From debbugs-submit-bounces@debbugs.gnu.org Fri May 18 13:09:30 2018 Received: (at 31479) by debbugs.gnu.org; 18 May 2018 17:09:30 +0000 Received: from localhost ([127.0.0.1]:40023 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJisk-0007Rh-Fc for submit@debbugs.gnu.org; Fri, 18 May 2018 13:09:30 -0400 Received: from mout01.posteo.de ([185.67.36.65]:45510) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJisi-0007RQ-Rt for 31479@debbugs.gnu.org; Fri, 18 May 2018 13:09:29 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id A79C8211B5 for <31479@debbugs.gnu.org>; Fri, 18 May 2018 19:09:22 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1526663362; bh=DDpIW7/QB13TcVYYIxTRlwch7nAVuzDgQSGQ7JJlz1Q=; h=From:To:Cc:Subject:Date:From; b=AIA1sm1BtCg9Mw7eGa9v3EPFd+jFiEHXId/ppgeirC5lZ8ndqZBtibMBbP0LG2Xd3 h30LZ6PGM47HXOdio71d0XKpL7sPXTS7BHVqGiBFdbqvIBHxhau95mipqM8tTnAK8I 1pYfU2LxjV/CTwnTzRuPlsN4/B/NSwnnsOomEZS/CD/jqMgIYf+txatL43/Vk+eNEz 5MBhenXnA523pfZYWsyNyzKEj+J1SGmgUO8FuRmMM9GIyTXXhZDPklC0DAMIP1Ta55 TcjINdHrOk99IBnM06dALX7NGdcuLJNIDpB0N5yjAOLenNU8XPPXXN9jetHFhje2X3 bKLEAWVl2k3sg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40nZQn0B8Mz9rxS; Fri, 18 May 2018 19:09:20 +0200 (CEST) From: Kei Kebreau To: Jonathan Brielmaier Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. References: <20180516231957.1827-1-kkebreau@posteo.net> <20180516231957.1827-2-kkebreau@posteo.net> <874lj7w5f2.fsf@posteo.net> <0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de> <0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de> Date: Fri, 18 May 2018 13:08:57 -0400 In-Reply-To: <0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de> (Jonathan Brielmaier's message of "Fri, 18 May 2018 07:58:50 +0200") Message-ID: <87muww6gd2.fsf@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 31479 Cc: 31479@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --==-=-= Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Jonathan Brielmaier writes: > On 17/05/2018 13:39, Jonathan Brielmaier wrote: >> On 17/05/2018 01:24, Kei Kebreau wrote: >>> >>> These patches are really just to upgrade Octave, but the old Shogun >>> couldn't find the new version of Octave. The shogun update patch is a >>> WIP, but I don't have enough RAM (only 3.8GB) to make it through Shogun= 's >>> build process reliably. Could someone else help out with this patch? >>> >>=20 >> I build shogun now, lets see how it goes :) > > Unfortunately there was a build error for shogun. I attached the build > log where it fails. It has something to do with the eigen library... > > > > $ /pre-inst-env guix build shogun > [...] > [ 50%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/mathematic= s/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp.o > cd /tmp/guix-build-shogun-6.1.3.drv-0/build/src/shogun && /gnu/store/cfdn= 69spjc44x4sd0acrwhxq6yay3rbc-gcc-5.5.0/bin/c++ -I/tmp/guix-build-shogun-= 6.1.3.drv-0/shogun-6.1.3/src -I/tmp/guix-build-shogun-6.1.3.drv-0/build/src= -I/tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src/gpl -isystem /gnu/st= ore/iwzn3vhwmzkvhq7sqs6c4bjp2xld17kc-eigen-3.3.4/include/eigen3 -isystem /g= nu/store/5s9am1dgn83wj5q5kwfcasqws8zd85zz-rxcpp-4.0.0 -I/gnu/store/mllyvfy3= 9npzra984jsmcm8ksn3x8094-glpk-4.65/include -I/gnu/store/wnw0gv5hgmhlw3jz1pg= w4n017bhj9f2z-arpack-ng-3.5.0/lib/../include -I/gnu/store/mv9m6bxdhijhlfvxp= ja3km6v599b4pv5-libxml2-2.9.7/include/libxml2 -I/gnu/store/27jrvwbg5xa9la6j= wnqz6ys4k7pfyykl-hdf5-1.8.19/include -I/gnu/store/9hd38bkw8bq8gq6lcv6vd8xjp= csbyzlm-zlib-1.2.11/include -I/gnu/store/77l8sxh9py133cy1p9kypshji4q9wv0w-b= zip2-1.0.6/include -I/gnu/store/kgaf671a9a76k0ql1pwwjxjbj80x22mj-xz-5.2.3/i= nclude -I/gnu/store/33m86ycak50vh2p0q7qb0byh990hrkjn-lzo-2.10/include -Wal= l -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -= Wno-unknown-pragmas -Wno-deprecated -O2 -g -DNDEBUG -fPIC -fopenmp -std= =3Dc++11 -o CMakeFiles/libshogun.dir/mathematics/linalg/ratapprox/logdet/op= func/DenseMatrixExactLog.cpp.o -c /tmp/guix-build-shogun-6.1.3.drv-0/shogun= -6.1.3/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExa= ctLog.cpp > /tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src/shogun/mathematics/li= nalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp:15:45: fatal error: un= supported/Eigen/MatrixFunctions: No such file or directory > compilation terminated. > make[2]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:11456: src/s= hogun/CMakeFiles/libshogun.dir/mathematics/linalg/ratapprox/logdet/opfunc/D= enseMatrixExactLog.cpp.o] Error 1 > make[2]: *** Waiting for unfinished jobs.... > make[2]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build' > make[1]: *** [CMakeFiles/Makefile2:126: src/shogun/CMakeFiles/libshogun.d= ir/all] Error 2 > make[1]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build' > make: *** [Makefile:153: all] Error 2 > phase `build' failed after 493.7 seconds > builder for `/gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.drv= ' failed with exit code 1 > @ build-failed /gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.d= rv - 1 builder for `/gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.= 3.drv' failed with exit code 1 > guix build: error: build failed: build of `/gnu/store/mjnmhzdx6zmwcvspmlj= srjw2aazfvnv7-shogun-6.1.3.drv' failed So it turns out that Eigen's source code comes with some functions that are officially unsupported by the developers but still available for use. Guix just doesn't install them. I've attached a patch that *should* properly install the unsupported files to Eigen's include path. Also, thanks for helping with this shogun patch! --=-=-= Content-Type: text/plain Content-Disposition: attachment; filename=0003-gnu-eigen-Install-unsupported-header-files.patch Content-Transfer-Encoding: quoted-printable From=20eed3dcce3714bc16ccb378d261d9e1bd8db3c249 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 18 May 2018 12:46:57 -0400 Subject: [PATCH 3/4] gnu: eigen: Install unsupported header files. * gnu/packages/algebra.scm (eigen)[arguments]: Add 'install-unsupported' ph= ase. Use invoke instead of system*. =2D-- gnu/packages/algebra.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 03a61be47..51be58ee2 100644 =2D-- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -750,6 +750,14 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transf= orm} (DHT).") #:build-type "Release" =20 #:phases (modify-phases %standard-phases + (add-after 'install 'install-unsupported + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (include (string-append out "/include/eigen3"= ))) + (copy-recursively "unsupported" + (string-append include + "/unsupported")) + #t))) (replace 'check (lambda _ (let* ((cores (parallel-job-count)) @@ -757,11 +765,11 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Trans= form} (DHT).") (setenv "EIGEN_SEED" "1") ;for reproducibility ;; First build the tests, in parallel. See ;; . =2D (and (zero? (system* "make" "buildtests" dash-j)) + (and (invoke "make" "buildtests" dash-j) =20 ;; Then run 'CTest' with -V so we get more ;; details upon failure. =2D (zero? (system* "ctest" "-V" dash-j))))))))) + (invoke "ctest" "-V" dash-j)))))))) (home-page "http://eigen.tuxfamily.org") (synopsis "C++ template library for linear algebra") (description =2D-=20 2.17.0 --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAlr/CKoACgkQ5qXuPBlG eg2V7RAAmVC+dENQkqavr41b3GDjdkFiA2hqaphm8st2mG6KphgnlXbTHM8x7MIB vnvo+PIKoRRZu9pieGY9pYVQxkaByRM+SaLw9ip4dc8aJ8bCmYJbYCUzsmdFM9Qx MdOXc7wGm/jnbsxMmiiWicfEXm2ZCm7pAYIBgjJomy2YPFJoId3F64YhBYmLNyzg U1S3JGMjtaZzVDK1Oyl88OscQJwKgM0RPLFwvXHP8WzVvSPLM7OoKRGAtR8nK6fB hVc7LwAMVqYCtN1VPaeEbeAWnVMMjinFwlETsXRfWrHbUkrWjP0er3VyEK+oQWef rc1Z3RbElhgakSt8g3gFq//JH4Sfl0WiKvf7szk9XGcqAp7fsLGQ6Ny6NxAu8Z4D vFfO6XPrPkkStL2yAN83vqFQrzoLho79VxfZ2KAUJePjXXYmqnJR1k2KJ9ZRfP2/ oLqrHfkw1EIdZydRlUzf3qGpJ2EW6tS0BLOj6tHqxNQHr1i8cWoCXee4WVlgTtno OCmgIy/ro4KNv8ftYH13Tp99RiR78i6LJNuXyJldt5C1M/ri6V+mUzHPl9p5NSbd MF+Hmf7YNXjB1K2jcP8Tx49ghUnOUcL/vNx4XDEn8rYOkvZWVdkV4Pgjoo8Kp2Ks Ov+msIBtLaCqjSZJnsmK9avmTxau4xr+tmgK2WLOSCXImsVruPI= =D7iJ -----END PGP SIGNATURE----- --==-=-=--