From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 4A49F1387FD for ; Mon, 9 Jun 2014 21:33:46 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EBFB4E0959; Mon, 9 Jun 2014 21:33:43 +0000 (UTC) Received: from cantvb.canterbury.ac.nz (cantvb.canterbury.ac.nz [132.181.2.28]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id CDAC0E0881 for ; Mon, 9 Jun 2014 21:33:42 +0000 (UTC) Received: from CONVERSION-DAEMON.it.canterbury.ac.nz by it.canterbury.ac.nz (PMDF V6.6-x1 #32072) id <01P8UDUSH8KWC4KXXK@it.canterbury.ac.nz> for gentoo-science@lists.gentoo.org; Tue, 10 Jun 2014 09:33:38 +1300 (NEW ZEALAND DAYLIGHT TIME) Received: from qcd-nzi3.localnet (QCD-nzi3.canterbury.ac.nz [132.181.64.206]) by it.canterbury.ac.nz (PMDF V6.6-x1 #32072) with ESMTPS id <01P8UDUS846MC7IIUS@it.canterbury.ac.nz> for gentoo-science@lists.gentoo.org; Tue, 10 Jun 2014 09:33:38 +1300 (NEW ZEALAND DAYLIGHT TIME) Date: Tue, 10 Jun 2014 09:33:37 +1200 From: =?ISO-8859-1?Q?Fran=E7ois?= Bissey Subject: Re: [gentoo-science] Trouble building scipy-0.14.0 against acml In-reply-to: <5395FFDF.3000502@arcor.de> To: gentoo-science@lists.gentoo.org Message-id: <3554982.Vr7BGyNh6U@qcd-nzi3> Organization: BlueFern Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: quoted-printable User-Agent: KMail/4.12.5 (Linux/3.8.13-gentoo; KDE/4.12.5; x86_64; ; ) References: <53959961.1060000@bastian-loeffler.de> <4054FC76-6D38-434E-8DAC-3433619F9222@gmail.com> <5395FFDF.3000502@arcor.de> X-Archives-Salt: 284efaf2-a228-4772-8894-37156bc35287 X-Archives-Hash: 397845719d6b0b7033886d8bb01d8546 OK, thanks for the file. I think it is a bug in the pkgconfig file for=20= blas with acml. You should also have=20 library_dirs =3D //opt/acml5.3.1/gfortran64/lib:/usr/lib64 in the blas section, not just in the lapack one. Do you have a=20 Gentoo bugzilla account? If not I'll fill the report. Francois On Mon, 09 Jun 2014 20:41:35 Bastian L=F6ffler wrote: > Hi, >=20 > this is >=20 > /var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7/si= te.cfg: >=20 > [blas] > include_dirs =3D > library_dirs =3D :/usr/lib64 > blas_libs =3D > [lapack] > library_dirs =3D //opt/acml5.3.1/gfortran64/lib:/usr/lib64 > lapack_libs =3D acml >=20 > Buliding numpy is ago. This is any scipy update. >=20 > Am 09.06.2014 13:51, schrieb Fran=E7ois Bissey: > > numpy not bumpy. Sorry for the noise. > >=20 > > On 9/06/2014, at 23:42, Fran=E7ois Bissey wr= ote: > >> Hi, > >>=20 > >> Could you post the file: > >> /var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2_7= /site.c > >> fg > >> for our perusal? You obviously managed to merge bumpy which fundam= entally > >> should have the exact same problem. > >> Was it just before scipy or a while ago? > >>=20 > >> Fran=E7ois > >>=20 > >> On 9/06/2014, at 23:25, Bastian L=F6ffler =20 wrote: > >>> Hi all, > >>>=20 > >>> I can not build scipy 0.14.0 agaonst the currenct aclm since it > >>> complains a missing blas: > >>>=20 > >>> numpy.distutils.system_info.BlasNotFoundError: > >>> Blas ( > >>>=20 > >>> http://www.netlib.org/blas/ > >>> ) libraries not found. > >>>=20 > >>> Directories to search for the libraries can be specified in th= e > >>> numpy/distutils/site.cfg file (section [blas]) or by setting > >>> the BLAS environment variable. > >>>=20 > >>> * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase): > >>> * (no error message) > >>> * > >>> * Call stack: > >>> * ebuild.sh, line 93: Called src_compile > >>> * environment, line 4075: Called distutils-r1_src_compile > >>> * environment, line 1421: Called _distutils-r1_run_foreach_imp= l > >>> 'python_compile' > >>> * environment, line 312: Called python_parallel_foreach_impl > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 3808: Called multibuild_parallel_foreach_v= ariant > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_com= pile' > >>> * environment, line 2855: Called multibuild_foreach_variant > >>> '_multibuild_parallel' '_python_multibuild_wrapper' > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 2798: Called _multibuild_run > >>> '_multibuild_parallel' '_python_multibuild_wrapper' > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 2796: Called _multibuild_parallel > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_com= pile' > >>> * environment, line 2846: Called _python_multibuild_wrapper > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 914: Called distutils-r1_run_phase > >>> 'python_compile' > >>> * environment, line 1412: Called python_compile > >>> * environment, line 3315: Called distutils-r1_python_compile > >>> 'config_fc' '--noopt' '--noarch' > >>> * environment, line 1292: Called esetup.py 'build' 'config_fc'= > >>> '--noopt' '--noarch' > >>> * environment, line 1862: Called die > >>> * The specific snippet of code: > >>> * "${@}" || die > >>> * > >>> * If you need support, post the output of `emerge --info > >>> '=3Dsci-libs/scipy-0.14.0::gentoo'`, > >>> * the complete build log and the output of `emerge -pqv > >>> '=3Dsci-libs/scipy-0.14.0::gentoo'`. > >>> * The complete build log is located at > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'. > >>> * The ebuild environment file is located at > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'. > >>> * Working directory: > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python2= _7' > >>> * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0' > >>> /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (66= 75) - > >>> No such process > >>> blas_opt_info: > >>>=20 > >>> system_info: > >>> NOT AVAILABLE > >>>=20 > >>> blas_info: > >>> libraries not found in ['/usr/lib64'] > >>> NOT AVAILABLE > >>>=20 > >>> blas_src_info: > >>> NOT AVAILABLE > >>>=20 > >>> /usr/lib64/python3.3/distutils/dist.py:258: UserWarning: Unknown > >>> distribution option: 'test_suite' > >>>=20 > >>> warnings.warn(msg) > >>>=20 > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py= :1511: > >>>=20 > >>> UserWarning: > >>> Atlas ( > >>>=20 > >>> http://math-atlas.sourceforge.net/ > >>> ) libraries not found. > >>>=20 > >>> Directories to search for the libraries can be specified in th= e > >>> numpy/distutils/site.cfg file (section [atlas]) or by setting > >>> the ATLAS environment variable. > >>> =20 > >>> warnings.warn(AtlasNotFoundError.__doc__) > >>>=20 > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py= :566: > >>> UserWarning: Specified path is invalid. > >>>=20 > >>> warnings.warn('Specified path %s is invalid.' % d) > >>>=20 > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py= :1520: > >>>=20 > >>> UserWarning: > >>> Blas ( > >>>=20 > >>> http://www.netlib.org/blas/ > >>> ) libraries not found. > >>>=20 > >>> Directories to search for the libraries can be specified in th= e > >>> numpy/distutils/site.cfg file (section [blas]) or by setting > >>> the BLAS environment variable. > >>> =20 > >>> warnings.warn(BlasNotFoundError.__doc__) > >>>=20 > >>> /usr/lib64/python3.3/site-packages/numpy/distutils/system_info.py= :1523: > >>>=20 > >>> UserWarning: > >>> Blas ( > >>>=20 > >>> http://www.netlib.org/blas/ > >>> ) sources not found. > >>>=20 > >>> Directories to search for the sources can be specified in the > >>> numpy/distutils/site.cfg file (section [blas_src]) or by setti= ng > >>> the BLAS_SRC environment variable. > >>> =20 > >>> warnings.warn(BlasSrcNotFoundError.__doc__) > >>>=20 > >>> Traceback (most recent call last): > >>> File "setup.py", line 237, in > >>> =20 > >>> setup_package() > >>> =20 > >>> File "setup.py", line 234, in setup_package > >>> =20 > >>> setup(**metadata) > >>> =20 > >>> File "/usr/lib64/python3.3/site-packages/numpy/distutils/core.py= ", > >>>=20 > >>> line 135, in setup > >>>=20 > >>> config =3D configuration() > >>> =20 > >>> File "setup.py", line 173, in configuration > >>> =20 > >>> config.add_subpackage('scipy') > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py"= , line > >>> 966, in add_subpackage > >>>=20 > >>> caller_level =3D 2) > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py"= , line > >>> 935, in get_subpackage > >>>=20 > >>> caller_level =3D caller_level + 1) > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py"= , line > >>> 872, in _get_configuration_from_setup_py > >>>=20 > >>> config =3D setup_module.configuration(*args) > >>> =20 > >>> File "scipy/setup.py", line 12, in configuration > >>> =20 > >>> config.add_subpackage('integrate') > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py"= , line > >>> 966, in add_subpackage > >>>=20 > >>> caller_level =3D 2) > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py"= , line > >>> 935, in get_subpackage > >>>=20 > >>> caller_level =3D caller_level + 1) > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/misc_util.py"= , line > >>> 872, in _get_configuration_from_setup_py > >>>=20 > >>> config =3D setup_module.configuration(*args) > >>> =20 > >>> File "scipy/integrate/setup.py", line 12, in configuration > >>> =20 > >>> blas_opt =3D get_info('blas_opt',notfound_action=3D2) > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.p= y", > >>> line 340, in get_info > >>>=20 > >>> return cl().get_info(notfound_action) > >>> =20 > >>> File > >>>=20 > >>> "/usr/lib64/python3.3/site-packages/numpy/distutils/system_info.p= y", > >>> line 499, in get_info > >>>=20 > >>> raise self.notfounderror(self.notfounderror.__doc__) > >>>=20 > >>> numpy.distutils.system_info.BlasNotFoundError: > >>> Blas ( > >>>=20 > >>> http://www.netlib.org/blas/ > >>> ) libraries not found. > >>>=20 > >>> Directories to search for the libraries can be specified in th= e > >>> numpy/distutils/site.cfg file (section [blas]) or by setting > >>> the BLAS environment variable. > >>>=20 > >>> * ERROR: sci-libs/scipy-0.14.0::gentoo failed (compile phase): > >>> * (no error message) > >>> * > >>> * Call stack: > >>> * ebuild.sh, line 93: Called src_compile > >>> * environment, line 4075: Called distutils-r1_src_compile > >>> * environment, line 1421: Called _distutils-r1_run_foreach_imp= l > >>> 'python_compile' > >>> * environment, line 312: Called python_parallel_foreach_impl > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 3808: Called multibuild_parallel_foreach_v= ariant > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_com= pile' > >>> * environment, line 2855: Called multibuild_foreach_variant > >>> '_multibuild_parallel' '_python_multibuild_wrapper' > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 2798: Called _multibuild_run > >>> '_multibuild_parallel' '_python_multibuild_wrapper' > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 2796: Called _multibuild_parallel > >>> '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_com= pile' > >>> * environment, line 2846: Called _python_multibuild_wrapper > >>> 'distutils-r1_run_phase' 'python_compile' > >>> * environment, line 914: Called distutils-r1_run_phase > >>> 'python_compile' > >>> * environment, line 1412: Called python_compile > >>> * environment, line 3315: Called distutils-r1_python_compile > >>> 'config_fc' '--noopt' '--noarch' > >>> * environment, line 1292: Called esetup.py 'build' 'config_fc'= > >>> '--noopt' '--noarch' > >>> * environment, line 1862: Called die > >>> * The specific snippet of code: > >>> * "${@}" || die > >>> * > >>> * If you need support, post the output of `emerge --info > >>> '=3Dsci-libs/scipy-0.14.0::gentoo'`, > >>> * the complete build log and the output of `emerge -pqv > >>> '=3Dsci-libs/scipy-0.14.0::gentoo'`. > >>> * The complete build log is located at > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/build.log'. > >>> * The ebuild environment file is located at > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/temp/environment'. > >>> * Working directory: > >>> '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0-python3= _3' > >>> * S: '/var/tmp/portage/sci-libs/scipy-0.14.0/work/scipy-0.14.0' > >>> /usr/lib64/portage/bin/isolated-functions.sh: line 226: kill: (66= 75) - > >>> No such process > >>>=20 > >>>>>> Failed to emerge sci-libs/scipy-0.14.0, Log file: