Gentoo Archives: gentoo-science

From: rose@××××××××××××××.de
To: gentoo-science@l.g.o, Steven Trogdon <strogdon@×××××.edu>
Subject: Re: [gentoo-science] sci-mathematics/sage-4.7.1 and numpy version
Date: Wed, 24 Aug 2011 22:22:25
Message-Id: 20110825002133.54j5on98iswwo808@webmail.uni-potsdam.de
In Reply to: Re: [gentoo-science] sci-mathematics/sage-4.7.1 and numpy version by Steven Trogdon
Quoting Steven Trogdon <strogdon@×××××.edu>:

> On Wed, 24 Aug 2011 12:03:19 +0200 > rose@××××××××××××××.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 conflict: >> >> dev-python/numpy:0 >> >> (dev-python/numpy-1.6.1::gentoo, ebuild scheduled for merge) >> 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="doc emacs java odbc smp >> ssl tk wxwidgets -halfword -hipe -kpoll -sctp" 98,075 kB >> [ebuild N ] dev-db/couchdb-1.1.0 USE="-test" 1,063 kB >> [ebuild U ] dev-python/numpy-1.6.1 [1.5.1] USE="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=371099 > > is resolved (sog) sage requires ~numpy-1.5.1 > > I'm not sure exactly the impact on your system of masking > >=numpy-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 >=pexpect-2.4 > > Steve >
Thanks Steve, OK, I masked:
> =dev-python/numpy-1.6.0 > =dev-python/pexpect-2.4
The following installation of couchdb was no problem, also 'emerge -puvDN world' did not complain about any conflicts. But I made the mistake to delete scipy. Now 'emerge scipy' fails with: ... RefactoringTool: /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/sparse/linalg/isolve/setup.py RefactoringTool: /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/setup.py /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/__init__.py /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/matlab/mio4.py ... /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/ode.py /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/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=ATLAS Warning: No configuration returned, assuming unavailable./usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:527: UserWarning: Specified path is 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: 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 <module> ... File "/usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py", 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="2.7" 'emerge -v1 scipy'

Replies

Subject Author
Re: [gentoo-science] sci-mathematics/sage-4.7.1 and numpy version fbissey@××××××××××××.nz
Re: [gentoo-science] sci-mathematics/sage-4.7.1 and numpy version Juergen Rose <rose@××××××××××××××.de>