[khmer] Problem installing khmer

Cooper, Joshua T. jtcooper at ou.edu
Thu Sep 5 08:59:59 PDT 2013


Hi Titus,

I was figuring it was something to do with disabling i386, as like you said, I'm not sure quite how to do that either, Ha!

Looking at the AppStore, it appears I have the latest Xcode 4.6.3 installed and the command line tools from within preferences also installed.

Could have something to do with the python installation itself? 
 Where Python 2.7.5 Mac OS X 64-bit/32-bit x86-64/i386 Installer, I think it was installed it from the .dmg from    python.org, installing both x86_64 and i386 libraries. But maybe that has nothing to do with it? Just a thought.

Cheers,

Josh

________________________________________
From: C. Titus Brown [ctb at msu.edu]
Sent: Tuesday, September 03, 2013 7:35 PM
To: Cooper, Joshua T.
Cc: khmer at lists.idyll.org
Subject: Re: [khmer] Problem installing khmer

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




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