[R] Using R and Python together

Kankana Shukla shukla.kank at gmail.com
Tue Apr 4 22:26:55 CEST 2017


Installation of pyper gives me error code 1.  I used pip install on my
ubuntu machine.  How to install Pyper correctly?

Here is the debug log file:

------------------------------------------------------------
/usr/bin/pip run on Tue Apr  4 15:07:58 2017
Downloading/unpacking pyper
  Getting page https://pypi.python.org/simple/pyper/
  URLs to search for versions for pyper:
  * https://pypi.python.org/simple/pyper/
YV  Analyzing links from page https://pypi.python.org/simple/pyper/
    Found link
https://pypi.python.org/packages/0f/46/47a5ebf039d1982a5cf7ed4f53ef1dcfccf57358566da973732cfc2ac31d/PypeR-1.1.1.tar.gz#md5=8f1708b06e1cdd73d3f03b4342c7c948
(from https://pypi.python.org/sim$
    Found link
https://pypi.python.org/packages/4f/c2/957c9eb9ced95cedd04e6330ac446485d6e48f2d198f21f30aba0fe637cc/PypeR-1.0.1.tar.gz#md5=fc05ad098ef370deb7fffee34497fa82
(from https://pypi.python.org/sim$
    Found link
https://pypi.python.org/packages/56/fa/d6d58ace212c2dac27c08fe03c603eede4f1190a46d11917946db74bd1e8/PypeR-1.1.0.tar.gz#md5=6a186b5399d75f32f0eb29275c7e01b3
(from https://pypi.python.org/sim$
    Found link
https://pypi.python.org/packages/6c/87/a19361e922311aa86697edcbd95f3af85c69240350836136c629b7b29b38/PypeR-1.0.2.tar.gz#md5=73dd5f4b5dac2bd0a29425853c8de125
(from https://pypi.python.org/sim$
    Found link
https://pypi.python.org/packages/7e/4d/8167a3f7b3897b15ac5c2424886579cefa852705ac4c925dbdb8740f8838/PypeR-1.0.tar.gz#md5=eb05aa5ccee55e5175ea8f36e2d42591
(from https://pypi.python.org/simpl$
    Found link
https://pypi.python.org/packages/7f/44/4c063481bed01a9f18e34b823c796af7b8f59f458a8e67fd171263a96488/PypeR-1.0.3.tar.gz#md5=b8b9535e825d88dc6f15aff13c6e180c
(from https://pypi.python.org/sim$
    Found link
https://pypi.python.org/packages/e6/3e/4ed8b7c23333f7a1d3b18ecb37b09b4867fee95151a3a59c43c20376678e/PypeR-1.1.2.tar.gz#md5=d056a481a13d07300a5ffc6848b34d1e
(from https://pypi.python.org/sim$
    Found link
https://pypi.python.org/packages/eb/5a/2991b67ad276c55234ffff04b77eeb9c30e01cbda9920c9da9b20d656dc2/PypeR-1.0.4.tar.gz#md5=40b0ccaa645c7b936cc25ce86527aba6
(from https://pypi.python.org/sim$
  Using version 1.1.2 (newest of versions: 1.1.2, 1.1.1, 1.1.0, 1.0.4,
1.0.3, 1.0.2, 1.0.1, 1.0)
  Downloading PypeR-1.1.2.tar.gz
  Downloading from URL
https://pypi.python.org/packages/e6/3e/4ed8b7c23333f7a1d3b18ecb37b09b4867fee95151a3a59c43c20376678e/PypeR-1.1.2.tar.gz#md5=d056a481a13d07300a5ffc6848b34d1e
(from https://pypi.python$
  Running setup.py (path:/tmp/pip_build_root/pyper/setup.py) egg_info for
package pyper
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/tmp/pip_build_root/pyper/setup.py", line 13, in <module>
        py_modules=['pyper'], # copy to site-packages
      File "/usr/lib/python2.7/distutils/core.py", line 111, in setup
        _setup_distribution = dist = klass(attrs)
      File "/usr/local/lib/python2.7/dist-packages/setuptools/dist.py",
line 320, in __init__
        _Distribution.__init__(self, attrs)
      File "/usr/lib/python2.7/distutils/dist.py", line 287, in __init__
        self.finalize_options()
      File "/usr/local/lib/python2.7/dist-packages/setuptools/dist.py",
line 386, in finalize_options
        ep.require(installer=self.fetch_build_egg)
      File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2100,
in require
        working_set.resolve(self.dist.requires(self.extras),env,installer)))
      File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 620,
in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 858,
in best_match
        return self.obtain(req, installer) # try and download/install
      File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 870,
in obtain
        return installer(requirement)
      File "/usr/local/lib/python2.7/dist-packages/setuptools/dist.py",
line 416, in fetch_build_egg
        from setuptools.command.easy_install import easy_install
      File
"/usr/local/lib/python2.7/dist-packages/setuptools/command/easy_install.py",
line 51, in <module>
        from setuptools.archive_util import unpack_archive
      File
"/usr/local/lib/python2.7/dist-packages/setuptools/archive_util.py", line
11, in <module>
        from pkg_resources import ensure_directory, ContextualZipFile
    ImportError: cannot import name ContextualZipFile
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/tmp/pip_build_root/pyper/setup.py", line 13, in <module>
    py_modules=['pyper'], # copy to site-packages

  File "/usr/lib/python2.7/distutils/core.py", line 111, in setup

    _setup_distribution = dist = klass(attrs)

  File "/usr/local/lib/python2.7/dist-packages/setuptools/dist.py", line
320, in __init__

    _Distribution.__init__(self, attrs)

  File "/usr/lib/python2.7/distutils/dist.py", line 287, in __init__

    self.finalize_options()

  File "/usr/local/lib/python2.7/dist-packages/setuptools/dist.py", line
386, in finalize_options

    ep.require(installer=self.fetch_build_egg)

  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2100, in
require

    working_set.resolve(self.dist.requires(self.extras),env,installer)))

  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 620, in
resolve

    dist = best[req.key] = env.best_match(req, ws, installer)

  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 858, in
best_match


    return self.obtain(req, installer) # try and download/install

  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 870, in
obtain

    return installer(requirement)

  File "/usr/local/lib/python2.7/dist-packages/setuptools/dist.py", line
416, in fetch_build_egg

    from setuptools.command.easy_install import easy_install

  File
"/usr/local/lib/python2.7/dist-packages/setuptools/command/easy_install.py",
line 51, in <module>

    from setuptools.archive_util import unpack_archive

  File "/usr/local/lib/python2.7/dist-packages/setuptools/archive_util.py",
line 11, in <module>

    from pkg_resources import ensure_directory, ContextualZipFile

ImportError: cannot import name ContextualZipFile

----------------------------------------
Cleaning up...
  Removing temporary dir /tmp/pip_build_root...
Command python setup.py egg_info failed with error code 1 in
/tmp/pip_build_root/pyper
Exception information:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 122, in
main
    status = self.run(options, args)
  File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line
278, in run
    requirement_set.prepare_files(finder, force_root_egg_info=self.bundle,
bundle=self.bundle)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1230, in
prepare_files
    req_to_install.run_egg_info()
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 326, in
run_egg_info
    command_desc='python setup.py egg_info')
  File "/usr/lib/python2.7/dist-packages/pip/util.py", line 715, in
call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command python setup.py egg_info failed with error code
1 in /tmp/pip_build_root/pyper

-------------------------------------------

On Fri, Mar 31, 2017 at 1:35 PM, Wensui Liu <liuwensui at gmail.com> wrote:

> In https://statcompute.wordpress.com/?s=rpy2, you can find examples of
> rpy2.
>
> In https://statcompute.wordpress.com/?s=pyper, you can find examples of
> pyper.
>
> On Fri, Mar 31, 2017 at 11:38 AM, Kankana Shukla <shukla.kank at gmail.com>
> wrote:
> > I'm not great at rpy2.  Are there any good examples I could see to learn
> > how to do that?  My R code is very long and complicated.
> >
> > On Fri, Mar 31, 2017 at 7:08 AM, Stefan Evert <stefanML at collocations.de>
> > wrote:
> >
> >>
> >> > On 30 Mar 2017, at 23:37, Kankana Shukla <shukla.kank at gmail.com>
> wrote:
> >> >
> >> > I have searched for examples using R and Python together, and rpy2
> seems
> >> > like the way to go, but is there another (easier) way to do it?
> >>
> >> Rpy2 would seem to be a very easy and convenient solution.  What do you
> >> need that can't easily be down with rpy2?
> >>
> >> Best regards,
> >> Stefan
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

	[[alternative HTML version deleted]]



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