From: | rose@××××××××××××××.de | ||
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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 |

1 | Quoting Steven Trogdon <strogdon@×××××.edu>: |

2 | |

3 | > On Wed, 24 Aug 2011 12:03:19 +0200 |

4 | > rose@××××××××××××××.de wrote: |

5 | > |

6 | >> Hi, |

7 | >> |

8 | >> I just installed more or less succesful sage. During the installation |

9 | >> numpy was downgraded from numpy-1.6.1 to numpy-1.5.1. |

10 | >> Now every 'emerge -uvDN world' complaines about; |

11 | >> |

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

13 | >> |

14 | >> dev-python/numpy:0 |

15 | >> |

16 | >> (dev-python/numpy-1.6.1::gentoo, ebuild scheduled for merge) |

17 | >> conflicts with |

18 | >> ~dev-python/numpy-1.5.1 required by |

19 | >> (sci-mathematics/sage-4.7.1::sage-on-gentoo, installed) |

20 | >> |

21 | >> dev-python/pexpect:0 |

22 | >> |

23 | >> (dev-python/pexpect-2.4-r1::sage-on-gentoo, ebuild scheduled for |

24 | >> merge) conflicts with |

25 | >> ~dev-python/pexpect-2.0 required by |

26 | >> (sci-mathematics/sage-4.7.1::sage-on-gentoo, installed) |

27 | >> |

28 | >> If I try to install couchdb, numpy-1.6.1 will be installed again: |

29 | >> |

30 | >> root@caiman:/root(4)# emerge -pvuDN couchdb |

31 | >> |

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

33 | >> |

34 | >> Calculating dependencies... done! |

35 | >> [ebuild N ] dev-lang/erlang-14.2.3 USE="doc emacs java odbc smp |

36 | >> ssl tk wxwidgets -halfword -hipe -kpoll -sctp" 98,075 kB |

37 | >> [ebuild N ] dev-db/couchdb-1.1.0 USE="-test" 1,063 kB |

38 | >> [ebuild U ] dev-python/numpy-1.6.1 [1.5.1] USE="doc lapack -test" 0 kB |

39 | >> |

40 | >> Should I mask numpy-1.6.1 or how are the chances that sage will work |

41 | >> with numpy-1.6.1? |

42 | >> |

43 | > At least until this Bug |

44 | > |

45 | > https://bugs.gentoo.org/show_bug.cgi?id=371099 |

46 | > |

47 | > is resolved (sog) sage requires ~numpy-1.5.1 |

48 | > |

49 | > I'm not sure exactly the impact on your system of masking |

50 | > >=numpy-1.6.0 but you |

51 | > could try that and see what emerge -puDNv world gives. I don't see which |

52 | > component, if any, of couchdb is pulling in numpy or where else numpy is |

53 | > needed on your system. Oh, and you will also have to mask >=pexpect-2.4 |

54 | > |

55 | > Steve |

56 | > |

57 | |

58 | Thanks Steve, |

59 | |

60 | OK, I masked: |

61 | |

62 | > =dev-python/numpy-1.6.0 |

63 | > =dev-python/pexpect-2.4 |

64 | |

65 | The following installation of couchdb was no problem, also 'emerge |

66 | -puvDN world' did not complain about any conflicts. But I made the |

67 | mistake to delete scipy. Now 'emerge scipy' fails with: |

68 | ... |

69 | RefactoringTool: |

70 | /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/sparse/linalg/isolve/setup.py |

71 | RefactoringTool: |

72 | /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/setup.py |

73 | /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/__init__.py |

74 | /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/io/matlab/mio4.py |

75 | ... |

76 | /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/ode.py |

77 | /var/tmp/portage/sci-libs/scipy-0.9.0-r1/work/scipy-0.9.0/build/py3k/scipy/integrate/quadpack.py |

78 | blas_opt_info: |

79 | blas_mkl_info: |

80 | libraries mkl,vml,guide not found in /usr/local/lib64 |

81 | libraries mkl,vml,guide not found in /usr/local/lib |

82 | libraries mkl,vml,guide not found in /usr/lib64 |

83 | libraries mkl,vml,guide not found in /usr/lib |

84 | NOT AVAILABLE |

85 | |

86 | atlas_blas_threads_info: |

87 | Setting PTATLAS=ATLAS |

88 | Warning: No configuration returned, assuming |

89 | unavailable./usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:527: UserWarning: Specified path is |

90 | invalid. |

91 | warnings.warn('Specified path %s is invalid.' % d) |

92 | libraries atlcblas,f77blas,m,atlas not found in /usr/lib64 |

93 | NOT AVAILABLE |

94 | ... |

95 | blas_src_info: |

96 | NOT AVAILABLE |

97 | |

98 | /usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py:1411: |

99 | UserWarning: |

100 | Blas (http://www.netlib.org/blas/) sources not found. |

101 | Directories to search for the sources can be specified in the |

102 | numpy/distutils/site.cfg file (section [blas_src]) or by setting |

103 | the BLAS_SRC environment variable. |

104 | warnings.warn(BlasSrcNotFoundError.__doc__) |

105 | Traceback (most recent call last): |

106 | File "setup.py", line 181, in <module> |

107 | ... |

108 | File |

109 | "/usr/lib64/python3.2/site-packages/numpy/distutils/system_info.py", |

110 | line 461, in get_info |

111 | raise self.notfounderror(self.notfounderror.__doc__) |

112 | numpy.distutils.system_info.BlasNotFoundError: |

113 | Blas (http://www.netlib.org/blas/) libraries not found. |

114 | Directories to search for the libraries can be specified in the |

115 | numpy/distutils/site.cfg file (section [blas]) or by setting |

116 | the BLAS environment variable. |

117 | * ERROR: sci-libs/scipy-0.9.0-r1 failed (compile phase): |

118 | * Building failed with CPython 3.2 in distutils_building() function |

119 | |

120 | |

121 | USE_PYTHON="2.7" 'emerge -v1 scipy' |

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> |

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