Installation problems in python 3

[cebel]

1. made a "clean" python enviroment with
   mkvirtualenv -p /usr/bin/python3 pypath
   version check:
   src/pypath/__version__:0.7.17
2. Install
   pip install git+git://github.com/saezlab/pypath.git
   traceback from install:

complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>                                                                                                                                                                                                                                     
      File "/tmp/pip-build-tip722io/fisher/setup.py", line 2, in <module>                                                                                                                                                                                                      
        import numpy as np                                                                                                                                                                                                                                                     
    ImportError: No module named 'numpy'

3. Then I did a
   pip install numpy
4. Again:
   pip install git+git://github.com/saezlab/pypath.git
   traceback:

    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "/tmp/pip-build-pwnyxrtw/pycurl/setup.py", line 103, in configure_unix
        stdout=subprocess.PIPE, stderr=subprocess.PIPE)
      File "/usr/lib/python3.5/subprocess.py", line 947, in __init__
        restore_signals, start_new_session)
      File "/usr/lib/python3.5/subprocess.py", line 1551, in _execute_child
        raise child_exception_type(errno_num, err_msg)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-pwnyxrtw/pycurl/setup.py", line 823, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-build-pwnyxrtw/pycurl/setup.py", line 497, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-build-pwnyxrtw/pycurl/setup.py", line 71, in __init__
        self.configure()
      File "/tmp/pip-build-pwnyxrtw/pycurl/setup.py", line 107, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-pwnyxrtw/pycurl/

Hope this helps

[deeenes]

Indeed this issue was still present because fisher imports numpy in egg_info. Now we get fisher from the repo of Fabio Tinocci who applied a workaround but the developer of fisher unfortunately did not merge their pull request. Overall the issue got fixed in 0.7.53.

[cebel]

Dear deeenes,

thanks for your quick fixes, but I have still problems. The problem above I think was the missing libcurl4-openssl-dev

This time:
mkvirtualenv -p /usr/bin/python3 pypath
git clone git://github.com/saezlab/pypath.git

src/pypath/version:7.0.53

I additionally installed (on Ubuntu):

sudo apt-get install libcurl4-openssl-dev
sudo apt-get install python-igraph
sudo apt-get install libxml2
libxml2 is already the newest version (2.9.3+dfsg1-1ubuntu0.2)

cd pypath
pip install -e .

error message:
[...]
/usr/bin/ld: cannot find -lxml2
collect2: error: ld returned 1 exit status
Makefile:2357: recipe for target 'libigraph.la' failed
make[3]: *** [libigraph.la] Error 1
make[3]: Leaving directory '/tmp/pip-build-fo6s1cwx/python-igraph/tmp/igraph.bywmswzr/igraph-0.7.1/src'
Makefile:1377: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/tmp/pip-build-fo6s1cwx/python-igraph/tmp/igraph.bywmswzr/igraph-0.7.1/src'
Makefile:480: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/tmp/pip-build-fo6s1cwx/python-igraph/tmp/igraph.bywmswzr/igraph-0.7.1'
Makefile:382: recipe for target 'all' failed
make: *** [all] Error 2
Could not download and compile the C core of igraph.
----------------------------------------
Command
"/home/ceb/.virtualenvs/pypath/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-fo6s1cwx/python-igraph/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-p0ru8skl-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/ceb/.virtualenvs/pypath/include/site/python3.5/python-igraph" failed with error code 1 in /tmp/pip-build-fo6s1cwx/python-igraph/

[deeenes]

Hi Christian, Does it occure only on Ubuntu or also on Mac? 2017-09-05 9:56 GMT+02:00 Christian Ebeling <notifications@github.com>:

…

Dear deeenes, thanks for your quick fixes, but I have still problems. The problem above I think was the missing libcurl4-openssl-dev This time: mkvirtualenv -p /usr/bin/python3 pypath git clone git://github.com/saezlab/pypath.git src/pypath/*version*:7.0.53 I additionally installed (on Ubuntu): sudo apt-get install libcurl4-openssl-dev sudo apt-get install python-igraph sudo apt-get install libxml2 libxml2 is already the newest version (2.9.3+dfsg1-1ubuntu0.2) cd pypath pip install -e . error message: [...] /usr/bin/ld: cannot find -lxml2 collect2: error: ld returned 1 exit status Makefile:2357: recipe for target 'libigraph.la' failed make[3]: *** [libigraph.la] Error 1 make[3]: Leaving directory '/tmp/pip-build-fo6s1cwx/ python-igraph/tmp/igraph.bywmswzr/igraph-0.7.1/src' Makefile:1377: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/tmp/pip-build-fo6s1cwx/ python-igraph/tmp/igraph.bywmswzr/igraph-0.7.1/src' Makefile:480: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/tmp/pip-build-fo6s1cwx/ python-igraph/tmp/igraph.bywmswzr/igraph-0.7.1' Makefile:382: recipe for target 'all' failed make: *** [all] Error 2 Could not download and compile the C core of igraph. ---------------------------------------- Command "/home/ceb/.virtualenvs/pypath/bin/python3 -u -c "import setuptools, tokenize;*file*='/tmp/pip-build-fo6s1cwx/python-igraph/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-p0ru8skl-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/ceb/.virtualenvs/pypath/ include/site/python3.5/python-igraph" failed with error code 1 in /tmp/pip-build-fo6s1cwx/python-igraph/ — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACjkUev_zryXOAn-Ceb1w4_C0jYGb9wfks5sfP6QgaJpZM4PICB1> .

-- Denes Turei, Ph.D. postdoc @ EMBL +4915166299976 Germany +447442970610 UK denes@ebi.ac.uk http://www.ebi.ac.uk/~denes public key: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x5706A4B609DD65A6

[mschubert]

@cebel You likely need libxml2-dev, not just libxml2

[cebel]

Many thanks, that's it!!!!!