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 6/14/14 10:24 PM, Irjohn Junus wrote:
> Here's my /usr/local/lib/compat/pkg:
> [ijunus at mars /]$ ls /usr/local/lib/compat/pkg
> libXau.so.0libgd.so.4libxcb-sync.so.0
> libaprutil-1.so.3libpcre.so.1libxcb-xkb.so.0
> libatalk.so.3libpcre16.so.0libxcb.so.2
> libffi.so.5libpixman-1.so.30lxml-3.1.0-py2.7.egg-info
> libfreetype.so.9libsvn_ra_neon-1.so.0
> libgcrypt.so.18libxcb-randr.so.1

Irjohn,

None of that looks suspicious to me.

I'm sorry to leave you hanging like this, but I'm at a loss for how to
proceed. If you have any updates, like things you've tried or---even
better---that the problem cleared up on its own, please let us know. In
the mean time, perhaps somebody else will have some insight into what's
going on.

-John

> On Wed, May 28, 2014 at 7:58 PM, John W. O'Brien <john at saltant.com
> <mailto:john at saltant.com>> wrote:
> 
>     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.


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