[khmer] Problem installing khmer

[C. Titus Brown]

Excellent -- we'll put this in the docs somewhere!

thanks,
--titus

On Thu, Sep 05, 2013 at 11:53:08PM +0000, Cooper, Joshua T. wrote:
> Thanks Jordan and Titus!
> 
> Hi Jordan, I did just as you said, and I downloaded the git and simply used
> 
> make ARCHFLAGS="-arch x86_64"
> 
> and it works perfectly!!!! I'm also very glad it works!
> 
> Thank you so much!!
> 
> Cheers,
> 
> Josh
> ________________________________________
> From: Jordan Fish [jrdn.fish at gmail.com]
> Sent: Tuesday, September 03, 2013 8:54 PM
> To: C. Titus Brown
> Cc: Cooper, Joshua T.; khmer at lists.idyll.org
> Subject: Re: [khmer] Problem installing khmer
> 
> ./jumping in late
> 
> If you just want to get it working:
> 
> My best suggestion would be to just clone khmer again and build it
> from scratch (checking that you have the latest version of xcode
> couldn't hurt either). I just checked the latest version of khmer
> master from github on an osx 10.7 machine with python 2.7.5 and just
> running  `make` produces a valid, usable module.
> 
> First to jump back to the very first question, the lines:
> 
> ld: warning: ignoring file ../lib/*.o, file was built for unsupported
> file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0
> 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked
> (i386): ../lib/*.o
> 
> in the make output can be safely ignored, by default python will try
> to build libraries for all the supported architectures (this can be
> controlled with the ARCHFLAGS="-arch x86_64" environmental variable),
> on intel macs this defaults to i386, x86_64.  The c++ code for khmer
> build chain isn't designed to support that.
> 
> 
> 
> Next, the nosetest output, from make test(Symbol not found:
> __ZNKSt5ctypeIcE13_M_widen_initEv), does indicate an error, but it's
> uh...a doozy, it seems to indicate something going very awry with
> something inside the python build chain.
> 
> 
> 
> Finally, for a complete record, the assembly errors (bad register name
> xxx) stem from forcing the python build tools to use the gcc when it
> is still using g++ command line options (although I'm not quite sure
> how to force it to do that though...).
> 
> On Tue, Sep 3, 2013 at 8:35 PM, C. Titus Brown <ctb at msu.edu> wrote:
> > 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
> >
> > _______________________________________________
> > khmer mailing list
> > khmer at lists.idyll.org
> > http://lists.idyll.org/listinfo/khmer

-- 
C. Titus Brown, ctb at msu.edu