Trying to install RSeQC-python package

Question

[KG]

I am trying to install RSeQC

http://rseqc.sourceforge.net/

but keep getting error listed below although I have Python-lzo installed. Please help

Failed building wheel for python-lzo
  Running setup.py clean for python-lzo
Failed to build python-lzo
Installing collected packages: pysam, six, numpy, python-lzo, bx-python, cython, RSeQC
  Running setup.py install for python-lzo ... error
    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_5SgaO/python-lzo/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-iT8urN-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
    running install
    running build
    running build_ext
    building 'lzo' extension
    creating build
    creating build/temp.linux-x86_64-2.7
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-nbjU53/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/lzo -I/usr/include/python2.7 -c lzomodule.c -o build/temp.linux-x86_64-2.7/lzomodule.o
    lzomodule.c:35:10: fatal error: lzo/lzo1x.h: No such file or directory
     #include <lzo/lzo1x.h>
              ^~~~~~~~~~~~~
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

    ----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_5SgaO/python-lzo/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-iT8urN-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-_5SgaO/python-lzo/

[finswimmer]

Hello KG,

how have you tried to installed in? From source or via pip?

And please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

fin swimmer

[KG]

Thanks a lot. I tried both ways via pip as well as from source. same error both ways.

Thanks again

[mohammadhassanj]

Hi, Have you seen this https://stackoverflow.com/questions/40424097/file-not-found-error-when-pip-installing-python-lzo

Answer 1

[vimalkvn]

You haven't mentioned what Linux distribution this is. If you are on a Debian/Ubuntu system, you need to install the system library that python-lzo requires i.e., liblzo2-dev. On RPM based systems like Fedora or openSUSE, this package is most likely named lzo2-devel.