Bug 207750 - math/py-numpy: Run-time errors as it can't find /usr/local/lib/gcc48/libgfortran.so.3
Summary: math/py-numpy: Run-time errors as it can't find /usr/local/lib/gcc48/libgfort...
Status: Closed Overcome By Events
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Only Me
Assignee: freebsd-python (Nobody)
Keywords: needs-qa
: 217968 (view as bug list)
Depends on: 208120
  Show dependency treegraph
Reported: 2016-03-06 18:58 UTC by Zane C. Bowers-Hadley
Modified: 2018-01-16 13:08 UTC (History)
8 users (show)

See Also:
bugzilla: maintainer-feedback? (python)

py-numpy build log (319.73 KB, text/plain)
2016-03-06 18:58 UTC, Zane C. Bowers-Hadley
no flags Details

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Description Zane C. Bowers-Hadley 2016-03-06 18:58:04 UTC
Created attachment 167772 [details]
py-numpy build log

Attempting to run something like osmocom_fft results in the issue below...

[kitsune@vixen42]/home/kitsune% osmocom_fft 
Traceback (most recent call last):
  File "/usr/local/bin/osmocom_fft", line 34, in <module>
    from gnuradio import blocks
  File "/usr/local/lib/python2.7/site-packages/gnuradio/blocks/__init__.py", line 34, in <module>
    from stream_to_vector_decimator import *
  File "/usr/local/lib/python2.7/site-packages/gnuradio/blocks/stream_to_vector_decimator.py", line 23, in <module>
    from gnuradio import gr
  File "/usr/local/lib/python2.7/site-packages/gnuradio/gr/__init__.py", line 44, in <module>
    from top_block import *
  File "/usr/local/lib/python2.7/site-packages/gnuradio/gr/top_block.py", line 30, in <module>
    from hier_block2 import hier_block2
  File "/usr/local/lib/python2.7/site-packages/gnuradio/gr/hier_block2.py", line 25, in <module>
    import pmt
  File "/usr/local/lib/python2.7/site-packages/pmt/__init__.py", line 58, in <module>
    from pmt_to_python import pmt_to_python as to_python
  File "/usr/local/lib/python2.7/site-packages/pmt/pmt_to_python.py", line 22, in <module>
    import numpy
  File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 180, 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/gcc48/libgfortran.so.3 not found
Exit 1

[kitsune@vixen42]/home/kitsune% uname -a
FreeBSD vixen42.vulpes.vvelox.net 10.3-BETA3 FreeBSD 10.3-BETA3 #1 r296090: Fri Feb 26 06:29:58 CST 2016     kitsune@vixen42.vulpes.vvelox.net:/usr/obj/usr/src/sys/GENERIC  amd64

[root@vixen42]/arc/src/ports/math/py-numpy# make showconfig
===> The following configuration options are available for py27-numpy-1.10.4,1:
     DOCS=off: Build and/or install documentation
     SUITESPARSE=on: Use AMD and UMFPACK in SuiteSparse
     TESTS=off: Install test suite requirements
====> Options available for the single BLASLIB: you have to select exactly one of them
     ATLAS=off: ATLAS blas implementation
     NETLIB=on: Blas implementation from Netlib
     OPENBLAS=off: OpenBLAS blas implementation
===> Use 'make config' to modify these settings

[root@vixen42]/arc/src/ports/math/py-numpy# cat /etc/src.conf 

[root@vixen42]/arc/src/ports/math/py-numpy# cat /etc/make.conf 
DEFAULT_VERSIONS+=    perl5=5.22
Comment 1 VK freebsd_triage 2016-06-14 17:05:34 UTC
I have tried replicating this issue as there was just another inquiry about that same failure in #freebsd@Freenode, but I couldn't. It wasn't related to osmocom_fft but merely importing numpy would trigger it.

I tried importing numpy and specifically, repeat that last import before the ImportError in this report, it didn't fail.

I built numpy with poudriere, and only had to change math/suitesparse config to use Netlib, because Openblas fails to build like that.

FreeBSD 10.3-p5 (amd64), ports from SVN head. Clean poudriere jail just for this test.
Comment 2 Olivier Duchateau freebsd_committer 2016-06-14 18:35:52 UTC
It's not Numpy's problem, but rather GNU Radio. I already encountered this error with several applications (especially Pitivi devel release, Flowblade).

Import of modules with Numpy is very "fragile", it doesn't support circular import (in fact relative import). GNU Radio must import each own modules globally (it's not a trivial process, especially when there are many).

Using sys.path() method is generally helpful.
Comment 3 Ryder Dain 2016-06-14 19:35:37 UTC
(In reply to Vladimir Krstulja from comment #1)

Hi Vlad, that was me inquiring, btw: yes, the port will build in poudriere just fine with math/suitesparse set to the same.

However, the (single) bug here probably bears repeating: 'import numpy' while using the interactive shell throws the same error as seen and reported in bug #188114, and can be solved the same way. Calling the shell as

    env LD_LIBRARY_PATH=/usr/local/lib/gcc48 python 

removes the problem. However, this *only* affected me in the interactive shell, which indicates it may likely be my problem – I'm building a clean instance now to try this out on without any prior settings, and I'll leave another comment if and when I find out what the difference was.
Comment 4 Shane 2016-06-15 08:31:29 UTC
This has come up a few times. Setting LD_LIBRARY_PATH is a known workaround. If you have several apps with this issue then you may want to set this in your shell startup file (.cshrc or .bashrc) or create a substitute script that is found in your path before the real app that sets this and then calls the real app.

bug #208120 is looking at a way to fix this properly.
Comment 5 Shawn Webb 2017-01-25 22:46:12 UTC
I'm seeing this, too. This is preventing me from running comms/gnuradio successfully.
Comment 6 Jason W. Bacon freebsd_committer 2017-03-21 13:48:34 UTC
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

<<<ROOT@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
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Unknown media type in type 'chemical/x-alchemy'
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<<<ROOT@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    
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Checking integrity... done (0 conflicting)
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[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


For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
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:


More information about port maintainership is available at:


FreeBSD unixdev.ceas  bacon ~ 405: python junk.py
Comment 7 Mark Linimon freebsd_committer freebsd_triage 2017-03-23 22:00:10 UTC
*** Bug 217968 has been marked as a duplicate of this bug. ***
Comment 8 Walter Schwarzenfeld freebsd_triage 2018-01-16 13:07:55 UTC
This port is deprecated; you may wish to reconsider installing it:

Unsupported by upstream. Use GCC 6 or newer instead..

seems overcome by events.