Error about pbtranscript-tofu installation
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Entering edit mode
5.4 years ago
Ginsea Chen ▴ 130

Dear all! I tried to install pbtranscript-tofu as follows:https://github.com/PacificBiosciences/cDNA_primer/wiki/Setting-up-virtualenv-and-installing-pbtranscript-tofu

While a error message reported in the "make" step,

git clone git://github.com/PacificBiosciences/cDNA_primer.git
cd cDNA_primer/pbtranscript-tofu/pbtranscript/pbtools/pbtranscript/branch/C/
python setup2.py build_ext --inplace
cd ../../../../
**make**(This step)

The error message was pasted here:

make
+ make
python setup.py build --executable="/usr/bin/env python"
Not found: ../../third-party/
Download error on https://pypi.python.org/simple/setuptools_cython/: [Errno 110]                                                                                         Connection timed out -- Some packages may not be found!
Download error on https://pypi.python.org/simple/setuptools-cython/: [Errno 110] Connection timed out -- Some packages may not be found!
Couldn't find index page for 'setuptools_cython' (maybe misspelled?)
Download error on https://pypi.python.org/simple/: [Errno 110] Connection timed out -- Some packages may not be found!
No local packages or download links found for setuptools-cython
Traceback (most recent call last):
  File "setup.py", line 74, in <module>
    zip_safe=False,
  File "/share/nas2/workdir/lius/software/smrtanalysis/current/redist/python2.7/lib/python2.7/distutils/core.py", line 112, in setup
    _setup_distribution = dist = klass(attrs)
  File "/home/chenzx/workdir/biosoft/VENV_TOFU/lib/python2.7/site-packages/setuptools/dist.py", line 260, in __init__
    self.fetch_build_eggs(attrs.pop('setup_requires'))
  File "/home/chenzx/workdir/biosoft/VENV_TOFU/lib/python2.7/site-packages/setuptools/dist.py", line 285, in fetch_build_eggs
    replace_conflicting=True
  File "/home/chenzx/workdir/biosoft/VENV_TOFU/lib/python2.7/site-packages/pkg_resources.py", line 631, in resolve
    dist = best[req.key] = env.best_match(req, ws, installer)
  File "/home/chenzx/workdir/biosoft/VENV_TOFU/lib/python2.7/site-packages/pkg_resources.py", line 871, in best_match
    return self.obtain(req, installer)
  File "/home/chenzx/workdir/biosoft/VENV_TOFU/lib/python2.7/site-packages/pkg_resources.py", line 883, in obtain
    return installer(requirement)
  File "/home/chenzx/workdir/biosoft/VENV_TOFU/lib/python2.7/site-packages/setuptools/dist.py", line 335, in fetch_build_egg
    return cmd.easy_install(req)
  File "/home/chenzx/workdir/biosoft/VENV_TOFU/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 589, in easy_install
    raise DistutilsError(msg)
distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('setuptools-cython')
make: *** [build] Error 1

I don't know what happened, if anyone have some ways, please tell me here. Thanks!

pbtranscript-tofu pacbio installation python • 2.0k views
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Hi ,Ginsea, I have the same problem to yours. Do you have solutions?

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