[khmer] Problem installing khmer

Cooper, Joshua T. jtcooper at ou.edu
Thu Sep 5 16:53:08 PDT 2013


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
>
> _______________________________________________
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> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer




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