[khmer] (no subject)

Jordan Fish jrdn.fish at gmail.com
Wed Oct 30 07:30:12 PDT 2013


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

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

sudo apt-get install python-dev


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

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