Opened 10 years ago

Closed 10 years ago

## #14617 closed enhancement (fixed)

# Update scipy to 0.12

Reported by: | Jean-Pierre Flori | Owned by: | Jeroen Demeyer |
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Priority: | major | Milestone: | sage-5.10 |

Component: | packages: standard | Keywords: | scipy spkg |

Cc: | Merged in: | sage-5.10.beta5 | |

Authors: | Jean-Pierre Flori | Reviewers: | Volker Braun |

Report Upstream: | N/A | Work issues: | |

Branch: | Commit: | ||

Dependencies: | Stopgaps: |

### Description (last modified by )

### Change History (15)

### comment:1 Changed 10 years ago by

Description: | modified (diff) |
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### comment:2 Changed 10 years ago by

My, bad, it is. I read the wrong README in the tarball and got a wrong feeling.

### comment:5 Changed 10 years ago by

The way I read it, scipy's arpack has been renamed to arpack-ng. Nothing has been replaced, but there are a bunch of bugfixes to arpack in the new release.

### comment:6 Changed 10 years ago by

Hum, anyway arpack-ng is just a fork of arpack, so would basically fit with "rename and fix bugs" because upstream was not active anymore. See:

### comment:8 Changed 10 years ago by

Description: | modified (diff) |
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I've reposted an spkg which now compiles (the only patch we used was now upstream). I've not tested Volker's one, whence the change in the ticket description, but if anyone (including Volker :)) feels it is better, feel free to change it back.

### comment:10 Changed 10 years ago by

Great, so I'll have a look at your spkg and give it positive review when my tests finish.

### comment:11 Changed 10 years ago by

Authors: | → Jean-Pierre Flori |
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Reviewers: | → Volker Braun |

Status: | new → needs_review |

### comment:12 Changed 10 years ago by

Status: | needs_review → positive_review |
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### comment:13 Changed 10 years ago by

On `hawk`

, importing `scipy`

fails with

sage -t --long devel/sage/sage/plot/plot3d/list_plot3d.py ********************************************************************** File "devel/sage/sage/plot/plot3d/list_plot3d.py", line 87, in sage.plot.plot3d.list_plot3d.list_plot3d Failed example: list_plot3d(m, texture='yellow', interpolation_type='nn',frame_aspect_ratio=[1,1,1/3]) Exception raised: Traceback (most recent call last): File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 466, in _run self.execute(example, compiled, test.globs) File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 825, in execute exec compiled in globs File "<doctest sage.plot.plot3d.list_plot3d.list_plot3d[5]>", line 1, in <module> list_plot3d(m, texture='yellow', interpolation_type='nn',frame_aspect_ratio=[Integer(1),Integer(1),Integer(1)/Integer(3)]) File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/plot/plot3d/list_plot3d.py", line 174, in list_plot3d return list_plot3d_tuples(l,interpolation_type,texture,**kwds) File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/plot/plot3d/list_plot3d.py", line 356, in list_plot3d_tuples from scipy import interpolate File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/scipy/interpolate/__init__.py", line 160, in <module> from .ndgriddata import * File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/scipy/interpolate/ndgriddata.py", line 10, in <module> from .interpnd import LinearNDInterpolator, NDInterpolatorBase, \ ImportError: ld.so.1: python2.7: fatal: relocation error: file /export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/scipy/interpolate/interpnd.so: symbol __sync_fetch_and_add_4: referenced symbol not found **********************************************************************

This seems to come from GCC, so I'll try again with Sage's GCC (the error above was with GCC-4.4.3)

### comment:14 Changed 10 years ago by

Indeed. Some pointers:

and a bunch of similar ones on other systems alos closed as invalid, or

For GCC 4.4.x you should explicitely pass -march=something-that-works to get that function, whereas for more recent GCCs it seems to be implied automatically from the value of target.

### comment:15 Changed 10 years ago by

Merged in: | → sage-5.10.beta5 |
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Resolution: | → fixed |

Status: | positive_review → closed |

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This won't fix the problem with updated ATLAS as ARPACK-NG is not in 0.12 unfortunately, but in the git repo only: https://github.com/scipy/scipy/pull/386