https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=207750
Jason Bacon <bacon4...@gmail.com> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |bacon4...@gmail.com
--- Comment #6 from Jason Bacon <bacon4...@gmail.com> ---
I was able to solve this permanently by deleting gcc and everything that
depends on it, and then reinstalling numpy.
If I can narrow it down more, I'll report back, but this appears to be a pkg
upgrade failure of some sort.
FreeBSD unixdev.ceas bacon ~ 402: cat junk.py
#!/usr/bin/env python
import sys,os
import numpy
print 'Hello!\n'
FreeBSD unixdev.ceas bacon ~ 403: python2 junk.py
Traceback (most recent call last):
File "junk.py", line 4, in <module>
import numpy
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
<<<r...@unixdev.ceas>>> /home/bacon 1005 # pkg delete -y gcc\*
[snip irrelevant pkg output]
ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by
/usr/local/lib/gcc49/libgfortran.so.3 not found
Proceed with deinstalling packages? [y/N]: y
[1/84] Deinstalling py27-qiime-1.9.1...
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[2/84] Deinstalling py27-statsmodels-0.6.1_1...
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Unknown media type in type 'chemical/x-alchemy'
Unknown media type in type 'chemical/x-cache'
Unknown media type in type 'chemical/x-cactvs-ascii'
Unknown media type in type 'chemical/x-cactvs-binary'
Unknown media type in type 'chemical/x-cactvs-table'
Unknown media type in type 'chemical/x-cdx'
Unknown media type in type 'chemical/x-cdxml'
Unknown media type in type 'chemical/x-chem3d'
Unknown media type in type 'chemical/x-cif'
Unknown media type in type 'chemical/x-cml'
Unknown media type in type 'chemical/x-daylight-smiles'
Unknown media type in type 'chemical/x-dmol'
Unknown media type in type 'chemical/x-gamess-input'
Unknown media type in type 'chemical/x-gamess-output'
Unknown media type in type 'chemical/x-gaussian-input'
Unknown media type in type 'chemical/x-gaussian-log'
Unknown media type in type 'chemical/x-genbank'
Unknown media type in type 'chemical/x-gulp'
Unknown media type in type 'chemical/x-hin'
Unknown media type in type 'chemical/x-inchi'
Unknown media type in type 'chemical/x-inchi-xml'
Unknown media type in type 'chemical/x-jcamp-dx'
Unknown media type in type 'chemical/x-macromodel-input'
Unknown media type in type 'chemical/x-mdl-molfile'
Unknown media type in type 'chemical/x-mdl-rdfile'
Unknown media type in type 'chemical/x-mdl-rxnfile'
Unknown media type in type 'chemical/x-mdl-sdfile'
Unknown media type in type 'chemical/x-mdl-tgf'
Unknown media type in type 'chemical/x-mmcif'
Unknown media type in type 'chemical/x-mol2'
Unknown media type in type 'chemical/x-mopac-graph'
Unknown media type in type 'chemical/x-mopac-input'
Unknown media type in type 'chemical/x-mopac-out'
Unknown media type in type 'chemical/x-msi-car'
Unknown media type in type 'chemical/x-msi-hessian'
Unknown media type in type 'chemical/x-msi-mdf'
Unknown media type in type 'chemical/x-msi-msi'
Unknown media type in type 'chemical/x-ncbi-asn1'
Unknown media type in type 'chemical/x-ncbi-asn1-binary'
Unknown media type in type 'chemical/x-ncbi-asn1-xml'
Unknown media type in type 'chemical/x-pdb'
Unknown media type in type 'chemical/x-shelx'
Unknown media type in type 'chemical/x-vmd'
Unknown media type in type 'chemical/x-xyz'
Unknown media type in type 'all/all'
Unknown media type in type 'all/allfiles'
[37/84] Deinstalling getdp-2.8.0_1...
[37/84] Deleting files for getdp-2.8.0_1: 100%
[38/84] Deinstalling py27-numpy-1.11.2_2,1...
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[42/84] Deinstalling xlapack-3.5.0_3...
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[43/84] Deinstalling hs-random-1.1...
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[44/84] Deinstalling hs-primitive-0.6...
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[45/84] Deinstalling hs-mtl-2.2.1...
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[46/84] Deinstalling hs-text-1.2.1.3...
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[51/84] Deinstalling lapack-3.5.0_1...
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pkg: /usr/local/share/doc/ghc-7.10.2/html/libraries/doc-index.html different
from original checksum, not removing
[70/84] Deleting files for ghc-7.10.2_1: 100%
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[84/84] Deinstalling gcc-ecj-4.5...
[84/84] Deleting files for gcc-ecj-4.5: 100%
<<<r...@unixdev.ceas>>> /home/bacon 1006 # pkg install py27-numpy
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
The following 8 package(s) will be affected (of 0 checked):
New packages to be INSTALLED:
py27-numpy: 1.11.2_2,1
suitesparse: 4.0.2_5
openblas: 0.2.19,1
gcc: 4.9.4
gcc-ecj: 4.5
lapack: 3.5.0_1
blas: 3.5.0_3
cblas: 1.0_5
Number of packages to be installed: 8
The process will require 576 MiB more space.
18 MiB to be downloaded.
Proceed with this action? [y/N]: y
[1/8] suitesparse-4.0.2_5.txz : 3% 48 KiB 49.2kB/s
00:2[1/8] suitesparse-4.0.2_5.txz : 100% 1 MiB 1.3MB/s
00:01
[2/8] openblas-0.2.19,1.txz : 10% 1 MiB 1.1MB/s
00:0[2/8] openblas-0.2.19,1.txz : 37% 4 MiB 2.6MB/s
00:0[2/8] openblas-0.2.19,1.txz : 64% 6 MiB 2.7MB/s
00:0[2/8] openblas-0.2.19,1.txz : 90% 9 MiB 2.6MB/s
00:0[2/8] openblas-0.2.19,1.txz : 100% 9 MiB 2.5MB/s
00:04
[3/8] gcc-ecj-4.5.txz : 58% 800 KiB 819.2kB/s
00:0[3/8] gcc-ecj-4.5.txz : 100% 1 MiB 1.4MB/s
00:01
[4/8] lapack-3.5.0_1.txz : 27% 2 MiB 1.8MB/s
00:0[4/8] lapack-3.5.0_1.txz : 67% 4 MiB 2.6MB/s
00:0[4/8] lapack-3.5.0_1.txz : 100% 6 MiB 3.2MB/s
00:02
[5/8] blas-3.5.0_3.txz : 100% 128 KiB 131.3kB/s
00:01
[6/8] cblas-1.0_5.txz : 100% 48 KiB 48.8kB/s
00:01
Checking integrity... done (0 conflicting)
[1/8] Installing gcc-ecj-4.5...
[1/8] Extracting gcc-ecj-4.5: 100%
[2/8] Installing gcc-4.9.4...
[2/8] Extracting gcc-4.9.4: 100%
[3/8] Installing openblas-0.2.19,1...
[3/8] Extracting openblas-0.2.19,1: 100%
[4/8] Installing blas-3.5.0_3...
[4/8] Extracting blas-3.5.0_3: 100%
[5/8] Installing suitesparse-4.0.2_5...
[5/8] Extracting suitesparse-4.0.2_5: 100%
[6/8] Installing lapack-3.5.0_1...
Extracting lapack-3.5.0_1: 100%
[1/8] Installing cblas-1.0_5...
[1/8] Extracting cblas-1.0_5: 100%
[2/8] Installing py27-numpy-1.11.2_2,1...
[2/8] Extracting py27-numpy-1.11.2_2,1: 100%
Message from gcc-4.9.4:
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc49
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
Message from cblas-1.0_5:
===> NOTICE:
The cblas port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port
FreeBSD unixdev.ceas bacon ~ 405: python junk.py
Hello
--
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You are the assignee for the bug.
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