Re: [gentoo-science] sci-mathematics/sage-4.7.1 and numpy version

Quoting rose@××××××××××××××.de:

> 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'
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