[khmer] (no subject)

[Jordan Fish]

Hi,

First things first, the khmer mailing list moved from librelist to
khmer at lists.idyll.org, you can register for the mailing list at
http://lists.idyll.org/listinfo/khmer.

Your problem installing khmer stems from not having the python
development package installed, on ubuntu you can install it with the
command

sudo apt-get install python-dev

Jordan

On Wed, Oct 30, 2013 at 4:13 AM, Mamoon Rashid <rashidmamoon at gmail.com> wrote:
> Hi there,
> I need help to install and run khmer on my local system [Linux kw12979
> 3.2.0-45-generic #70-Ubuntu SMP Wed May 29 20:12:06 UTC 2013 x86_64 x86_64
> x86_64 GNU/Linux].
> I am following this tutorial
> [http://ged.msu.edu/angus/diginorm-2012/tutorial.html] and installed
> "screed" as root it was ok, BUT doing "make test" in khmer directory throws
> following errors-
> [
> rashm0a at kw12979:~/software/diginorm/khmer$ sudo make test
> cd lib && make
> make[1]: Entering directory `/home/rashm0a/software/diginorm/khmer/lib'
> make[1]: Nothing to be done for `all'.
> make[1]: Leaving directory `/home/rashm0a/software/diginorm/khmer/lib'
> cd python && python setup.py build_ext -i
> running build_ext
> building 'khmer._khmermodule' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -fPIC -I../lib -I/usr/include/python2.7 -c
> _khmermodule.cc -o build/temp.linux-x86_64-2.7/_khmermodule.o -g
> cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
> Ada/C/ObjC but not for C++ [enabled by default]
> _khmermodule.cc:7:20: fatal error: Python.h: No such file or directory
> compilation terminated.
> error: command 'gcc' failed with exit status 1
> make: *** [python_files] Error 1
> ]
>
> please help me to install it correctly.
> Thanks in anticipation
> Mamoon
>
> --
> Mamoon Rashid, PhD
> Post-Doctoral Fellow
> Marine Microbial Ecology Lab
> Red Sea Research Center
> 4700 King Abdullah University of Science and Technology (KAUST)
> Room 2217-WS03, Ibn Al-Haytham Building (2)
> 4700 King Abdullah University of Science and Technology
> Thuwal 23955-6900, Kingdom of Saudi Arabia
> Office: +966 (0) 2 808-2671