From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1QwLq5-0007rI-Et for garchives@archives.gentoo.org; Wed, 24 Aug 2011 22:22:25 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1B94521C4E4; Wed, 24 Aug 2011 22:22:05 +0000 (UTC) Received: from cl-mail.uni-potsdam.de (cl-mail.rz.uni-potsdam.de [141.89.68.1]) by pigeon.gentoo.org (Postfix) with ESMTP id C458021C4F1 for ; Wed, 24 Aug 2011 22:21:49 +0000 (UTC) Received: from arnim.rz.uni-potsdam.de (arnim.rz.uni-potsdam.de [141.89.68.11]) by n-mail-4.rz.uni-potsdam.de (8.14.4/8.14.4) with ESMTP id p7OMLYKY016061 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO); Thu, 25 Aug 2011 00:21:34 +0200 (CEST) Received: from uni-potsdam.de (localhost.localdomain [127.0.0.1]) by arnim.rz.uni-potsdam.de (8.13.8/8.13.8) with ESMTP id p7OMLXqd032474; Thu, 25 Aug 2011 00:21:33 +0200 Received: from p57B9ACB0.dip.t-dialin.net (p57B9ACB0.dip.t-dialin.net [87.185.172.176]) by webmail.uni-potsdam.de (Horde MIME library) with HTTP; Thu, 25 Aug 2011 00:21:33 +0200 Message-ID: <20110825002133.54j5on98iswwo808@webmail.uni-potsdam.de> Date: Thu, 25 Aug 2011 00:21:33 +0200 From: rose@rz.uni-potsdam.de To: gentoo-science@lists.gentoo.org, Steven Trogdon Subject: Re: [gentoo-science] sci-mathematics/sage-4.7.1 and numpy version References: <20110824120319.b46xhd35wgss00os@webmail.uni-potsdam.de> <20110824104700.47e095f2@pavilion64.home.lan> In-Reply-To: <20110824104700.47e095f2@pavilion64.home.lan> 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; DelSp="Yes"; format="flowed" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable User-Agent: Internet Messaging Program (IMP) H3 (4.1.6) X-Miltered: at n-mail-4 with ID 4E55796E.000 by Joe's j-chkmail (http : // j-chkmail dot ensmp dot fr)! X-j-chkmail-Enveloppe: 4E55796E.000 from arnim.rz.uni-potsdam.de/arnim.rz.uni-potsdam.de/141.89.68.11/arnim.rz.uni-potsdam.de/ X-j-chkmail-Score: MSGID : 4E55796E.000 on n-mail-4.rz.uni-potsdam.de : j-chkmail score : . : R=. U=. O=. B=0.000 -> S=0.000 X-j-chkmail-Status: Ham X-Archives-Salt: X-Archives-Hash: 5d373d6e938155b70d1c6162691800d1 Quoting Steven Trogdon : > On Wed, 24 Aug 2011 12:03:19 +0200 > rose@rz.uni-potsdam.de wrote: > >> Hi, >> >> I just installed more or less succesful sage. During the installation >> numpy was downgraded from numpy-1.6.1 to numpy-1.5.1. >> Now every 'emerge -uvDN world' complaines about; >> >> WARNING: One or more updates have been skipped due to a dependency confli= ct: >> >> dev-python/numpy:0 >> >> (dev-python/numpy-1.6.1::gentoo, ebuild scheduled for merge) =20 >> conflicts with >> ~dev-python/numpy-1.5.1 required by >> (sci-mathematics/sage-4.7.1::sage-on-gentoo, installed) >> >> dev-python/pexpect:0 >> >> (dev-python/pexpect-2.4-r1::sage-on-gentoo, ebuild scheduled for >> merge) conflicts with >> ~dev-python/pexpect-2.0 required by >> (sci-mathematics/sage-4.7.1::sage-on-gentoo, installed) >> >> If I try to install couchdb, numpy-1.6.1 will be installed again: >> >> root@caiman:/root(4)# emerge -pvuDN couchdb >> >> These are the packages that would be merged, in order: >> >> Calculating dependencies... done! >> [ebuild N ] dev-lang/erlang-14.2.3 USE=3D"doc emacs java odbc smp >> ssl tk wxwidgets -halfword -hipe -kpoll -sctp" 98,075 kB >> [ebuild N ] dev-db/couchdb-1.1.0 USE=3D"-test" 1,063 kB >> [ebuild U ] dev-python/numpy-1.6.1 [1.5.1] USE=3D"doc lapack -test" = 0 kB >> >> Should I mask numpy-1.6.1 or how are the chances that sage will work >> with numpy-1.6.1? >> > At least until this Bug > > https://bugs.gentoo.org/show_bug.cgi?id=3D371099 > > is resolved (sog) sage requires ~numpy-1.5.1 > > I'm not sure exactly the impact on your system of masking =20 > >=3Dnumpy-1.6.0 but you > could try that and see what emerge -puDNv world gives. I don't see which > component, if any, of couchdb is pulling in numpy or where else numpy is > needed on your system. Oh, and you will also have to mask >=3Dpexpect-2.4 > > Steve > Thanks Steve, OK, I masked: > =3Ddev-python/numpy-1.6.0 > =3Ddev-python/pexpect-2.4 The following installation of couchdb was no problem, also 'emerge =20 -puvDN world' did not complain about any conflicts. But I made the =20 mistake to delete scipy. Now 'emerge scipy' fails with: ... RefactoringTool: =20 /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/s= parse/linalg/isolve/setup.py RefactoringTool: =20 /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/i= ntegrate/setup.py /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/i= o/__init__.py /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/i= o/matlab/mio4.py ... /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/i= ntegrate/ode.py /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/i= ntegrate/quadpack.py blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=3DATLAS Warning: No configuration returned, assuming =20 unavailable./usr/lib64/python3.2/site-packages/numpy/distutils/system_info.p= y:527: UserWarning: Specified path is =20 invalid. warnings.warn('Specified path %s is invalid.' % d) libraries atlcblas,f77blas,m,atlas not found in /usr/lib64 NOT AVAILABLE ... blas_src_info: NOT AVAILABLE /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1411: =20 UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 181, in ... File =20 "/usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py", =20 line 461, in get_info raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. * ERROR: sci-libs/scipy-0.9.0-r1 failed (compile phase): * Building failed with CPython 3.2 in distutils_building() function USE_PYTHON=3D"2.7" 'emerge -v1 scipy'