sci-libs/shogun: Fix buildproblems with atlas detection, #507304; be multilib friendl...

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-libs/shogun/ChangeLog b/sci-libs/shogun/ChangeLog
index a8873c3dac67dc13541ecf5003840d0224f2bc9f..2d7f3bb7e15ad9e51186a4dba8c2552796235302 100644 (file)
--- a/sci-libs/shogun/ChangeLog
+++ b/sci-libs/shogun/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-libs/shogun
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/ChangeLog,v 1.8 2014/04/06 01:47:16 bicatali Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/ChangeLog,v 1.9 2015/01/25 17:41:02 jlec Exp $
+
+  25 Jan 2015; Justin Lecher <jlec@gentoo.org> shogun-3.2.0.ebuild,
+  +files/shogun-3.2.0-atlas.patch, metadata.xml:
+  Fix buildproblems with atlas detection, #507304; be multilib friendly,
+  #531034; do not fetch gmock for tests, #528566
 
 *shogun-3.2.0 (06 Apr 2014)
 

diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index 4e9ae6295dcb6c67ffca9847d81e088421d724cc..8e8f08fc00786b348811d0c4c8a60672e8c82b10 100644 (file)
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,7 +1,11 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX shogun-1.1.0-as-needed.patch 2137 SHA256 de8bb8e6f42873b0fbc3c4f816869684b93d0ecceb6ea6db7c77e9e86bf79617 SHA512 c755d1f557eecd433ff8b2394ebb5d9687a5482ea081f2c9dd174492f5ab24f5bc4d50665491f40dbc01f8db1c6f5eec63c2e869f3f1ee3395e6587b227ef57a WHIRLPOOL 22421d20f345e3a8141d76fd6e0beebee32c9e1a0006f95331a3aaa2ef1736ddc18e5b0e3996ce42d0e9a540c8a91356832c7f84d6889edcb438769117a1f758
 AUX shogun-1.1.0-respect-ldflags.patch 342 SHA256 b92aa34f8410aa7f30286005cd7eb56616888cead0d4f96c1e8defe262e8e29f SHA512 46a920c6abaac325e394cd82055bbda4770f21b0ae4a9505d65945e2e1ee0e3e807384631f5d7b8e123e019352a48d8d35f630302e04b7ed229fc4d150e87c64 WHIRLPOOL 6599c7e7913d68cfff2d1a81789d0c16acbc70c17ffa947d64d5fda65d2db485e38803043ec0074dc701d8a7c16783abadb8dda3c32b24e6bac1f9409f35db25
 AUX shogun-1.1.0-test-readline.patch 352 SHA256 a8e0ecc78bf702bdfb8193fc94abd7745e8bfcee0fe1e6b4ba5efeac4c6df0cc SHA512 6963b8e66361b02b894d48e5b8b2dbc15b4569947ba5be7db56c4aeff142f2c949583cfbbc713cc5900815072e80999dd804f8a342011247b34c7ac30db0fd86 WHIRLPOOL f22f31a231a56f4d805539388ae96e4742f7bf99a0a49887daefad14bb1d13454e800050528df48b5bed0e5db51dd9d867812e148ec4e5533fd8b19758541bdf
 AUX shogun-1.1.0-test-snappy.patch 506 SHA256 ef0489b05cd1dd494c4a9b5070277dbd7733b920cfcf045e87d6abcbd871f01f SHA512 04b4f29ec7d23377fb31474c9ef9c7d243b8ed9ef8e81c6340462763a4dc6ac6361c4e067d680089192ccd5bf5d50ffc2fca6087d74e17341c9b4ae858851096 WHIRLPOOL 302365d7ecd2ed235536a886a3ff1d2834bf51885e4acd4dd0d2a581e8776c7cdcee8632a8470c6b2df969df7fe0cba1d5574c7c870323a866825a0235eb0b76
+AUX shogun-3.2.0-atlas.patch 936 SHA256 2c5d5a70bd1ddc10ff0251c5a648d5110850a01cc3b81715fc56f63a419412e9 SHA512 35df38bbeb0265a6e02f5b07a05746b796a3f201ee158947477e915b9f25e2666bf2a28a2c0d632181c27665d6da0d6e8f45c31eada6eeeaba8eea4e091676c4 WHIRLPOOL 924313a4350dee015268dab6550261f66ff1ae804656c7f5acc27c46b0bf8eb78eb7c039c148763bba1e602c8c512d7b2d9db0a6f327c29de5ed15f4e858745c
 DIST shogun-1.1.0.tar.bz2 3485714 SHA256 9f69638f0bc18995358c38cd6eed6437e6b90c1fceab7c6e64c9739b7e6cc40b SHA512 853168e3d68ad02ef543391b78c51682d004af46acddfa09a76b41e373e27199fc9be0598892207e116a82f24437e3f1c0dc97c3e28ca32879594fbe112bd157 WHIRLPOOL dd044ff2cc9fd9376b80f1efd9bbcf901b11765a2f85eb2325ddd640ea547e513df8c9da548634e49758ef124147666f86b6b4082e118c6d35ef2d5010527cf9
 DIST shogun-2.0.0.tar.bz2 4106437 SHA256 b18e30515b9f4432d02602d0dd66dbc57c70a46f71636275071afaee94e245ee SHA512 e7c8d515afbcb3198aade32d2962e8d94b669b9c79ddbcd7425f04bbb0379803f7353c50ba8897356842cddb401d303fefaf8a7f9dd6a2e751e176deba1e46f1 WHIRLPOOL aa9ef89f28acc012ee2894c4ff6858f7bf01585d02160d5b2df33159c7c87593ea352833765a7a78cc0ed16fd10713d285eb711606f0e3771ec685778f703570
 DIST shogun-3.2.0.tar.bz2 4217245 SHA256 bc416b615ed90aef80c58a30546c5e2da779347bebb8742ecf11657073fc8f72 SHA512 7c420da7bf10c8971954964bce4dc13a8f64c6ff2a0976293f54947414ad2fe7171b1747cef3e2ceb969cf936d8fe862e940582f642cd2367897cda3191b186b WHIRLPOOL bce007c01ebee0e225d5cf858e042561a540416b349015ac566cce82b77096e8206b2f9e51572d9ee8149651a39aa30d6438b28d37ba43eb5aba593b10c5e497
@@ -10,6 +14,25 @@ DIST shogun-data-0.4.tar.bz2 127377123 SHA256 103ef944c7211f64957833cd6ace85e326
 DIST shogun-data-0.8.tar.bz2 261905079 SHA256 a2a0c8ccd754f0b893d97d77cfb60e25fcdb4e7033731434fb07e5483514a047 SHA512 9ea48706aae5ca116e8cf3507d1fcd06e24a8384abe6f2ebaf3c81735237d3beceee26ce5af97b85af24409eb47da684f7e7a56c0800a82c40ed214e6382978f WHIRLPOOL 3a3120a8e982c90c670ec0c206635abdcb152ae5f312172ec58ae21e1ee11f15c406b382bd3b8e8a63300302290590b83a977bd4d90375160ceb8ae516409c12
 EBUILD shogun-1.1.0.ebuild 4480 SHA256 f7231e45448652f2e983811e8d36b8a7566d03121b5a7ba005a444c3dfd73c5d SHA512 cf28663e5b959bbe687ac0dcf31075bcb7959df4e70a808dff7f7a1e8f013f7c769926a39afdfe0db21cd25b6a2b5cf4687edcc67359b3c140fe62db8b8feed9 WHIRLPOOL cc20a34f43dfe3ba7d8ab4872cdd52eb30c3b133f38a3f5ae6050a08f0a43b98e8fd07906bd21be418399acc24f49402473c661e48c4c92660b517de96510019
 EBUILD shogun-2.0.0.ebuild 4652 SHA256 3e7f91775312731802079f6e149879895deabf867eca9d181bbf66529cd90981 SHA512 d1c38d785fb59611734629964d52c435812c13715d4fa67d5758371dc525c9beb3501d915101077c957a768517411bdca99b4d1a0c604b4d33ac08202db3434e WHIRLPOOL 1aa1789938334c754cdb0dedabae3a4d363c90f25885596bb87d31ce431dbf0bc3489ea2680e314dba583723f244267a90847da9b70ec931e737888877dcd5fa
-EBUILD shogun-3.2.0.ebuild 3445 SHA256 6aff106eb27184ae26a1e3a91345ef0119223c00806f04b83ae604ad875fe5a8 SHA512 d2b4ce65b147b6e80a07d6317c5d8e9cb0e66b325d3f3b0dbbb896616279d566d8672f0ae5aee5d6f5496c4b912e132f224c76d0573dfd1d674cb5da55c3abcf WHIRLPOOL 1f5eabab43fd708eae8b8d3a2fbbedeba99c085ff5f6ec6f0b463ab41bf2a15eac440a6b879ac7734fa0e9cff5be9651040da7c355620ba8ab2f2bca8fbaccc5
-MISC ChangeLog 1480 SHA256 ee19a95f20455c3c8e6853f585d830738a034c6e19712b45d5478802bc199399 SHA512 88a952d67f2b9444c2977750191fd6561bd2b1d456d847cd8384f852eb696da8284a9617f6d694f62b4d8f6a1d954bb7fd91f7d5b4a34c6f3ef83f0ac0c35a50 WHIRLPOOL f3ffdcab434f3e937de18c73c508e67319a02c80a9cc4ec647cd0918b91fcb1047da2e827d830a4374e48b5e69b4b069f2b0b8b4031142bca42628662c0aabc7
-MISC metadata.xml 2098 SHA256 4ff8f59c473d1cb5e52955fb29b51055ca85f511e29e167f9cdfec12f0025556 SHA512 94502d0fe4f7f56cf61a78bbc27c58ccd744967bb43792bd90667ed921d5a814aa5e6d3ac3b17b46d31dd68b3be177b53f81803f75b86c10a202279bedc59a7f WHIRLPOOL c7c995210f40d450a718f4257e9144d0eaf23fe8dae2441241336e1a6c7d12dba817117f1de9ff319cbfe992fd90e538918d40f5accc68a5337e6125170451f3
+EBUILD shogun-3.2.0.ebuild 3589 SHA256 30346046e5d122e49b2ee0b87acda1d1203985e80eb67ec9eb64fe023ce5f21f SHA512 093f84f048c1c5bc469031859509af70672007b620824920d4f5b471a7edf09a3e29dd4265c1c4e65070bc0cce9c23b95d92b17e7cfc5c0b208d97321b5be15e WHIRLPOOL 1115cf00e5941b38b871da33f04a1960536f507a1772e9cea147516c3953946c5f49f8918ff31f9ae09978a5ea35adcdcd18d1cd2f16e6f1141ff997869a455a
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+MISC metadata.xml 2126 SHA256 a4cb0acb7f2353453604cee3e25b9ad1678c8b022189f4f076c78fd4396da496 SHA512 660923062388b95673e81d4cd70fd65575a3d5a862f7c2a34425dbccbb3a3d58b7420be15fd132089bf60e2c42ababa7000e1367c25b52f626f615693151a205 WHIRLPOOL f820228dbedf890e0cebd3efe28362ed124403a1c65357106bfcdd055b2d2ad19e0008959ae06069319d2675988e8e7a2c57306fea93e060587c84fc678e9567
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0
+
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+-----END PGP SIGNATURE-----

diff --git a/sci-libs/shogun/files/shogun-3.2.0-atlas.patch b/sci-libs/shogun/files/shogun-3.2.0-atlas.patch
new file mode 100644 (file)
index 0000000..a4f5e1c
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-3.2.0-atlas.patch
@@ -0,0 +1,22 @@
+ cmake/FindAtlas.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/cmake/FindAtlas.cmake b/cmake/FindAtlas.cmake
+index 13f092d..8c2dd2f 100644
+--- a/cmake/FindAtlas.cmake
++++ b/cmake/FindAtlas.cmake
+@@ -20,10 +20,10 @@ if(ATLAS_LAPACK)
+   endif()
+   unset(CMAKE_REQUIRED_LIBRARIES CACHE)
+ else()
+-  find_file(ATLAS_LAPACK liblapack.so.3 PATHS /usr/lib/atlas /usr/lib64/atlas)
+-  find_library(ATLAS_LAPACK NAMES lapack)
+-  set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES} ${ATLAS_CBLAS})
+-  check_library_exists("${ATLAS_LAPACK}" clapack_dpotrf "" FOUND_CLAPACK)
++  # find_file(ATLAS_LAPACK liblapack.so.3 PATHS /usr/lib/atlas /usr/lib64/atlas)
++  # find_library(ATLAS_LAPACK NAMES lapack)
++  # set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES} ${ATLAS_CBLAS})
++  check_library_exists("${ATLAS_LIBRARIES}" clapack_dpotrf "" FOUND_CLAPACK)
+   if(NOT FOUND_CLAPACK)
+     unset(ATLAS_LAPACK CACHE)
+   endif()

diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
index 70e3e2616088750721df338714b48f936ae4b9b8..d0c30a0c09fbc8b7ed30fd269247222e2213a0b0 100644 (file)
--- a/sci-libs/shogun/metadata.xml
+++ b/sci-libs/shogun/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<longdescription lang="en">
+  <herd>sci</herd>
+  <longdescription lang="en">
   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
@@ -21,17 +21,17 @@
   (e.g. substracting the mean) can be attached to each feature object
   allowing for on-the-fly pre-processing.
 </longdescription>
-<use>
-  <flag name="arpack">Enable support for <pkg>sci-libs/arpack</pkg></flag>
-  <flag name="eigen">Enable support for matrix package <pkg>dev-cpp/eigen</pkg></flag>
-  <flag name="glpk">Enable support for <pkg>sci-mathematics/glpk</pkg></flag>
-  <flag name="json">Enable support for parsing JSON format</flag>
-  <flag name="lpsolve">Enable support for Linear Programming Solver</flag>
-  <flag name="nlopt">Enable support non linear optimization from
+  <use>
+    <flag name="arpack">Enable support for <pkg>sci-libs/arpack</pkg></flag>
+    <flag name="eigen">Enable support for matrix package <pkg>dev-cpp/eigen</pkg></flag>
+    <flag name="glpk">Enable support for <pkg>sci-mathematics/glpk</pkg></flag>
+    <flag name="json">Enable support for parsing JSON format</flag>
+    <flag name="lpsolve">Enable support for Linear Programming Solver</flag>
+    <flag name="nlopt">Enable support non linear optimization from
   <pkg>sci-libs/nlopt</pkg></flag>
-  <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
-  <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
-  <flag name="snappy">Enable support for snappy compression</flag>
-  <flag name="superlu">Enable support for <pkg>sci-libs/superlu</pkg></flag>
-</use>
+    <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
+    <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
+    <flag name="snappy">Enable support for snappy compression</flag>
+    <flag name="superlu">Enable support for <pkg>sci-libs/superlu</pkg></flag>
+  </use>
 </pkgmetadata>

diff --git a/sci-libs/shogun/shogun-3.2.0.ebuild b/sci-libs/shogun/shogun-3.2.0.ebuild
index e7e0b4d9570223cfeac5a493a9f5f06cfde92626..4bce5a8850a01217f4a071a727320773a585160f 100644 (file)
--- a/sci-libs/shogun/shogun-3.2.0.ebuild
+++ b/sci-libs/shogun/shogun-3.2.0.ebuild
@@ -1,27 +1,32 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/shogun-3.2.0.ebuild,v 1.1 2014/04/06 01:47:16 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/shogun/shogun-3.2.0.ebuild,v 1.2 2015/01/25 17:41:02 jlec Exp $
 
 EAPI=5
 
-PYTHON_COMPAT=( python{2_7,3_3} )
-inherit cmake-utils multilib versionator toolchain-funcs python-single-r1
+PYTHON_COMPAT=( python2_7 python{3,4} )
+
+inherit cmake-utils multilib python-single-r1 toolchain-funcs versionator
 
 MYPV=$(get_version_component_range 1-2)
 MYPD=${PN}-data-0.8
 
 DESCRIPTION="Large Scale Machine Learning Toolbox"
 HOMEPAGE="http://shogun-toolbox.org/"
-SRC_URI="ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2
+SRC_URI="
+       ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2
        test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )
        examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
 
 LICENSE="GPL-3 free-noncomm"
 SLOT="0/16"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
 IUSE="doc examples lua mono octave python R ruby static-libs test"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+REQUIRED_USE="
+       python? ( ${PYTHON_REQUIRED_USE} )
+       test? ( python )
+       "
 
 RDEPEND="
        app-arch/bzip2:=
@@ -62,13 +67,20 @@ DEPEND="${RDEPEND}
        python? ( >=dev-lang/swig-2.0.4 test? ( sci-libs/scipy ) )
        R? ( >=dev-lang/swig-2.0.4 )
        ruby? ( >=dev-lang/swig-2.0.4 )
-       test? ( dev-python/jinja )"
+       test? (
+               dev-python/jinja[${PYTHON_USEDEP}]
+               dev-cpp/gmock
+               )"
 
 # javamodular needs jblas (painful to package properly)
 # permodular work in progress (as 3.2.0)
 # could actually support multiple pythons, multiple rubys
 # feel free to do work for it
 
+PATCHES=(
+       "${FILESDIR}"/${P}-atlas.patch
+)
+
 pkg_setup() {
        use python && python-single-r1_pkg_setup
 }
@@ -88,6 +100,7 @@ src_configure() {
                -DENABLE_COVERAGE=OFF
                -DJavaModular=OFF
                -DPerlModular=OFF
+               -DLIB_INSTALL_DIR=$(get_libdir)
                $(cmake-utils_use lua LuaModular)
                $(cmake-utils_use mono CSharpModular)
                $(cmake-utils_use octave OctaveModular)