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compilation problem

compilation problem

From:
Haluk Dogan
Date:
2012-06-14 @ 21:00
Hi,

I got the following error during compilation. Do you have any solution for
this?

Thanks.

x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7 -c
_khmermodule.cc -o build/temp.linux-x86_64-2.7/_
khmermodule.o -g
In file included from /usr/include/python2.7/Python.h:8:0,
                 from _khmermodule.cc:7:
/usr/include/python2.7/pyconfig.h:1158:0: warning: "_POSIX_C_SOURCE"
redefined
/usr/include/features.h:164:0: note: this is the location of the previous
definition
/usr/include/python2.7/pyconfig.h:1180:0: warning: "_XOPEN_SOURCE" redefined
/usr/include/features.h:166:0: note: this is the location of the previous
definition
_khmermodule.cc: In function 'PyObject*
hash_abundance_distribution(PyObject*, PyObject*)':
_khmermodule.cc:1292:3: error: 'is_hashbits_obj' was not declared in this
scope
error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
make: *** [python_files] Error 1


-- 
HD

Re: [khmer] compilation problem

From:
Date:
2012-06-14 @ 23:17
Hi Haluk,

 From which Git repo did you clone? ged-lab/khmer? ctb/khmer? A  
different one? I.e., if you run the following commands in your working  
copy, what do they report:
   git status
   git remote -v

Thanks.

Quoting Haluk Dogan <hlk.dogan@gmail.com>:

> Hi,
>
> I got the following error during compilation. Do you have any solution for
> this?
>
> Thanks.
>
> x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7 -c
> _khmermodule.cc -o build/temp.linux-x86_64-2.7/_
> khmermodule.o -g
> In file included from /usr/include/python2.7/Python.h:8:0,
>                  from _khmermodule.cc:7:
> /usr/include/python2.7/pyconfig.h:1158:0: warning: "_POSIX_C_SOURCE"
> redefined
> /usr/include/features.h:164:0: note: this is the location of the previous
> definition
> /usr/include/python2.7/pyconfig.h:1180:0: warning: "_XOPEN_SOURCE" redefined
> /usr/include/features.h:166:0: note: this is the location of the previous
> definition
> _khmermodule.cc: In function 'PyObject*
> hash_abundance_distribution(PyObject*, PyObject*)':
> _khmermodule.cc:1292:3: error: 'is_hashbits_obj' was not declared in this
> scope
> error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
> make: *** [python_files] Error 1
>
>
> --
> HD
>


Re: [khmer] compilation problem

From:
azer
Date:
2012-06-15 @ 03:38
Error Message:
running build_ext
building 'khmer._khmermodule' extension
x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7 -c
_khmermodule.cc -o build/temp.linux-x86_64-2.7/_khmermodule.o -g
In file included from /usr/include/python2.7/Python.h:8,
                 from _khmermodule.cc:7:
/usr/include/python2.7/pyconfig.h:1158:1: warning: "_POSIX_C_SOURCE"
redefined
In file included from

/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
                 from

/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
                 from
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
                 from _khmermodule.cc:5:
/usr/include/features.h:163:1: warning: this is the location of the
previous definition
In file included from /usr/include/python2.7/Python.h:8,
                 from _khmermodule.cc:7:
/usr/include/python2.7/pyconfig.h:1180:1: warning: "_XOPEN_SOURCE" redefined
In file included from

/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
                 from

/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
                 from
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
                 from _khmermodule.cc:5:
/usr/include/features.h:165:1: warning: this is the location of the
previous definition
_khmermodule.cc: In function ‘PyObject*
hash_abundance_distribution(PyObject*, PyObject*)’:
_khmermodule.cc:1292: error: ‘is_hashbits_obj’ was not declared in this
scope
error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
make: *** [python_files] Error 1


$ git status
# On branch master
nothing to commit (working directory clean)

$ git remote -v
origin git://github.com/ctb/khmer.git (fetch)
origin git://github.com/ctb/khmer.git (push)

On Fri, Jun 15, 2012 at 7:17 AM, <em@msu.edu> wrote:

> Hi Haluk,
>
>  From which Git repo did you clone? ged-lab/khmer? ctb/khmer? A
> different one? I.e., if you run the following commands in your working
> copy, what do they report:
>   git status
>   git remote -v
>
> Thanks.
>
> Quoting Haluk Dogan <hlk.dogan@gmail.com>:
>
> > Hi,
> >
> > I got the following error during compilation. Do you have any solution
> for
> > this?
> >
> > Thanks.
> >
> > x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7
> -c
> > _khmermodule.cc -o build/temp.linux-x86_64-2.7/_
> > khmermodule.o -g
> > In file included from /usr/include/python2.7/Python.h:8:0,
> >                  from _khmermodule.cc:7:
> > /usr/include/python2.7/pyconfig.h:1158:0: warning: "_POSIX_C_SOURCE"
> > redefined
> > /usr/include/features.h:164:0: note: this is the location of the previous
> > definition
> > /usr/include/python2.7/pyconfig.h:1180:0: warning: "_XOPEN_SOURCE"
> redefined
> > /usr/include/features.h:166:0: note: this is the location of the previous
> > definition
> > _khmermodule.cc: In function 'PyObject*
> > hash_abundance_distribution(PyObject*, PyObject*)':
> > _khmermodule.cc:1292:3: error: 'is_hashbits_obj' was not declared in this
> > scope
> > error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
> > make: *** [python_files] Error 1
> >
> >
> > --
> > HD
> >
>
>
>
>

Re: [khmer] compilation problem

From:
Haluk Dogan
Date:
2012-06-15 @ 12:13
I comment out the line number 1292 [ assert(is_hashbits_obj(tracking_obj));
] in ./python/_khmermodule.cc and now it has compiled.

On Fri, Jun 15, 2012 at 6:38 AM, azer <azerxu@gmail.com> wrote:

> Error Message:
> running build_ext
> building 'khmer._khmermodule' extension
> x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7
> -c _khmermodule.cc -o build/temp.linux-x86_64-2.7/_khmermodule.o -g
> In file included from /usr/include/python2.7/Python.h:8,
>                  from _khmermodule.cc:7:
> /usr/include/python2.7/pyconfig.h:1158:1: warning: "_POSIX_C_SOURCE"
> redefined
> In file included from
> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
>                  from
> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
>                  from
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
>                  from _khmermodule.cc:5:
> /usr/include/features.h:163:1: warning: this is the location of the
> previous definition
> In file included from /usr/include/python2.7/Python.h:8,
>                  from _khmermodule.cc:7:
> /usr/include/python2.7/pyconfig.h:1180:1: warning: "_XOPEN_SOURCE"
> redefined
> In file included from
> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
>                  from
> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
>                  from
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
>                  from _khmermodule.cc:5:
> /usr/include/features.h:165:1: warning: this is the location of the
> previous definition
> _khmermodule.cc: In function ‘PyObject*
> hash_abundance_distribution(PyObject*, PyObject*)’:
> _khmermodule.cc:1292: error: ‘is_hashbits_obj’ was not declared in this
> scope
> error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
> make: *** [python_files] Error 1
>
>
> $ git status
> # On branch master
> nothing to commit (working directory clean)
>
> $ git remote -v
> origin git://github.com/ctb/khmer.git (fetch)
> origin git://github.com/ctb/khmer.git (push)
>
> On Fri, Jun 15, 2012 at 7:17 AM, <em@msu.edu> wrote:
>
>> Hi Haluk,
>>
>>  From which Git repo did you clone? ged-lab/khmer? ctb/khmer? A
>> different one? I.e., if you run the following commands in your working
>> copy, what do they report:
>>   git status
>>   git remote -v
>>
>> Thanks.
>>
>> Quoting Haluk Dogan <hlk.dogan@gmail.com>:
>>
>> > Hi,
>> >
>> > I got the following error during compilation. Do you have any solution
>> for
>> > this?
>> >
>> > Thanks.
>> >
>> > x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib
>> -I/usr/include/python2.7 -c
>> > _khmermodule.cc -o build/temp.linux-x86_64-2.7/_
>> > khmermodule.o -g
>> > In file included from /usr/include/python2.7/Python.h:8:0,
>> >                  from _khmermodule.cc:7:
>> > /usr/include/python2.7/pyconfig.h:1158:0: warning: "_POSIX_C_SOURCE"
>> > redefined
>> > /usr/include/features.h:164:0: note: this is the location of the
>> previous
>> > definition
>> > /usr/include/python2.7/pyconfig.h:1180:0: warning: "_XOPEN_SOURCE"
>> redefined
>> > /usr/include/features.h:166:0: note: this is the location of the
>> previous
>> > definition
>> > _khmermodule.cc: In function 'PyObject*
>> > hash_abundance_distribution(PyObject*, PyObject*)':
>> > _khmermodule.cc:1292:3: error: 'is_hashbits_obj' was not declared in
>> this
>> > scope
>> > error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
>> > make: *** [python_files] Error 1
>> >
>> >
>> > --
>> > HD
>> >
>>
>>
>>
>>
>


-- 
HD

Re: [khmer] compilation problem

From:
C. Titus Brown
Date:
2012-06-15 @ 12:22
On Fri, Jun 15, 2012 at 03:13:16PM +0300, Haluk Dogan wrote:
> I comment out the line number 1292 [ assert(is_hashbits_obj(tracking_obj));
> ] in ./python/_khmermodule.cc and now it has compiled.

OK, thanks -- it looks like the #define for is_hashbits_obj is below the
first use, which didn't matter for older versions of gcc but has since
become problematic, apparently.  Easy to fix -- thanks for letting us know!

cheers,
--titus

> On Fri, Jun 15, 2012 at 6:38 AM, azer <azerxu@gmail.com> wrote:
> 
> > Error Message:
> > running build_ext
> > building 'khmer._khmermodule' extension
> > x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7
> > -c _khmermodule.cc -o build/temp.linux-x86_64-2.7/_khmermodule.o -g
> > In file included from /usr/include/python2.7/Python.h:8,
> >                  from _khmermodule.cc:7:
> > /usr/include/python2.7/pyconfig.h:1158:1: warning: "_POSIX_C_SOURCE"
> > redefined
> > In file included from
> > 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
> >                  from
> > 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
> >                  from
> > /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
> >                  from _khmermodule.cc:5:
> > /usr/include/features.h:163:1: warning: this is the location of the
> > previous definition
> > In file included from /usr/include/python2.7/Python.h:8,
> >                  from _khmermodule.cc:7:
> > /usr/include/python2.7/pyconfig.h:1180:1: warning: "_XOPEN_SOURCE"
> > redefined
> > In file included from
> > 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
> >                  from
> > 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
> >                  from
> > /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
> >                  from _khmermodule.cc:5:
> > /usr/include/features.h:165:1: warning: this is the location of the
> > previous definition
> > _khmermodule.cc: In function ???PyObject*
> > hash_abundance_distribution(PyObject*, PyObject*)???:
> > _khmermodule.cc:1292: error: ???is_hashbits_obj??? was not declared in this
> > scope
> > error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
> > make: *** [python_files] Error 1
> >
> >
> > $ git status
> > # On branch master
> > nothing to commit (working directory clean)
> >
> > $ git remote -v
> > origin git://github.com/ctb/khmer.git (fetch)
> > origin git://github.com/ctb/khmer.git (push)
> >
> > On Fri, Jun 15, 2012 at 7:17 AM, <em@msu.edu> wrote:
> >
> >> Hi Haluk,
> >>
> >>  From which Git repo did you clone? ged-lab/khmer? ctb/khmer? A
> >> different one? I.e., if you run the following commands in your working
> >> copy, what do they report:
> >>   git status
> >>   git remote -v
> >>
> >> Thanks.
> >>
> >> Quoting Haluk Dogan <hlk.dogan@gmail.com>:
> >>
> >> > Hi,
> >> >
> >> > I got the following error during compilation. Do you have any solution
> >> for
> >> > this?
> >> >
> >> > Thanks.
> >> >
> >> > x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib
> >> -I/usr/include/python2.7 -c
> >> > _khmermodule.cc -o build/temp.linux-x86_64-2.7/_
> >> > khmermodule.o -g
> >> > In file included from /usr/include/python2.7/Python.h:8:0,
> >> >                  from _khmermodule.cc:7:
> >> > /usr/include/python2.7/pyconfig.h:1158:0: warning: "_POSIX_C_SOURCE"
> >> > redefined
> >> > /usr/include/features.h:164:0: note: this is the location of the
> >> previous
> >> > definition
> >> > /usr/include/python2.7/pyconfig.h:1180:0: warning: "_XOPEN_SOURCE"
> >> redefined
> >> > /usr/include/features.h:166:0: note: this is the location of the
> >> previous
> >> > definition
> >> > _khmermodule.cc: In function 'PyObject*
> >> > hash_abundance_distribution(PyObject*, PyObject*)':
> >> > _khmermodule.cc:1292:3: error: 'is_hashbits_obj' was not declared in
> >> this
> >> > scope
> >> > error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
> >> > make: *** [python_files] Error 1
> >> >
> >> >
> >> > --
> >> > HD
> >> >
> >>
> >>
> >>
> >>
> >
> 
> 
> -- 
> HD

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

Re: [khmer] compilation problem

From:
Eric McDonald
Date:
2012-06-15 @ 16:33
I was unable to reproduce the problem with GCC 4.4.5. I think the issue
is that different versions of the 'distutils' package are being used and
they are adding different flags by default. In particular, my build
mixes in the "-DNDEBUG" flag, which causes the 'assert' macros to expand
to nothing. The not-yet-defined macro inside the assert is thus not
invoked before its definition.

I do, however, agree that the fix is to ensure that macros are defined
before they are used.

Thanks for the bug report.

On 6/15/2012 8:22 AM, C. Titus Brown wrote:
> On Fri, Jun 15, 2012 at 03:13:16PM +0300, Haluk Dogan wrote:
>> I comment out the line number 1292 [ assert(is_hashbits_obj(tracking_obj));
>> ] in ./python/_khmermodule.cc and now it has compiled.
> 
> OK, thanks -- it looks like the #define for is_hashbits_obj is below the
> first use, which didn't matter for older versions of gcc but has since
> become problematic, apparently.  Easy to fix -- thanks for letting us know!
> 
> cheers,
> --titus
> 
>> On Fri, Jun 15, 2012 at 6:38 AM, azer <azerxu@gmail.com> wrote:
>>
>>> Error Message:
>>> running build_ext
>>> building 'khmer._khmermodule' extension
>>> x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7
>>> -c _khmermodule.cc -o build/temp.linux-x86_64-2.7/_khmermodule.o -g
>>> In file included from /usr/include/python2.7/Python.h:8,
>>>                  from _khmermodule.cc:7:
>>> /usr/include/python2.7/pyconfig.h:1158:1: warning: "_POSIX_C_SOURCE"
>>> redefined
>>> In file included from
>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
>>>                  from
>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
>>>                  from
>>> /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
>>>                  from _khmermodule.cc:5:
>>> /usr/include/features.h:163:1: warning: this is the location of the
>>> previous definition
>>> In file included from /usr/include/python2.7/Python.h:8,
>>>                  from _khmermodule.cc:7:
>>> /usr/include/python2.7/pyconfig.h:1180:1: warning: "_XOPEN_SOURCE"
>>> redefined
>>> In file included from
>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
>>>                  from
>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
>>>                  from
>>> /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
>>>                  from _khmermodule.cc:5:
>>> /usr/include/features.h:165:1: warning: this is the location of the
>>> previous definition
>>> _khmermodule.cc: In function ???PyObject*
>>> hash_abundance_distribution(PyObject*, PyObject*)???:
>>> _khmermodule.cc:1292: error: ???is_hashbits_obj??? was not declared in this
>>> scope
>>> error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
>>> make: *** [python_files] Error 1
>>>
>>>
>>> $ git status
>>> # On branch master
>>> nothing to commit (working directory clean)
>>>
>>> $ git remote -v
>>> origin git://github.com/ctb/khmer.git (fetch)
>>> origin git://github.com/ctb/khmer.git (push)
>>>
>>> On Fri, Jun 15, 2012 at 7:17 AM, <em@msu.edu> wrote:
>>>
>>>> Hi Haluk,
>>>>
>>>>  From which Git repo did you clone? ged-lab/khmer? ctb/khmer? A
>>>> different one? I.e., if you run the following commands in your working
>>>> copy, what do they report:
>>>>   git status
>>>>   git remote -v
>>>>
>>>> Thanks.
>>>>
>>>> Quoting Haluk Dogan <hlk.dogan@gmail.com>:
>>>>
>>>>> Hi,
>>>>>
>>>>> I got the following error during compilation. Do you have any solution
>>>> for
>>>>> this?
>>>>>
>>>>> Thanks.
>>>>>
>>>>> x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib
>>>> -I/usr/include/python2.7 -c
>>>>> _khmermodule.cc -o build/temp.linux-x86_64-2.7/_
>>>>> khmermodule.o -g
>>>>> In file included from /usr/include/python2.7/Python.h:8:0,
>>>>>                  from _khmermodule.cc:7:
>>>>> /usr/include/python2.7/pyconfig.h:1158:0: warning: "_POSIX_C_SOURCE"
>>>>> redefined
>>>>> /usr/include/features.h:164:0: note: this is the location of the
>>>> previous
>>>>> definition
>>>>> /usr/include/python2.7/pyconfig.h:1180:0: warning: "_XOPEN_SOURCE"
>>>> redefined
>>>>> /usr/include/features.h:166:0: note: this is the location of the
>>>> previous
>>>>> definition
>>>>> _khmermodule.cc: In function 'PyObject*
>>>>> hash_abundance_distribution(PyObject*, PyObject*)':
>>>>> _khmermodule.cc:1292:3: error: 'is_hashbits_obj' was not declared in
>>>> this
>>>>> scope
>>>>> error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
>>>>> make: *** [python_files] Error 1
>>>>>
>>>>>
>>>>> --
>>>>> HD
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>> -- 
>> HD
> 

Re: [khmer] compilation problem

From:
Eric McDonald
Date:
2012-06-15 @ 17:40
A fix has now been pushed to the 'master' branch 'ged-lab/khmer'
repository. For those using this repository, a simple:
  git pull
should suffice.

On 6/15/2012 12:33 PM, Eric McDonald wrote:
> I was unable to reproduce the problem with GCC 4.4.5. I think the issue
> is that different versions of the 'distutils' package are being used and
> they are adding different flags by default. In particular, my build
> mixes in the "-DNDEBUG" flag, which causes the 'assert' macros to expand
> to nothing. The not-yet-defined macro inside the assert is thus not
> invoked before its definition.
> 
> I do, however, agree that the fix is to ensure that macros are defined
> before they are used.
> 
> Thanks for the bug report.
> 
> On 6/15/2012 8:22 AM, C. Titus Brown wrote:
>> On Fri, Jun 15, 2012 at 03:13:16PM +0300, Haluk Dogan wrote:
>>> I comment out the line number 1292 [ assert(is_hashbits_obj(tracking_obj));
>>> ] in ./python/_khmermodule.cc and now it has compiled.
>>
>> OK, thanks -- it looks like the #define for is_hashbits_obj is below the
>> first use, which didn't matter for older versions of gcc but has since
>> become problematic, apparently.  Easy to fix -- thanks for letting us know!
>>
>> cheers,
>> --titus
>>
>>> On Fri, Jun 15, 2012 at 6:38 AM, azer <azerxu@gmail.com> wrote:
>>>
>>>> Error Message:
>>>> running build_ext
>>>> building 'khmer._khmermodule' extension
>>>> x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib -I/usr/include/python2.7
>>>> -c _khmermodule.cc -o build/temp.linux-x86_64-2.7/_khmermodule.o -g
>>>> In file included from /usr/include/python2.7/Python.h:8,
>>>>                  from _khmermodule.cc:7:
>>>> /usr/include/python2.7/pyconfig.h:1158:1: warning: "_POSIX_C_SOURCE"
>>>> redefined
>>>> In file included from
>>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
>>>>                  from
>>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
>>>>                  from
>>>> /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
>>>>                  from _khmermodule.cc:5:
>>>> /usr/include/features.h:163:1: warning: this is the location of the
>>>> previous definition
>>>> In file included from /usr/include/python2.7/Python.h:8,
>>>>                  from _khmermodule.cc:7:
>>>> /usr/include/python2.7/pyconfig.h:1180:1: warning: "_XOPEN_SOURCE"
>>>> redefined
>>>> In file included from
>>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/os_defines.h:39,
>>>>                  from
>>>> 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/x86_64-pc-linux-gnu/bits/c++config.h:243,
>>>>                  from
>>>> /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/include/g++-v4/iostream:39,
>>>>                  from _khmermodule.cc:5:
>>>> /usr/include/features.h:165:1: warning: this is the location of the
>>>> previous definition
>>>> _khmermodule.cc: In function ???PyObject*
>>>> hash_abundance_distribution(PyObject*, PyObject*)???:
>>>> _khmermodule.cc:1292: error: ???is_hashbits_obj??? was not declared in this
>>>> scope
>>>> error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
>>>> make: *** [python_files] Error 1
>>>>
>>>>
>>>> $ git status
>>>> # On branch master
>>>> nothing to commit (working directory clean)
>>>>
>>>> $ git remote -v
>>>> origin git://github.com/ctb/khmer.git (fetch)
>>>> origin git://github.com/ctb/khmer.git (push)
>>>>
>>>> On Fri, Jun 15, 2012 at 7:17 AM, <em@msu.edu> wrote:
>>>>
>>>>> Hi Haluk,
>>>>>
>>>>>  From which Git repo did you clone? ged-lab/khmer? ctb/khmer? A
>>>>> different one? I.e., if you run the following commands in your working
>>>>> copy, what do they report:
>>>>>   git status
>>>>>   git remote -v
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Quoting Haluk Dogan <hlk.dogan@gmail.com>:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I got the following error during compilation. Do you have any solution
>>>>> for
>>>>>> this?
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> x86_64-pc-linux-gnu-g++ -pthread -fPIC -I../lib
>>>>> -I/usr/include/python2.7 -c
>>>>>> _khmermodule.cc -o build/temp.linux-x86_64-2.7/_
>>>>>> khmermodule.o -g
>>>>>> In file included from /usr/include/python2.7/Python.h:8:0,
>>>>>>                  from _khmermodule.cc:7:
>>>>>> /usr/include/python2.7/pyconfig.h:1158:0: warning: "_POSIX_C_SOURCE"
>>>>>> redefined
>>>>>> /usr/include/features.h:164:0: note: this is the location of the
>>>>> previous
>>>>>> definition
>>>>>> /usr/include/python2.7/pyconfig.h:1180:0: warning: "_XOPEN_SOURCE"
>>>>> redefined
>>>>>> /usr/include/features.h:166:0: note: this is the location of the
>>>>> previous
>>>>>> definition
>>>>>> _khmermodule.cc: In function 'PyObject*
>>>>>> hash_abundance_distribution(PyObject*, PyObject*)':
>>>>>> _khmermodule.cc:1292:3: error: 'is_hashbits_obj' was not declared in
>>>>> this
>>>>>> scope
>>>>>> error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
>>>>>> make: *** [python_files] Error 1
>>>>>>
>>>>>>
>>>>>> --
>>>>>> HD
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>> -- 
>>> HD
>>