Quoting [email protected]:
Quoting Steven Trogdon <[email protected]>:
On Wed, 24 Aug 2011 12:03:19 +0200
[email protected] 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'
You replied while I was composing another answer :)
It looks like you are suffering from the bug mentioned by Steve. It may be
that using python-3.2 is a further element trigering it. This is interesting
info in and of itself that will need to be added to the bug.
The goal of Steve's suggestion was to avoid building scipy for python-3.2. It
obviously didn't work. So here are my instructions:
1) make sure numpy-1.5.1 is installed
2) if it is, get the scipy ebuild from
https://bugs.gentoo.org/show_bug.cgi?id=371099 and try it.
Francois
