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authorSébastien Fabbro <sebfabbro@gmail.com>2011-01-10 06:09:24 +0000
committerSébastien Fabbro <sebfabbro@gmail.com>2011-01-10 06:09:24 +0000
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parentmore removing (diff)
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-rw-r--r--docs/proj/#linalg.xml#551
-rw-r--r--sci-libs/shogun/Manifest4
-rw-r--r--sci-libs/shogun/files/shogun-0.9.3-lapack.patch18
-rw-r--r--sci-libs/shogun/metadata.xml22
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diff --git a/docs/proj/#linalg.xml# b/docs/proj/#linalg.xml#
deleted file mode 100644
index 3105039cc..000000000
--- a/docs/proj/#linalg.xml#
+++ /dev/null
@@ -1,551 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
-<!-- $Header: $ -->
-
-<guide link="/proj/en/science/linalg.xml">
-<title>Linear Algebra on Gentoo</title>
-
-<author title="Author">
- <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
-</author>
-
-<abstract>
- This guide explains the use of linear algebra libraries and focus on
- how to use the different implementations of BLAS and LAPACK available on Gentoo.
-</abstract>
-
-<!-- The content of this document is licensed under the CC-BY-SA license -->
-<!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
-<license/>
-
-<version>1.0</version>
-<date>2010-12-22</date>
-
-<chapter>
-<title>Introduction</title>
-<section>
-<body>
-
-<p>
- There are <uri link="http://en.wikipedia.org/wiki/List_of_numerical_libraries">many</uri>
- performant numerical libraries available.
- The Basic Linear Algebra Subprograms (BLAS) and the Linear Algebra PACKage (LAPACK)
- are well designed linear algebra libraries developed by the
- High Performance Computing (HPC) community. BLAS is an API of dense
- matrix and vectors products, while LAPACK provides routines for
- solving systems of linear equations. Both are widely used in
- many scientific applications and it is, therefore, important to
- have efficient implementations available.
-</p>
-
-<p>
- BLAS and LAPACK were originally written in FORTRAN 77. Since then, a
- number of additional language wrappers have been developed for
- languages like C, C++, FORTRAN 95, Java, Python, etc...
- Netlib offers exact implementations of the APIs and they are called
- "reference" libraries. There is also some parallel implementations
- for
-</p>
-
-<ul>
-<li>
- <uri link="http://www.netlib.org/blas/">BLAS</uri>: FORTRAN 77 and C
- (CBLAS) implementations of BLAS
-</li>
-<li>
- <uri link="http://www.netlib.org/lapack/">LAPACK</uri>: FORTRAN 77 and
- C (LAPACKE) implementations of LAPACK
-</li>
-</ul>
-
-<p>
-
-</p>
-
-<ul>
-<li>
- <uri link="http://www.netlib.org/blacs/">BLACS</uri>: FORTRAN 77 and C
- implementations of BLACS
-</li>
-<li>
- <uri link="http://www.netlib.org/scalapack/">ScaLAPACK</uri>: FORTRAN 77 and
- C implementations of PBLAS and ScaLAPACK
-</li>
-</ul>
-
-<p>
- In addition, Gentoo provides a number of optimized implementations
- of the above linear algebra libraries that will be described
- below. You can switch between implementations with the
- Gentoo's <c>eselect</c> system and the widely used <c>pkg-config</c>
- tool.
-</p>
-
-<p>
- It is important to note that if you require, e.g., a well performing
- BLAS implementation, simply emerging X over Y often is not enough. Rather, you will have
- to carefully benchmark your applications since performance may depend
- on many factors,
- such as hardware or network.
- If you are simply looking for a well performing and well tested
- implementation, the reference ebuilds will likely be your best choice.
-</p>
-
-
-</body>
-</section>
-</chapter>
-
-<chapter>
-<title>For Users</title>
-<section>
-<title>Installing</title>
-<body>
-
-<p>
- If best possible performance is not of paramount importance for you
- and you simply need BLAS and/or LAPACK, just emerge the virtual
- package:
-</p>
-
-<pre caption="Installing">
-# <i>emerge lapack</i>
-</pre>
-
-<p>
- This will install both <><> and <><> the reference packages from
- <uri>http://www.netlib.org/</uri> . They are well tested, easy to debug
- implementations. They should satisfy most users; if they're all you need, you're
- done reading.
-</p>
-
-<p>
-However, if:
-</p>
-
-<ul>
- <li>linear algebra libraries are critical for the speed of your applications</li>
- <li>you absolutely need to build the fastest computer</li>
- <li>you want to help Gentoo sci project to improve their packages</li>
-</ul>
-
-<p>
-... then read on, and be sure to file bugs both to Gentoo and upstream.
-</p>
-
-<p>
- There is a number of optimized implementations of these libraries in the Portage
- tree:
-</p>
-
-<ul>
- <li>
- <uri link="http://math-atlas.sourceforge.net">ATLAS</uri>: Automatically
- Tuned Linear Algebra Software is an open-source package that empirically
- tunes the library to the machine it is being compiled on. It provides BLAS
- (FORTRAN 77 and C), and LAPACK implementations on various architectures.
- </li>
- <li>
- <uri
- link="http://www.tacc.utexas.edu/tacc-projects/gotoblas2/">GotoBLAS</uri>:
- Goto BLAS provides open-source, free for academic use, hand-coded
- machine language, processor optimized versions of the FORTRAN 77
- and C BLAS routines. Still claims to be the fastest BLAS.
- </li>
- <li>
- <uri link="http://developer.amd.com/cpu/libraries/acml/Pages/default.aspx">ACML</uri>:
- AMD Core Math Library is a closed-source but free package containing BLAS (FORTRAN 77
- only) and LAPACK for x86 and x86_64 architectures, but also other math tools
- such as statistical libraries and FFTs.
- </li>
- <li>
- <uri link="http://software.intel.com/en-us/articles/intel-mkl/">MKL</uri>:
- Intel® Math Kernel Library is a closed-source but free package for
- non-commercial use on Linux systems containing implementations of all the linear
- algebra libraries mentioned here.
- </li>
-</ul>
-
-<p>
- Usually performance gain is noticeable mainly with BLAS, since LAPACK routines
- depend on BLAS kernels.
-</p>
-
-</body>
-</section>
-
-
-<section>
-<title>Developping with the installed linear algebra libraries</title>
-<body>
-
-<p>
- We took great care to make sure that each package provides
- consistent pkg-config files generated by us.
- Compiling and linking becomes straightforward:
-</p>
-
-<pre caption="Compiling and linking linear algebra libraries">
-# <i>pkg-config --libs blas</i> <comment>(To link with FORTRAN 77 BLAS library)</comment>
-# <i>pkg-config --cflags cblas</i> <comment>(To compile against C BLAS library)</comment>
-# <i>pkg-config --libs cblas</i> <comment>(To link with C BLAS library)</comment>
-# <i>pkg-config --libs scalapack</i> <comment>(To link with the ScaLAPACK library)</comment>
-</pre>
-
-<p>
- <c>pkg-config</c> files are available for all implementations and
- various alternatives within implementations. The default names of
- the implementations are: blas, cblas, lapack, lapacke, blacs and
- scalapack, and they can be chosen with <c>eselect</c>. You can also always compile or link
- with an library not selected for the
- More information on using <c>pkg-config</c> can be obtained with <c>man pkg-config</c>.
-</p>
-
-</body>
-</section>
-<section>
-<title>Selecting libraries</title>
-<body>
-
-<p>
- You can switch BLAS, CBLAS and LAPACK implementations with
- <c>eselect</c>. you can view which implementations of CBLAS
- are available.
-</p>
-
-<pre caption="Viewing available implementations of CBLAS">
-# <i>eselect cblas list</i>
-Installed CBLAS for library directory lib64
-[1] atlas
-[2] atlas-threads
-[3] gsl
-[4] mkl-threads *
-[5] reference
-</pre>
-
-<p>
- The implementation marked with an asterisk (*) is the currently
- selected implementation. To switch implementations, run:
-</p>
-
-<pre caption="Switching to the threaded ATLAS implementation of BLAS">
-# <i>eselect blas set atlas-threads</i>
-</pre>
-
-<p>
- To learn more about the <c>eselect</c> tool, visit the
- <uri link="http://www.gentoo.org/proj/en/eselect/user-guide.xml">eselect guide</uri>
-</p>
-
-<p>
- When selecting your linear algebra profiles try to avoid mixing
- different implementations since we don't have any mechanism to enforce
- reasonable profiles. However, here is a list of well performing
- profile combinations that have been used successfully in the past:
-</p>
-<ul>
- <li> performant on most CPUs:
- <ul>
- <li>blas, cblas: atlas (or atlas-threads with multi-processor)</li>
- <li>lapack, lapacke: atlas</li>
- </ul>
- </li>
- <li> performant on most CPUs:
- <ul>
- <li>blas, cblas: goto2 </li>
- <li>lapack, lapacke: reference</li>
- </ul>
- </li>
- <li> performant on AMD based CPUs:
- <ul>
- <li>blas, lapack: acml-gfortran (or acml-gfortran-openmp with
- multi-processors) </li>
- <li>cblas: reference</li>
- </ul>
- </li>
- <li> performant on Intel based CPUs:
- <ul>
- <li>blas,cblas,lapack: mkl-threads</li>
- </ul>
- </li>
-</ul>
-
-</body>
-</section>
-
-<section>
-<title>Choosing a compiler</title>
-<body>
-
-<p>
- All the above libraries have been tested with the GNU compiler
- collections (gcc, gfortran).
- There are many available C compilers and a few FORTRAN (ifort,
- Open64) compilers on Gentoo and many other FORTRAN compilers outside
- of Gentoo ().
-</p>
-
-<pre caption="Installing BLAS with the Intel FORTRAN compiler">
-# <i>F77=ifort FFLAGS="-O2 -mp1" emerge blas-reference</i>
-</pre>
-
-<p>
- Depending on your hardware, a small performance gain can be noticed thanks to
- vectorization. The <c>-mp</c> flag maintains floating-point precision, since by
- default ifort is pretty aggressive on floating point arithmetic, and we are
- actually compiling a math package. Try <c>man ifort</c> to see additional flags
- to fit your hardware.
-</p>
-
-<p>
- Some of the implementations let you specify the Intel® C compiler as
- well. Please beware that not all libraries compile with all
- combinations. You should receive an error during the emerge in case you have
- chosen an incompatible combination.
-</p>
-
-<p>
- As usual for Gentoo, there are many combinations of USE flags and
- compilers with which you could compile a package. Unfortunately
- switching compilers between BLAS and LAPACK might not be always
- compatible. For example:
-</p>
-
-<pre caption="Looking for trouble combinations">
-# <i>USE=ifort emerge acml</i>
-# <i>eselect blas set acml-ifort-openmp</i>
-# <i>FC=gfortran FFLAGS="-O2" emerge lapack-reference</i>
-</pre>
-
-<p>
- This will most likely break things or not even compile.
-</p>
-
-<p>
- Try to be consistent in your choice. Stay with the GCC most of the time will
- avoid you some trouble, unless you want to use the MKL, in which case the Intel
- compilers make a good combination.
-</p>
-
-</body>
-</section>
-<section>
-<title>Documentation</title>
-<body>
-
-<p>
- If you need BLAS or LAPACK to develop your own programs, the documentation
- becomes pretty handy. Setting the USE="doc" flag for the corresponding BLAS or
- LAPACK package will install man pages and quick reference sheets from the
- <c>app-doc/blas-docs</c> and <c>app-doc/lapack-docs</c> packages. They are
- standard and valid for all implementations. For optimized packages, the
- USE="doc" flags will usually install extra doc in PDF or HTML format.
-</p>
-
-</body>
-</section>
-</chapter>
-
-<chapter>
-<title>For ebuild developers</title>
-<section>
-
-<section>
-<title>Packages with BLAS/LAPACK dependencies</title>
-<body>
-
-<p>
- You need two things:
- set [R]DEPEND to <c>virtual/<imp></c>. To build some
- packages, you m need to use the pkg-config tool. If you are lucky, the
- package uses autotools together with the autoconf <>AX_BLAS and <>AX_LAPACK M4
- macros. In this case, the configuration step becomes simple. For example:
-</p>
-
-<pre caption="Sample package configuration with autotools">
-<keyword>econf</keyword> --with-blas="<var>$(pkg-config --libs blas)</var>"
-</pre>
-
-</body>
-</section>
-
-
-
-<title>Providing new implementations</title>
-<body>
-
-<p>
- The Portage tree contains many ebuilds that depend on the
- BLAS/CBLAS/LAPACK/BLACS/ScaLAPACK libraries. As there is more than
- one possible implementation, the Gentoo Science Project
- reorganized all the packages to provide <c>virtual</c>. All ebuilds using
- should depend on this virtual package, unless it is explicitly
- known to break with a specific implementation.
-</p>
-
-<p>
- To work with Gentoo's configuration tools
- <c>app-admin/eselect-{blas,cblas,lapack}</c>, and the virtual, every ebuild that
- installs a BLAS implementation must fulfill following requirements:
-</p>
-
-<ol>
-<li>
- The ebuild must install an eselect file for each profile it provides. The
- libraries should link to the ones in <path>/usr/$(get_libdir)</path>
- directories and the include files in <path>/usr/include</path>:
- <ul>
- <li>
- <path>libblas.so[.0]</path> - Shared object for FORTRAN BLAS
- applications
- </li>
- <li>
- <path>libblas.a</path> - Static library for FORTRAN BLAS applications
- </li>
- <li>
- <path>libcblas.so[.0]</path> - Shared object for C/C++ CBLAS applications
- </li>
- <li>
- <path>libcblas.a</path> - Static library for C/C++ CBLAS applications
- </li>
- <li><path>cblas.h</path> - Include header for C/C++ applications</li>
- <li>
- <path>liblapack.so[.0]</path> - Shared object for FORTRAN LAPACK
- applications
- </li>
- <li>
- <path>liblapack.a</path> - Static library for FORTRAN LAPACK applications
- </li>
- </ul>
- </li>
- <li>
- The ebuild must install a <path>blas.pc</path>, <path>cblas.pc</path> and/or
- <path>lapack.pc</path> pkg-config file and therefore RDEPEND on
- <c>dev-util/pkgconfig</c>. They should also be included in the eselect
- files, and link to the <path>/usr/$(get_libdir)/pkgconfig</path> directory:
- <ul>
- <li><path>blas.pc</path> - BLAS pkg-config file</li>
- <li><path>cblas.pc</path> - CBLAS pkg-config file</li>
- <li><path>lapack.pc</path> - LAPACK pkg-config file</li>
- </ul>
- </li>
- <li>Be included in the virtual package as a possible provider:
- <ul>
- <li><c>virtual/blas</c> - BLAS virtual package</li>
- <li><c>virtual/cblas</c> - CBLAS virtual package</li>
- <li><c>virtual/lapack</c> - LAPACK virtual package</li>
- </ul>
- </li>
-</ol>
-
-<p>
- The easiest way of understanding all this is probably getting inspiration from
- one of the available packages. Currently the Portage tree provide the following
- virtual packages:
-</p>
-
-<table>
-<tr>
- <th>Package name</th>
- <th>virtual/blas</th>
- <th>virtual/cblas</th>
- <th>virtual/lapack</th>
- <th>virtual/lapacke</th>
- <th>virtual/blacs</th>
- <th>virtual/scalapack</th>
-</tr>
-<tr>
- <ti><c>sci-libs/acml</c></ti>
- <ti>*</ti>
- <ti></ti>
- <ti>*</ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
-</tr>
-<tr>
- <ti><c>sci-libs/atlas</c></ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti></ti>
- <ti></ti>
-</tr>
-<tr>
- <ti><c>sci-libs/gotoblas2</c></ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
-</tr>
-<tr>
- <ti><c>sci-libs/blas-reference</c></ti>
- <ti>*</ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
-</tr>
-<tr>
- <ti><c>sci-libs/cblas-reference</c></ti>
- <ti></ti>
- <ti>*</ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
-</tr>
-<tr>
- <ti><c>sci-libs/gsl</c></ti>
- <ti></ti>
- <ti>*</ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
-</tr>
-<tr>
- <ti><c>sci-libs/lapack-reference</c></ti>
- <ti></ti>
- <ti></ti>
- <ti>*</ti>
- <ti></ti>
- <ti></ti>
- <ti></ti>
-</tr>
-<tr>
- <ti><c>sci-libs/mkl</c></ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti>*</ti>
- <ti>*</ti>
-</tr>
-</table>
-
-</body>
-</section>
-
-</chapter>
-
-<chapter>
-<title>Benchmarks</title>
-<section>
-<body>
-
-<p>
- If you feel inclined to write an ebuild for these, you
- are more than welcomed to file it on our <uri
- link="http://bugs.gentoo.org">Bugzilla</uri>.
-</p>
-
-</body>
-</section>
-</chapter>
-
-</guide>
diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
deleted file mode 100644
index a8c260cf2..000000000
--- a/sci-libs/shogun/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX shogun-0.9.3-lapack.patch 583 RMD160 e1e70f045fa448601e8f43b6a7603030981dbf97 SHA1 abef54b23c9041ef65faa7e0324e89fed52749c4 SHA256 b86cbcb4f0003754393c6e55f501b0721d3479ee6bed48c876f1ee564b9a2825
-DIST shogun-0.9.3.tar.bz2 2853271 RMD160 9638a6b747a1177b048720b8999c60f33c7df5ef SHA1 d559dff3e11f777a23f00278d78d259ad896b829 SHA256 597d08155c7eff894dfae64dff8d4b37a5aba1da4a87b335881bddcb1a587526
-EBUILD shogun-0.9.3.ebuild 1625 RMD160 79dfc02d159c84b6cfcd749150779979e8273cdc SHA1 17df8f64dbe4270ead4158f54a6928fa05095a76 SHA256 42e0e74ebf89cff12b1c461264067ccf32350abd63899404add950aa8d290968
-MISC metadata.xml 1297 RMD160 dcc89a39c7d7a60ae5c128b8778cd314646e1417 SHA1 9ffe75693797b1eeb466223d6332cd589b32c624 SHA256 84677e9d55cab8bed4c8d99fdb917a6a31d21904526f20b95137716e6fed63e0
diff --git a/sci-libs/shogun/files/shogun-0.9.3-lapack.patch b/sci-libs/shogun/files/shogun-0.9.3-lapack.patch
deleted file mode 100644
index 32e41aa1d..000000000
--- a/sci-libs/shogun/files/shogun-0.9.3-lapack.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- src/configure.orig 2010-06-01 19:49:30.000000000 +0100
-+++ src/configure 2010-06-01 19:52:05.000000000 +0100
-@@ -2421,13 +2421,13 @@
- }
- EOF
- echocheck "AMD ACML support"
-- if cc_check -lacml -lcblas -lgfortran
-+ if cc_check $(pkg-config --libs cblas lapack)
- then
- echores "yes"
- HAVE_ACML='#define HAVE_ACML 1'
- HAVE_LAPACK='#define HAVE_LAPACK 1'
- DEFINES="$DEFINES -DHAVE_ACML -DHAVE_LAPACK"
-- LINKFLAGS="$LINKFLAGS -lacml -lcblas -lgfortran"
-+ LINKFLAGS="$LINKFLAGS $(pkg-config --libs cblas lapack)"
- else
- echores "no"
-
diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
deleted file mode 100644
index b5cdff054..000000000
--- a/sci-libs/shogun/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<longdescription>
- SHOGUN is a new machine learning toolbox with focus on large scale kernel
- methods and especially on Support Vector Machines (SVM) with focus to
- bioinformatics. It provides a generic SVM object interfacing to several
- different SVM implementations. Each of the SVMs can be combined with a variety
- of the many kernels implemented. It can deal with weighted linear combination
- of a number of sub-kernels, each of which not necessarily working on the same
- domain, where an optimal sub-kernel weighting can be learned using Multiple
- Kernel Learning. Apart from SVM 2-class classification and regression
- problems, a number of linear methods like Linear Discriminant Analysis (LDA),
- Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to
- train hidden markov models are implemented. The input feature-objects can be
- dense, sparse or strings and of type int/short/double/char and can be
- converted into different feature types. Chains of preprocessors (e.g.
- substracting the mean) can be attached to each feature object allowing for
- on-the-fly pre-processing.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/shogun/shogun-0.9.3.ebuild b/sci-libs/shogun/shogun-0.9.3.ebuild
deleted file mode 100644
index 321959d93..000000000
--- a/sci-libs/shogun/shogun-0.9.3.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Large Scale Machine Learning Toolbox"
-HOMEPAGE="http://www.shogun-toolbox.org/"
-SRC_URI="http://shogun-toolbox.org/archives/shogun/releases/${PV:0:3}/sources/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="boost bz2 cplex doc glpk gzip hdf5 lapack lpsolve lzma lzo octave python R readline threads"
-
-RDEPEND="virtual/lapack
- bzip2? ( app-arch/bzip2 )
- cplex? ( sci-mathematics/cplex-bin )
- glpk? ( sci-mathematics/glpk )
- gzip? ( app-arch/gzip )
- hdf5? ( sci-libs/hdf5 )
- glpk? ( sci-mathematics/lpsolve )
- lzma? ( app-arch/xz-utils )
- lzo? ( dev-libs/lzo )
- octave? ( sci-mathematics/octave )
- python? ( dev-python/numpy )
- R? ( dev-lang/R )
- readline? ( sys-libs/readline )"
-
-DEPEND="${RDEPEND}
- dev-libs/boost
- dev-util/pkgconfig
- doc? ( app-doc/doxygen )"
-
-S="${WORKDIR}/${P}/src"
-
-src_configure() {
- # not an autotools configure (based on mplayer one)
- # disable svmlight based on debian comment
- ./configure \
- --cc=$(tc-getCC) \
- --cxx=$(tc-getCXX) \
- --prefix=/usr \
- --datadir=/usr/share/${PN} \
- --mandir=/usr/share/man \
- --confdir=/etc \
- --libdir=/usr/$(get_libdir) \
- --disable-cpudetection \
- --disable-svm-light \
- $(use_enable doc doxygen) \
- $(use_enable boost boost-serialization) \
- $(use_enable glpk) \
- $(use_enable hdf5) \
- $(use_enable lapack) \
- $(use_enable readline) \
- $(use_enable threads hmm-parallel)
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "emake install failed"
-}