[khmer] Problem installing khmer

[C. Titus Brown]

On Tue, Sep 03, 2013 at 10:47:37PM +0000, Cooper, Joshua T. wrote:
> 
> ________________________________________
> From: C. Titus Brown [ctb at msu.edu]
> Sent: Tuesday, September 03, 2013 2:21 PM
> To: Cooper, Joshua T.
> Subject: Re: [khmer] Problem installing khmer
> 
> could you send this on to the khmer mailing list, please?
> 
> thanks,
> --titus
> 
> On Tue, Sep 03, 2013 at 03:40:01PM +0000, Cooper, Joshua T. wrote:
> > Okay sounds great. I ran the command as instructed and it produced a very long output.
> >
> > make CC=gcc CXX=g++ clean all test
> >
> > Output. See below.

Hi Josh,

wow, interesting problem:

> > creating build
> > creating build/temp.macosx-10.6-intel-2.7
> > gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I../lib -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _khmermodule.cc -o build/temp.macosx-10.6-intel-2.7/_khmermodule.o -g
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:14:junk `@GOTPCREL' after expression
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:14:`__ZTVN5khmer9HashtableE at GOTPCREL(%rip)' is not a valid base/index expression
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:15:bad register name `%rax'
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:16:bad register name `%rax'
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:31:bad register name `%rdi)'
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:33:bad register name `%rax)'
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:34:bad register name `%rax'
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:53:junk `@GOTPCREL' after expression
> > /var/folders/n6/3rn93kgj1m74t1lfyw8t1d200000gn/T//ccKjiL6b.s:53:`__ZTVN5khmer9HashtableE at GOTPCREL(%rip)' is not a valid base/index expression

I've never seen this before, but (just guessing from some googling) you
might want to turn off '-arch i386', which is compiling in 32-bit mode.
I'm... not sure how to do that, however.

Before we chase that down, though: is your XCode installation up to date?

cheers,
--titus