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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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installation error #115

Closed francicco closed 5 years ago

francicco commented 5 years ago

Hi,

I'm trying to install progressiveCactus following your instructions:

git clone git://github.com/glennhickey/progressiveCactus.git
cd progressiveCactus
git pull
git submodule update --init
make

but make returns me this error

cd submodules && make all
make[1]: Entering directory `/home/fc464/software/progressiveCactus/submodules'
rm -f /home/fc464/software/progressiveCactus/submodules/../environment
python2.7 /home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py /home/fc464/software/progressiveCactus/python
New python executable in /home/fc464/software/progressiveCactus/python/bin/python2.7
Not overwriting existing python script /home/fc464/software/progressiveCactus/python/bin/python (you must use /home/fc464/software/progressiveCactus/python/bin/python2.7)
Installing setuptools, pip, wheel...
  Complete output from command /home/fc464/software...python/bin/python2.7 - setuptools pip wheel:
  Traceback (most recent call last):
  File "<stdin>", line 4, in <module>
  File "/home/fc464/miniconda2/lib/python2.7/tempfile.py", line 32, in <module>
    import io as _io
  File "/home/fc464/miniconda2/lib/python2.7/io.py", line 51, in <module>
    import _io
ImportError: /home/fc464/software/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so: undefined symbol: _PyCodec_LookupTextEncoding
----------------------------------------
...Installing setuptools, pip, wheel...done.
Traceback (most recent call last):
  File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 2331, in <module>
    main()
  File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 712, in main
    symlink=options.symlink)
  File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 943, in create_environment
    download=download,
  File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 900, in install_wheel
    call_subprocess(cmd, show_stdout=False, extra_env=env, stdin=SCRIPT)
  File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 796, in call_subprocess
    % (cmd_desc, proc.returncode))
OSError: Command /home/fc464/software...python/bin/python2.7 - setuptools pip wheel failed with error code 1
make[1]: *** [virtPyRule] Error 1
make[1]: Leaving directory `/home/fc464/software/progressiveCactus/submodules'
make: *** [all] Error 2
diekhans commented 5 years ago

I suspect this is a problem with your python install.

A couple of quick google indicate that this could be caused by multiple version of python on PYTHONPATH: https://lists.freebsd.org/pipermail/freebsd-questions/2016-October/273993.html

Francesco Cicconardi notifications@github.com writes:

Hi,

I'm trying to install progressiveCactus following your instructions:

git clone git://github.com/glennhickey/progressiveCactus.git cd progressiveCactus git pull git submodule update --init make

but make returns me this error

cd submodules && make all make[1]: Entering directory `/home/fc464/software/progressiveCactus/submodules' rm -f /home/fc464/software/progressiveCactus/submodules/../environment python2.7 /home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py /home/fc464/software/progressiveCactus/python New python executable in /home/fc464/software/progressiveCactus/python/bin/python2.7 Not overwriting existing python script /home/fc464/software/progressiveCactus/python/bin/python (you must use /home/fc464/software/progressiveCactus/python/bin/python2.7) Installing setuptools, pip, wheel... Complete output from command /home/fc464/software...python/bin/python2.7 - setuptools pip wheel: Traceback (most recent call last): File "", line 4, in File "/home/fc464/miniconda2/lib/python2.7/tempfile.py", line 32, in import io as _io File "/home/fc464/miniconda2/lib/python2.7/io.py", line 51, in import _io ImportError: /home/fc464/software/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so: undefined symbol: _PyCodec_LookupTextEncoding

...Installing setuptools, pip, wheel...done. Traceback (most recent call last): File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 2331, in main() File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 712, in main symlink=options.symlink) File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 943, in create_environment download=download, File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 900, in install_wheel call_subprocess(cmd, show_stdout=False, extra_env=env, stdin=SCRIPT) File "/home/fc464/software/progressiveCactus/submodules/virtualenv/virtualenv.py", line 796, in call_subprocess % (cmd_desc, proc.returncode)) OSError: Command /home/fc464/software...python/bin/python2.7 - setuptools pip wheel failed with error code 1 make[1]: [virtPyRule] Error 1 make[1]: Leaving directory `/home/fc464/software/progressiveCactus/submodules' make: [all] Error 2

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francicco commented 5 years ago

Could be the conda version of python interfering. Do I have to use the python in progressiveCactus or my own? F