From: | fbissey@××××××××××××.nz | ||
---|---|---|---|

To: | gentoo-science@l.g.o | ||

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

Date: | Wed, 24 Aug 2011 22:38:54 | ||

Message-Id: | 20110825103356.jwg0ggo0gk4woo44@webmail.slingshot.co.nz |
||

In Reply to: | Re: [gentoo-science] sci-mathematics/sage-4.7.1 and numpy version by rose@rz.uni-potsdam.de |

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 |

All times displayed are in UTC (GMT+0).

Contents reflect the opinion of the author, not the Gentoo project or the Gentoo Foundation.

Gentoo is a trademark of the Gentoo Foundation, Inc. The contents of this document, unless otherwise expressly stated, are licensed under the CC-BY-SA-4.0 license. The Gentoo Name and Logo Usage Guidelines apply.