Question: Trouble Installing Cutadapt On A Linux Machine
0
gravatar for agatorano
6.4 years ago by
agatorano40
agatorano40 wrote:

I run: sudo python setup.py build

this yields this error message

running build
running build_py
running build_ext
building 'cutadapt.calign' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.6 -c cutadapt/calignmodule.c -o build/temp.linux-x86_64-2.6/cutadapt/calignmodule.o
cutadapt/calignmodule.c:23:20: error: Python.h: No such file or directory
cutadapt/calignmodule.c:53: error: expected ‘)’ before string constant
cutadapt/calignmodule.c:95: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
cutadapt/calignmodule.c:263: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘methods’
cutadapt/calignmodule.c: In function ‘initcalign’:
cutadapt/calignmodule.c:297: error: ‘PyObject’ undeclared (first use in this function)
cutadapt/calignmodule.c:297: error: (Each undeclared identifier is reported only once
cutadapt/calignmodule.c:297: error: for each function it appears in.)
cutadapt/calignmodule.c:297: error: ‘module’ undeclared (first use in this function)
cutadapt/calignmodule.c:297: warning: implicit declaration of function ‘Py_InitModule’
cutadapt/calignmodule.c:297: error: ‘methods’ undeclared (first use in this function)
cutadapt/calignmodule.c:300: error: ‘NULL’ undeclared (first use in this function)
error: command 'gcc' failed with exit status 1

I have no clue whey this would occur but similar messages have popped up what installing other things as well.

linux • 3.0k views
ADD COMMENTlink written 6.4 years ago by agatorano40
4
gravatar for Pierre Lindenbaum
6.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

The Python.h file is not in under the '-I' path. Check that you have installed the development files for python. Under ubuntu it should be something like:

sudo apt-get install python-dev
ADD COMMENTlink written 6.4 years ago by Pierre Lindenbaum115k

Thank you! that did it. Wish I knew about all of these required installs before reaching all of these roadblocks

ADD REPLYlink written 6.4 years ago by agatorano40
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