math/py-numpy cannot satisfy libgfortran dependency on libgcc_s/GCC_4.6.0 [WAS: Re: py27-pandas-0.13.1_1 conflict with py27-MySQLdb-1.2.3_4]

[John W. O'Brien]

On 5/18/14 12:30 AM, Irjohn Junus wrote:
> Thank you for looking at this. Apologies for my late reply it's been
> crazy busy at work lately.

I completely understand. As you can probably tell, my situation is similar.

> Here's answers to your questions:

>>    1.  What is the rpath stored in your copy of those numpy files?
>>        That is, what is the output from
>>
>>            cd /usr/local/lib/python2.7/site-packages/numpy/linalg
>>            readelf -d _umath_linalg.so | grep RPATH
>>            readelf -d lapack_lite.so | grep RPATH
>>
>>        ?

> readelf -d _umath_linalg.so | grep RPATH
>  0x000000000000000f (RPATH)              Library rpath:
> [/usr/local/lib/gcc47]
> readelf -d lapack_lite.so | grep RPATH
>  0x000000000000000f (RPATH)              Library rpath:
> [/usr/local/lib/gcc47]

That looks correct to me.

>>    2.  What is the contents of
>>    /usr/local/lib/python2.7/site-packages/numpy/distutils/site.cfg on your
>>    machine?

> cat /usr/local/lib/python2.7/site-packages/numpy/distutils/site.cfg
> [DEFAULT]
> lapack_type=atlas
> library_dirs =
> /usr/lib:/usr/local/lib:/usr/local/lib/gcc47/gcc/x86_64-portbld-freebsd9.1/4.7.3/../../../
> include_dirs =
> /usr/include:/usr/local/include:/usr/local/include/suitesparse
> src_dirs = /usr/local/src
> # search static libraries (.a) in preference to shared ones (.so)
> search_static_first = 0
> [atlas]
> library_dirs =
> /usr/local/lib:/usr/local/lib/gcc47/gcc/x86_64-portbld-freebsd9.1/4.7.3/../../../
> atlas_libs = lapack, blas

Just like mine.

>>    2.  What is the contents of /etc/make.conf on your machine?

> cat /etc/make.conf
> # added by use.perl 2013-03-25 18:12:09
> PERL_VERSION=5.12.4
> #WITH_MPM=worker

Totally innocuous.

>>     4.  How to you install and upgrade your ports? Build from source
>>         by hand? Build from source with the help of portmaster,
>>         poudriere, etc?
>>         Install binary packages with pkg_* or ports-mgmt/pkg (pkgng)?

> 4.
> I use portmaster exclusively, to install:
> portmaster --packages-build --delete-build-only port-name
> to upgrade:
> portmaster --dwv port-name

I'm taking a stab in the dark here. Based on the '-w' option, might
there be any stale libs hanging around in /usr/local/lib/compat/pkg?

I haven't been able to reproduce this, so I'm not sure which tree to
bark up next.

-John

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