1 |
Quoting rose@××××××××××××××.de: |
2 |
|
3 |
> Quoting Steven Trogdon <strogdon@×××××.edu>: |
4 |
> |
5 |
>> On Wed, 24 Aug 2011 12:03:19 +0200 |
6 |
>> rose@××××××××××××××.de wrote: |
7 |
>> |
8 |
>>> Hi, |
9 |
>>> |
10 |
>>> I just installed more or less succesful sage. During the installation |
11 |
>>> numpy was downgraded from numpy-1.6.1 to numpy-1.5.1. |
12 |
>>> Now every 'emerge -uvDN world' complaines about; |
13 |
>>> |
14 |
>>> WARNING: One or more updates have been skipped due to a dependency |
15 |
>>> conflict: |
16 |
>>> |
17 |
>>> dev-python/numpy:0 |
18 |
>>> |
19 |
>>> (dev-python/numpy-1.6.1::gentoo, ebuild scheduled for merge) |
20 |
>>> conflicts with |
21 |
>>> ~dev-python/numpy-1.5.1 required by |
22 |
>>> (sci-mathematics/sage-4.7.1::sage-on-gentoo, installed) |
23 |
>>> |
24 |
>>> dev-python/pexpect:0 |
25 |
>>> |
26 |
>>> (dev-python/pexpect-2.4-r1::sage-on-gentoo, ebuild scheduled for |
27 |
>>> merge) conflicts with |
28 |
>>> ~dev-python/pexpect-2.0 required by |
29 |
>>> (sci-mathematics/sage-4.7.1::sage-on-gentoo, installed) |
30 |
>>> |
31 |
>>> If I try to install couchdb, numpy-1.6.1 will be installed again: |
32 |
>>> |
33 |
>>> root@caiman:/root(4)# emerge -pvuDN couchdb |
34 |
>>> |
35 |
>>> These are the packages that would be merged, in order: |
36 |
>>> |
37 |
>>> Calculating dependencies... done! |
38 |
>>> [ebuild N ] dev-lang/erlang-14.2.3 USE="doc emacs java odbc smp |
39 |
>>> ssl tk wxwidgets -halfword -hipe -kpoll -sctp" 98,075 kB |
40 |
>>> [ebuild N ] dev-db/couchdb-1.1.0 USE="-test" 1,063 kB |
41 |
>>> [ebuild U ] dev-python/numpy-1.6.1 [1.5.1] USE="doc lapack -test" 0 kB |
42 |
>>> |
43 |
>>> Should I mask numpy-1.6.1 or how are the chances that sage will work |
44 |
>>> with numpy-1.6.1? |
45 |
>>> |
46 |
>> At least until this Bug |
47 |
>> |
48 |
>> https://bugs.gentoo.org/show_bug.cgi?id=371099 |
49 |
>> |
50 |
>> is resolved (sog) sage requires ~numpy-1.5.1 |
51 |
>> |
52 |
>> I'm not sure exactly the impact on your system of masking |
53 |
>> >=numpy-1.6.0 but you |
54 |
>> could try that and see what emerge -puDNv world gives. I don't see which |
55 |
>> component, if any, of couchdb is pulling in numpy or where else numpy is |
56 |
>> needed on your system. Oh, and you will also have to mask >=pexpect-2.4 |
57 |
>> |
58 |
>> Steve |
59 |
>> |
60 |
> |
61 |
> Thanks Steve, |
62 |
> |
63 |
> OK, I masked: |
64 |
> |
65 |
>> =dev-python/numpy-1.6.0 |
66 |
>> =dev-python/pexpect-2.4 |
67 |
> |
68 |
> The following installation of couchdb was no problem, also 'emerge |
69 |
> -puvDN world' did not complain about any conflicts. But I made the |
70 |
> mistake to delete scipy. Now 'emerge scipy' fails with: |
71 |
> ... |
72 |
> RefactoringTool: |
73 |
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/sparse/linalg/isolve/setup.py |
74 |
> RefactoringTool: |
75 |
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/setup.py |
76 |
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/__init__.py |
77 |
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/matlab/mio4.py |
78 |
> ... |
79 |
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/ode.py |
80 |
> /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/quadpack.py |
81 |
> blas_opt_info: |
82 |
> blas_mkl_info: |
83 |
> libraries mkl,vml,guide not found in /usr/local/lib64 |
84 |
> libraries mkl,vml,guide not found in /usr/local/lib |
85 |
> libraries mkl,vml,guide not found in /usr/lib64 |
86 |
> libraries mkl,vml,guide not found in /usr/lib |
87 |
> NOT AVAILABLE |
88 |
> |
89 |
> atlas_blas_threads_info: |
90 |
> Setting PTATLAS=ATLAS |
91 |
> Warning: No configuration returned, assuming |
92 |
> unavailable./usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:527: UserWarning: Specified path |
93 |
> is |
94 |
> invalid. |
95 |
> warnings.warn('Specified path %s is invalid.' % d) |
96 |
> libraries atlcblas,f77blas,m,atlas not found in /usr/lib64 |
97 |
> NOT AVAILABLE |
98 |
> ... |
99 |
> blas_src_info: |
100 |
> NOT AVAILABLE |
101 |
> |
102 |
> /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1411: |
103 |
> UserWarning: |
104 |
> Blas (http://www.netlib.org/blas/) sources not found. |
105 |
> Directories to search for the sources can be specified in the |
106 |
> numpy/distutils/site.cfg file (section [blas_src]) or by setting |
107 |
> the BLAS_SRC environment variable. |
108 |
> warnings.warn(BlasSrcNotFoundError.__doc__) |
109 |
> Traceback (most recent call last): |
110 |
> File "setup.py", line 181, in <module> |
111 |
> ... |
112 |
> File |
113 |
> "/usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py", |
114 |
> line 461, in get_info |
115 |
> raise self.notfounderror(self.notfounderror.__doc__) |
116 |
> numpy.distutils.system_info.BlasNotFoundError: |
117 |
> Blas (http://www.netlib.org/blas/) libraries not found. |
118 |
> Directories to search for the libraries can be specified in the |
119 |
> numpy/distutils/site.cfg file (section [blas]) or by setting |
120 |
> the BLAS environment variable. |
121 |
> * ERROR: sci-libs/scipy-0.9.0-r1 failed (compile phase): |
122 |
> * Building failed with CPython 3.2 in distutils_building() function |
123 |
> |
124 |
> |
125 |
> USE_PYTHON="2.7" 'emerge -v1 scipy' |
126 |
You replied while I was composing another answer :) |
127 |
It looks like you are suffering from the bug mentioned by Steve. It may be |
128 |
that using python-3.2 is a further element trigering it. This is interesting |
129 |
info in and of itself that will need to be added to the bug. |
130 |
|
131 |
The goal of Steve's suggestion was to avoid building scipy for python-3.2. It |
132 |
obviously didn't work. So here are my instructions: |
133 |
1) make sure numpy-1.5.1 is installed |
134 |
2) if it is, get the scipy ebuild from |
135 |
https://bugs.gentoo.org/show_bug.cgi?id=371099 and try it. |
136 |
|
137 |
Francois |