An error in installation of HTSeq with numpy

[hibachings2013]

Hi,


I am trying to install HTSeq and i already checked out if numpy is installed well. but still got an error message that i need to install numpy before installation of HTSeq, i am not sure why it happens.
is there anyone who can advise me?

****
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> exit()
dhcp128036165072:HTSeq-0.5.1p3 chuck$ python setup.py install
Could not import 'setuptools', falling back to 'distutils'.
Setup script for HTSeq: Failed to import 'numpy'.
Please install numpy and then try again to install HTSeq.
dhcp128036165072:HTSeq-0.5.1p3 chuck$

****




many thanks in advance!

[hibachings2013]

More details Here:

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dhcp128036165072:HTSeq-0.5.1p3 chuck$ arch -i386 python
Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> exit()
dhcp128036165072:HTSeq-0.5.1p3 chuck$ python setup.py install
Could not import 'setuptools', falling back to 'distutils'.
Setup script for HTSeq: Failed to import 'numpy'.
Please install numpy and then try again to install HTSeq.
dhcp128036165072:HTSeq-0.5.1p3 chuck$

************

[Buprestid]

I'm bumping this thread because I am having the same problem.

I'm running Ubuntu 12.04 in VirtualBox on a Windows 7 machine.

I followed the instructions on the HTSeq install page to install numpy and matplotlib.
After unpackaging the HTSeq source tarball (HTSeq-0.5.4p3) and navigating to the correct directory I entered:

python setup.py build

and get the following error

Could not import 'setuptools', falling back to 'distutils'.
Setup script for HTSeq: Failed to import 'numpy'.
Please install numpy and then try again to install HTSeq.

If I re-run

sudo apt-get install build-essential python2.7-dev python-numpy python-matplotlib

Then I get this output:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
python-numpy is already the newest version.
python-matplotlib is already the newest version.
build-essential is already the newest version.
python2.7-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 526 not upgraded.

If I run:

sudo python setup.py install

I get the following:

Could not import 'setuptools', falling back to 'distutils'.
running install
running build
running build_py
creating build
creating build/lib.linux-i686-2.7
creating build/lib.linux-i686-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.linux-i686-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.linux-i686-2.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.linux-i686-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.linux-i686-2.7/HTSeq
creating build/lib.linux-i686-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.linux-i686-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.linux-i686-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.linux-i686-2.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.linux-i686-2.7
creating build/temp.linux-i686-2.7/src
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c src/_HTSeq.c -o build/temp.linux-i686-2.7/src/_HTSeq.o -w
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-i686-2.7/src/_HTSeq.o -o build/lib.linux-i686-2.7/HTSeq/_HTSeq.so
building 'HTSeq._StepVector' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.linux-i686-2.7/src/StepVector_wrap.o -w
cc1plus: warning: command line option вЂ˜-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-i686-2.7/src/StepVector_wrap.o -o build/lib.linux-i686-2.7/HTSeq/_StepVector.so
running build_scripts
creating build/scripts-2.7
copying and adjusting scripts/htseq-qa -> build/scripts-2.7
copying and adjusting scripts/htseq-count -> build/scripts-2.7
changing mode of build/scripts-2.7/htseq-qa from 644 to 755
changing mode of build/scripts-2.7/htseq-count from 644 to 755
running install_lib
copying build/lib.linux-i686-2.7/HTSeq/_StepVector.so -> /usr/local/lib/python2.7/dist-packages/HTSeq
copying build/lib.linux-i686-2.7/HTSeq/_HTSeq.so -> /usr/local/lib/python2.7/dist-packages/HTSeq
running install_scripts
copying build/scripts-2.7/htseq-count -> /usr/local/bin
copying build/scripts-2.7/htseq-qa -> /usr/local/bin
changing mode of /usr/local/bin/htseq-count to 755
changing mode of /usr/local/bin/htseq-qa to 755
running install_egg_info
Removing /usr/local/lib/python2.7/dist-packages/HTSeq-0.5.4p3.egg-info
Writing /usr/local/lib/python2.7/dist-packages/HTSeq-0.5.4p3.egg-info

I checked the install by running python and trying to import HTSeq and get:

>>> import htseq
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named htseq

Can anyone tell me what's going on?

[Simon Anders]

At the last step, you are supposed to type "import HTSeq". capitalization matters.

[Buprestid]

Thank you for the incredibly fast reply, Simon. I re-tried this with capitlization:

>>> import HTSeq
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named HTSeq

[Simon Anders]

Somthing seems to be broken with your Python installation.

You could check, with "import sys; print sys.path" where Python looks for libraries, and check whether the directory where you installed it to is listed.

[Buprestid]

Thanks again. Here is the result of print sys.path

['', '/home/CCP4/ccp4-6.2.0/share/python', '/home', '/home/CCP4/Python-2.6.7/lib/python26.zip',
 '/home/CCP4/Python-2.6.7/lib/python2.6', '/home/CCP4/Python-2.6.7/lib/python2.6/plat-linux2', 
'/home/CCP4/Python-2.6.7/lib/python2.6/lib-tk', '/home/CCP4/Python-2.6.7/lib/python2.6/lib-old',
 '/home/CCP4/Python-2.6.7/lib/python2.6/lib-dynload', '/home/CCP4/Python-2.6.7/lib/python2.6/site-packages']

I'll have to talk to my PI - the install was from a disk image he set up

[Simon Anders]

This look like you have two Python installations on your system: once in /usr and one in /home, and depending on whether you used 'sudo' or not, the command worked either on one or on the other.

I suppose you need to clean up this mess before proceeding.