False alarm, I let it sit overnight and it appeared to pass after about 6 
hours of running. 

However, no surprise, another package halted the build with the error: 

cat ../gf2x/gf2x-thresholds.h > tuned_thresholds.h
./update-thresholds -o tuned_thresholds.h < tunetoom.res
/bin/sh: ./update-thresholds: Permission denied
Makefile:2205: recipe for target 'tune-toom' failed
make[4]: *** [tune-toom] Error 126
make[4]: Leaving directory 
'/home/evan.oman/sage-6.1/local/var/tmp/sage/build/gf2x-1.1.p0/src/src'
Makefile:976: recipe for target 'tune-toom' failed
make[3]: *** [tune-toom] Error 2
make[3]: Leaving directory 
'/home/evan.oman/sage-6.1/local/var/tmp/sage/build/gf2x-1.1.p0/src'
Error: Failed to tune gf2x.

What does it mean "Permission Denied"? Is that something to do with my 
system configuration and permissions?

I tried installing the spkg here <http://trac.sagemath.org/ticket/15014> but 
that didn't work and there seems to be some relevant discussion here 
<http://trac.sagemath.org/ticket/15316>along with a patch but I am not sure 
how to apply it or if it addresses my issue. 

This is beginning to seem like an exercise in futility, suppose thats what 
might happen when you try to use things that "Almost 
Work"<http://wiki.sagemath.org/SupportedPlatforms#Almost_works>
 haha.

Thank you all again for putting up with my amateur questions!

On Wednesday, March 12, 2014 5:15:10 AM UTC-5, Jean-Pierre Flori wrote:
>
>
>
> On Wednesday, March 12, 2014 11:10:40 AM UTC+1, Jean-Pierre Flori wrote:
>>
>>
>>
>> On Wednesday, March 12, 2014 11:07:38 AM UTC+1, Dima Pasechnik wrote:
>>>
>>> On 2014-03-12, Evan Oman <eva...@gmail.com> wrote: 
>>> > Hmm, it is just sitting there on that line again, is it expecting 
>>> input? It 
>>> > seems to be passing all of the tests. 
>>>
>>> you might instead just install the relevant Cygwin libs, and use them, 
>>> instead of building Altas. 
>>> See SAGE_ATLAS_LIB in 
>>>
>>> http://www.sagemath.org/doc/installation/source.html#environment-variables 
>>>
>>> Not sure this works anymore (because of me...). 
>>
> Just checked and it should still work.
> But note that the use of ATLAS in Sage on Cygwin (and other systems) is 
> kind of hackish and broken.
> See http://trac.sagemath.org/ticket/14390 and 
> http://trac.sagemath.org/ticket/15839 
>

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