e7b67d9772a174f2 SHA512 854906dfe13a654627e07ff850d598a23736d2a7d2efcdf5127ed58ea1466b4240d7b229081da319486dbda00311b16ee1dc1ec9be0369160da1fdfacb161387 WHIRLPOOL 7aacc9c305b83a2de740f03cf731511c641cf53bda2f887f0d55a86777fe936fad81fe9914fb1d47b0bfcfbf22bc20d7ac775ce373d9586a448be67c8428a80b
diff --git a/sci-misc/mendeleydesktop/mendeleydesktop-1.13.ebuild b/sci-misc/mendeleydesktop/mendeleydesktop-1.13.ebuild
new file mode 100644
index 000000000..8855f7558
--- /dev/null
+++ b/sci-misc/mendeleydesktop/mendeleydesktop-1.13.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils fdo-mime multilib
+
+MY_P_AMD64="${P}-linux-x86_64"
+MY_P_X86="${P}-linux-i486"
+
+DESCRIPTION="A free research management tool for desktop and web"
+HOMEPAGE="http://www.mendeley.com/"
+SRC_URI="amd64? ( ${MY_P_AMD64}.tar.bz2 )
+ x86? ( ${MY_P_X86}.tar.bz2 )
+ amd64-linux? ( ${MY_P_AMD64}.tar.bz2 )
+ x86-linux? ( ${MY_P_X86}.tar.bz2 )"
+
+LICENSE="Mendeley-terms"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND=""
+RDEPEND="
+ dev-qt/qtcore:4
+ dev-qt/qtgui:4
+ dev-qt/qtsvg:4
+ dev-qt/qtwebkit:4
+ dev-qt/qtxmlpatterns:4"
+
+QA_PREBUILT="/opt/mendeleydesktop/.*"
+
+pkg_nofetch() {
+ elog "Please download ${A} from:"
+ elog "http://www.mendeley.com/download-mendeley-desktop/"
+ elog "and move it to ${DISTDIR}"
+}
+
+src_unpack() {
+ unpack ${A}
+
+ cd "${WORKDIR}" || die
+
+ if use amd64 || use amd64-linux ; then
+ mv -f "${MY_P_AMD64}" "${P}" || die
+ else
+ mv -f "${MY_P_X86}" "${P}" || die
+ fi
+}
+
+src_prepare() {
+ # remove bundled Qt libraries
+ rm -r lib/mendeleydesktop/plugins \
+ || die "failed to remove plugin directory"
+ rm -r lib/qt || die "failed to remove qt libraries"
+
+ # force use of system Qt libraries
+ sed -i "s:sys\.argv\.count(\"--force-system-qt\") > 0:True:" \
+ bin/mendeleydesktop || die "failed to patch startup script"
+
+ # fix library paths
+ sed -i \
+ -e "s:lib/mendeleydesktop:$(get_libdir)/mendeleydesktop:g" \
+ -e "s:MENDELEY_BASE_PATH + \"/lib/\":MENDELEY_BASE_PATH + \"/$(get_libdir)/\":g" \
+ bin/mendeleydesktop || die "failed to patch library path"
+}
+
+src_install() {
+ # install menu
+ domenu share/applications/${PN}.desktop
+
+ # install application icons
+ insinto /usr/share/icons
+ doins -r share/icons/hicolor
+
+ # install default icon
+ insinto /usr/share/pixmaps
+ doins share/icons/hicolor/48x48/apps/${PN}.png
+
+ # install documentation, but no license file
+ dodoc share/doc/${PN}/Readme.txt
+
+ # install binary
+ into /opt/${PN}
+ dobin bin/*
+
+ # install libraries
+ dolib.so lib/lib*.so*
+
+ # install programs
+ exeinto /opt/mendeleydesktop/$(get_libdir)/mendeleydesktop/libexec
+ doexe lib/mendeleydesktop/libexec/*
+
+ # install shared files
+ insinto /opt/${PN}/share
+ doins -r share/mendeleydesktop
+
+ # install launch script
+ into /opt
+ make_wrapper ${PN} "/opt/${PN}/bin/${PN} --unix-distro-build"
+}
+
+pkg_postinst() {
+ fdo-mime_desktop_database_update
+ fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+ fdo-mime_desktop_database_update
+ fdo-mime_mime_database_update
+}
diff --git a/sci-misc/mendeleydesktop/metadata.xml b/sci-misc/mendeleydesktop/metadata.xml
new file mode 100644
index 000000000..067828793
--- /dev/null
+++ b/sci-misc/mendeleydesktop/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription>
+Mendeley(TM) is a free reference manager and academic social network that can
+help you organize your research, collaborate with others online, and discover
+the latest research.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-physics/geant-vmc/ChangeLog b/sci-physics/geant-vmc/ChangeLog
index 1a52d9e24..c8c3e8278 100644
--- a/sci-physics/geant-vmc/ChangeLog
+++ b/sci-physics/geant-vmc/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-physics/geant-vmc
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 13 Jan 2015; Oliver Freyermuth <o.freyermuth@googlemail.com>
+ geant-vmc-9999.ebuild:
+ version_number-file not provided anymore.
+
26 Jul 2014; Oliver Freyermuth <o.freyermuth@googlemail.com>
geant-vmc-9999.ebuild:
Fix doxygen-generation, adapt to now working way to run the test-suite
diff --git a/sci-physics/geant-vmc/geant-vmc-9999.ebuild b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
index f0a1ebe86..e73ea6201 100644
--- a/sci-physics/geant-vmc/geant-vmc-9999.ebuild
+++ b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -65,6 +65,6 @@ src_test() {
src_install() {
cmake-utils_src_install
- dodoc README history version_number
+ dodoc README history
use doc && dohtml -r Geant4VMC.html doc/*
}
diff --git a/sci-physics/qcl/ChangeLog b/sci-physics/qcl/ChangeLog
index 587799cd7..d01d0e99b 100644
--- a/sci-physics/qcl/ChangeLog
+++ b/sci-physics/qcl/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-physics/qcl
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 11 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>,
+ qcl-0.6.4.ebuild, qcl-0.6.3-r1.ebuild:
+ Move to EAPI=5, cleanup ebuilds
+
*qcl-0.6.4 (02 Jun 2014)
02 Jun 2014; Jauhien Piatlicki <jauhien@gentoo.org> +qcl-0.6.4.ebuild,
diff --git a/sci-physics/qcl/qcl-0.6.3-r1.ebuild b/sci-physics/qcl/qcl-0.6.3-r1.ebuild
index 6419134e9..c67baa64b 100644
--- a/sci-physics/qcl/qcl-0.6.3-r1.ebuild
+++ b/sci-physics/qcl/qcl-0.6.3-r1.ebuild
@@ -1,8 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=2
+EAPI=5
+
inherit eutils flag-o-matic
DESCRIPTION="Quantum Computation Language with an emulator of a quantum computer"
@@ -21,19 +22,21 @@ DEPEND="media-libs/plotutils
sys-libs/readline"
RDEPEND="${DEPEND}"
+PATCHES=(
+ "${FILESDIR}/${P}"-gcc43.patch
+ "${FILESDIR}/${P}"-makefile.patch
+)
+
src_prepare() {
- epatch "${FILESDIR}"/${P}-gcc43.patch
- epatch "${FILESDIR}"/${P}-makefile.patch
+ epatch ${PATCHES[@]}
}
src_install() {
emake \
QCLDIR="${D}/usr/share/${PN}" \
- QCLBIN="${D}/usr/bin" install \
- || die "emake install failed"
+ QCLBIN="${D}/usr/bin" install
dodoc README CHANGES
if use doc; then
- insinto /usr/share/doc/${PF}
- doins "${DISTDIR}"/{structquprog,qcldoc,quprog}.pdf || die
+ dodoc {structquprog,qcldoc,quprog}.pdf
fi
}
diff --git a/sci-physics/qcl/qcl-0.6.4.ebuild b/sci-physics/qcl/qcl-0.6.4.ebuild
index 9338be1cd..a709a580d 100644
--- a/sci-physics/qcl/qcl-0.6.4.ebuild
+++ b/sci-physics/qcl/qcl-0.6.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -22,8 +22,13 @@ DEPEND="media-libs/plotutils
sys-libs/readline"
RDEPEND="${DEPEND}"
+PATCHES=(
+ "${FILESDIR}/${PN}"-0.6.3-gcc43.patch
+ "${FILESDIR}/${P}"-makefile.patch
+)
+
src_prepare() {
- epatch "${FILESDIR}/${PN}-0.6.3-gcc43.patch" "${FILESDIR}/${P}-makefile.patch"
+ epatch ${PATCHES[@]}
}
src_install() {
@@ -32,7 +37,6 @@ src_install() {
QCLBIN="${D}/usr/bin" install
dodoc README CHANGES
if use doc; then
- insinto /usr/share/doc/${PF}
- doins "${DISTDIR}"/{structquprog,qcldoc,quprog}.pdf || die
+ dodoc {structquprog,qcldoc,quprog}.pdf
fi
}