Numpy in Jupyter GCC-4.6 error

[Peter Sprague]

I have Jupyterhub running in a FreeBSD jail with Python 3.5.

$ pip3 install numpy

installs with no errors

$ python35
>> import numpy
>> [aka no error]

In notebook cell:

ln[]: import numpy as np

Gives error:
ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by /usr/local/lib/gcc48/libgfortran.so.3 not found

Ports installed include lapack, openblas, gcc (4.8), gcc46, cblas, pkgconfig

$ pip3 install scipy

Throws all kinds of errors related back to gcc 4.6 fortran

Any ideas how to fix this? Haven't found anything that works so far.

[Peter Sprague]

Setting LD_LIBRARY_PATH had worked with Python 2.7 in the past.  Doesn't help now.

https://groups.google.com/forum/#!msg/jupyter/pYqPONG0BBQ/4irri6TkAgAJ;context-place=forum/jupyter

[MinRK]

Can you compare os.environ in the two contexts? And `sys.executable` and `sys.path`?

-Min

On Sun, Oct 2, 2016 at 10:20 PM, Peter Sprague <geovisionen...@gmail.com> wrote:

Setting LD_LIBRARY_PATH had worked with Python 2.7 in the past.  Doesn't help now.

https://groups.google.com/forum/#!msg/jupyter/pYqPONG0BBQ/4irri6TkAgAJ;context-place=forum/jupyter

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[Peter Sprague]

Brute force solution:

Code:

$ portmaster gcc5
$ ln -s /usr/local/lib/gcc5 /usr/local/lib/gcc
$ ln -s /usr/local/bin/gcc5 /usr/local/lib/gcc

For this jail:
in /etc/make.conf

Code:

.if !empty(.CURDIR:M/usr/ports/*) && exists(/usr/local/bin/gcc5)
CC=gcc49
CXX=g++49
CPP=cpp49
.endif

Edit /etc/libmap.conf:

Code:

libgcc_s.so.1   gcc5/libgcc_s.so.1
libgomp.so.1    gcc5/libgomp.so.1
libobjc.so.3    gcc5/libobjc.so.4
libssp.so.0     gcc5/libssp.so.0
libstdc++.so.6  gcc5/libstdc++.so.6

See: http://unix.stackexchange.com/questions/130639/how-do-i-install-the-latest-gcc-on-freebsd