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[Bug 217968] math/py-numpy: Possible regression with fortran linkage

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[Bug 217968] math/py-numpy: Possible regression with fortran linkage

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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=217968

            Bug ID: 217968
           Summary: math/py-numpy: Possible regression with fortran
                    linkage
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Only Me
          Priority: ---
         Component: Individual Port(s)
          Assignee: [hidden email]
          Reporter: [hidden email]
          Assignee: [hidden email]
             Flags: maintainer-feedback?([hidden email])

The following error started appearing since running pkg upgrade this morning.
The qiime-test script had been working for the past couple weeks and there have
been no major changes to the qiime port lately.

I can still build and run fortran programs using
-Wl,-rpath,/usr/local/lib/gcc49.

This looks to me like a numpy link error, maybe failing to use rpath to load
the correct libgcc?

Thanks,

    Jason

FreeBSD unixdev.ceas  bacon ~ 403: ./qiime-test qiime-tests/
Traceback (most recent call last):
  File "./all_tests.py", line 10, in <module>
    from qiime.util import (parse_command_line_parameters, get_options_lookup,
  File "/usr/local/lib/python2.7/site-packages/qiime/util.py", line 35, in
<module>
    from numpy import (array, zeros, shape, vstack, ndarray, asarray,
  File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 142, in
<module>
    from . import add_newdocs
  File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13,
in <module>
    from numpy.lib import add_newdoc
  File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8,
in <module>
    from .type_check import *
  File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line
11, in <module>
    import numpy.core.numeric as _nx
  File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line
14, in <module>
    from . import multiarray
ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by
/usr/local/lib/gcc49/libgfortran.so.3 not found

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maintainer-feedback requested: [Bug 217968] math/py-numpy: Possible regression with fortran linkage

bugzilla-noreply
Jason Bacon <[hidden email]> has reassigned Bugzilla Automation
<[hidden email]>'s request for maintainer-feedback to FreeBSD Python
<[hidden email]>:
Bug 217968: math/py-numpy: Possible regression with fortran linkage
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=217968



--- Description ---
The following error started appearing since running pkg upgrade this morning.
The qiime-test script had been working for the past couple weeks and there have
been no major changes to the qiime port lately.

I can still build and run fortran programs using
-Wl,-rpath,/usr/local/lib/gcc49.

This looks to me like a numpy link error, maybe failing to use rpath to load
the correct libgcc?

Thanks,

    Jason

FreeBSD unixdev.ceas  bacon ~ 403: ./qiime-test qiime-tests/
Traceback (most recent call last):
  File "./all_tests.py", line 10, in <module>
    from qiime.util import (parse_command_line_parameters, get_options_lookup,
  File "/usr/local/lib/python2.7/site-packages/qiime/util.py", line 35, in
<module>
    from numpy import (array, zeros, shape, vstack, ndarray, asarray,
  File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 142, in
<module>
    from . import add_newdocs
  File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13,
in <module>
    from numpy.lib import add_newdoc
  File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8,
in <module>
    from .type_check import *
  File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line
11, in <module>
    import numpy.core.numeric as _nx
  File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line
14, in <module>
    from . import multiarray
ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by
/usr/local/lib/gcc49/libgfortran.so.3 not found
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[Bug 217968] math/py-numpy: Possible regression with fortran linkage

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In reply to this post by bugzilla-noreply
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=217968

Shane <[hidden email]> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |[hidden email]

--- Comment #1 from Shane <[hidden email]> ---
Duplicate of bug #207750

A workaround is setting LD_LIBRARY_PATH

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[Bug 217968] math/py-numpy: Possible regression with fortran linkage

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In reply to this post by bugzilla-noreply
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=217968

Mark Linimon <[hidden email]> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         Resolution|---                         |DUPLICATE
             Status|New                         |Closed
           Assignee|[hidden email]          |[hidden email]

--- Comment #2 from Mark Linimon <[hidden email]> ---


*** This bug has been marked as a duplicate of bug 207750 ***

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