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

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

[rose]

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?

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

[Steven Trogdon]

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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 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

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

[rose]

Quoting Steven Trogdon <strogdon@d.umn.edu>:

> 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 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'

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

[fbissey]

Quoting Steven Trogdon <strogdon@d.umn.edu>:

> 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 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
>
Hi all,

Sorry I needed to have a little break. numpy-1.6+ is not compatible with sage
at the moment:
http://trac.sagemath.org/sage_trac/ticket/11334
so don't try it. I suspect numpy wants to upgrade to 1.6.1 for you for the
following reason:
1) you put numpy in your package.keywords file
2) numpy is part of your world set. It is upgraded independently of any
dependency requirement. The fact that it is pulled just by -D is 
somewhat a bug
in portage - although there could be a web of dependencies leading to numpy.
emerge -puNv couchdb probably won't pick it.

If you downgraded from numpy-1.6.x to 1.5.1 don't forget to rebuild scipy.

Francois

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

[fbissey]

Quoting rose@rz.uni-potsdam.de:

> Quoting Steven Trogdon <strogdon@d.umn.edu>:
>
>> 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 
>>> 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

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

[P Purkayastha]

On 08/25/2011 06:24 AM, fbissey@slingshot.co.nz wrote:
> Quoting Steven Trogdon <strogdon@d.umn.edu>:
>
>> 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
>>> 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
>>
> Hi all,
>
> Sorry I needed to have a little break. numpy-1.6+ is not compatible with
> sage
> at the moment:
> http://trac.sagemath.org/sage_trac/ticket/11334
> so don't try it. I suspect numpy wants to upgrade to 1.6.1 for you for the
> following reason:
> 1) you put numpy in your package.keywords file
> 2) numpy is part of your world set. It is upgraded independently of any
> dependency requirement. The fact that it is pulled just by -D is
> somewhat a bug
> in portage - although there could be a web of dependencies leading to
> numpy.
> emerge -puNv couchdb probably won't pick it.
>
> If you downgraded from numpy-1.6.x to 1.5.1 don't forget to rebuild scipy.
>
> Francois
>

I think it is a limitation of portage, in that it doesn't do reverse 
dependency checking every time you upgrade a package by its name.

~> emerge -p numpy

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     U  ] dev-python/numpy-1.6.0 [1.5.1]
~> emerge -p numpy sage

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] dev-python/numpy-1.5.1
[ebuild   R   ~] sci-mathematics/sage-4.7.1

WARNING: One or more updates have been skipped due to a dependency conflict:

dev-python/numpy:0

   (dev-python/numpy-1.6.0::gentoo, ebuild scheduled for merge) 
conflicts with
     ~dev-python/numpy-1.5.1 required by 
(sci-mathematics/sage-4.7.1::sage-on-gentoo, ebuild scheduled for merge)

~> emerge -pu numpy sage

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     U  ] dev-python/numpy-1.6.0 [1.5.1]
~> emerge -puD numpy sage

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N     ] virtual/pam-0

WARNING: One or more updates have been skipped due to a dependency conflict:

dev-python/numpy:0

   (dev-python/numpy-1.6.0::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)

~>

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

[Juergen Rose]

Am Donnerstag, den 25.08.2011, 00:21 +0200 schrieb
rose@rz.uni-potsdam.de:

..
> 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'

My last mail was not complete.  I wanted to say 'emerge -v1 scipy' fails
after downgrading numpy, but 'USE_PYTHON="2.7" emerge -v1 scipy' works.

And I reemerged also matplotlib, but as described in an other thread 

sage -testall

still generates still between about 150 and 220 errors.

Regards

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

[Steven Trogdon]

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On Thu, 25 Aug 2011 19:22:17 +0200
Juergen Rose <rose@rz.uni-potsdam.de> wrote:

> Am Donnerstag, den 25.08.2011, 00:21 +0200 schrieb
> rose@rz.uni-potsdam.de:
>
> ..
> > 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'
>
> My last mail was not complete.  I wanted to say 'emerge -v1 scipy' fails
> after downgrading numpy, but 'USE_PYTHON="2.7" emerge -v1 scipy' works.
>
> And I reemerged also matplotlib, but as described in an other thread
>
> sage -testall
>
> still generates still between about 150 and 220 errors.
>
> Regards
>
>
>

Juergen,

Do you by chance have singular-3.1.3.1 or any other singular except the sog
singular (singular-3.1.1.4-r1) installed. If so, you should install the sog
singular. When I have an incorrect singular installed I get things like:

sage -t -force_lib "devel/sage/doc/fr/tutorial/tour_advanced.rst"
// ** Could not open dynamic library: /usr/lib/singular/p_Procs_FieldQ.so
// ** Error message from system: /usr/lib/singular/p_Procs_FieldQ.so:
undefined symbol: _Z17nlShort3_noinlineP7snumber
// ** Singular will work properly, but much slower.
// ** See the INSTALL section in the Singular manual for details.

which appear in your sage_test_impala.log file. This will not cure all your
problems but perhaps is a start. I suspect, for some reason, you have
unstable packages installed that do not play well with sage (my guess).
Could you post the output of

Tools/list-compare-deps sci-mathematics/sage

Tools is a folder under the sog overlay. I believe the tool still reports
things correctly. This may give an indication of what you have installed.

Steve

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