error installation
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- Python
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Description
I am getting this error while trying to install clodius.
`sudo pip install clodius`
> Collecting clodius
> Downloading https://files.pythonhosted.org/packages/7f/f4/9409fa3e1917cd8de859943de7dd77286391873c7aa0f55bccfdfad86cb2/clodius-0.9.3.tar.gz (90kB)
> 100% |████████████████████████████████| 92kB 2.1MB/s
> Requirement already satisfied: cython in /usr/local/lib64/python3.6/site-packages (from clodius) (0.28.5)
> Requirement already satisfied: numpy in /usr/local/lib64/python3.6/site-packages (from clodius) (1.15.1)
> Requirement already satisfied: negspy in /usr/local/lib/python3.6/site-packages (from clodius) (0.2.20)
> Requirement already satisfied: pysam in /usr/local/lib64/python3.6/site-packages (from clodius) (0.15.0)
> Requirement already satisfied: requests in /usr/lib/python3.6/site-packages (from clodius) (2.18.4)
> Requirement already satisfied: h5py in /usr/local/lib64/python3.6/site-packages (from clodius) (2.8.0)
> Requirement already satisfied: pandas in /usr/local/lib64/python3.6/site-packages (from clodius) (0.23.4)
> Requirement already satisfied: slugid in /usr/local/lib/python3.6/site-packages (from clodius) (1.0.7)
> Requirement already satisfied: sortedcontainers in /usr/local/lib/python3.6/site-packages (from clodius) (2.0.5)
> Requirement already satisfied: nose in /usr/local/lib/python3.6/site-packages (from clodius) (1.3.7)
> Requirement already satisfied: Click in /usr/local/lib64/python3.6/site-packages (from clodius) (6.7)
> Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /usr/lib/python3.6/site-packages (from requests->clodius) (3.0.4)
> Requirement already satisfied: idna<2.7,>=2.5 in /usr/lib/python3.6/site-packages (from requests->clodius) (2.5)
> Requirement already satisfied: urllib3<1.23,>=1.21.1 in /usr/lib/python3.6/site-packages (from requests->clodius) (1.22)
> Requirement already satisfied: six in /usr/lib/python3.6/site-packages (from h5py->clodius) (1.11.0)
> Requirement already satisfied: pytz>=2011k in /usr/lib/python3.6/site-packages (from pandas->clodius) (2017.2)
> Requirement already satisfied: python-dateutil>=2.5.0 in /usr/local/lib/python3.6/site-packages (from pandas->clodius) (2.7.3)
> Installing collected packages: clodius
> Running setup.py install for clodius ... error
> Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-t95klw2h/clodius/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-vpzh88ol/install-record.txt --single-version-externally-managed --compile:
> packages: ['clodius', 'scripts', 'test', 'clodius.cli']
> running install
> running build
> running build_py
> creating build
> creating build/lib.linux-x86_64-3.6
> creating build/lib.linux-x86_64-3.6/clodius
> copying clodius/describe_dataset.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/save_tiles.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/__init__.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/tiles.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/hdf_tiles.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/fpark.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/higlass_getter.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/chromosomes.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/db_tiles.py -> build/lib.linux-x86_64-3.6/clodius
> copying clodius/multivec.py -> build/lib.linux-x86_64-3.6/clodius
> creating build/lib.linux-x86_64-3.6/clodius/cli
> copying clodius/cli/utils.py -> build/lib.linux-x86_64-3.6/clodius/cli
> copying clodius/cli/__init__.py -> build/lib.linux-x86_64-3.6/clodius/cli
> copying clodius/cli/convert.py -> build/lib.linux-x86_64-3.6/clodius/cli
> copying clodius/cli/aggregate.py -> build/lib.linux-x86_64-3.6/clodius/cli
> running build_ext
> building 'clodius.fast' extension
> creating build/temp.linux-x86_64-3.6
> creating build/temp.linux-x86_64-3.6/clodius
> gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -mcet -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python3.6m -I/usr/local/lib64/python3.6/site-packages/numpy/core/include -I/usr/local/lib64/python3.6/site-packages/numpy/core/include -c clodius/fast.c -o build/temp.linux-x86_64-3.6/clodius/fast.o
> clodius/fast.c:24:10: fatal error: Python.h: No such file or directory
> #include "Python.h"
> ^~~~~~~~~~
> compilation terminated.
> error: command 'gcc' failed with exit status 1
>
> ----------------------------------------
> Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-t95klw2h/clodius/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-vpzh88ol/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-t95klw2h/clodius/
>
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