[Pyrex] (no subject)

[Kevin Conway]

-----Original Message-----
From: Greg Ewing [mailto:greg.ewing at canterbury.ac.nz] 
Sent: Monday, February 10, 2014 7:06 PM
To: pyrex at lists.copyleft.no
Cc: Kevin Conway
Subject: Re: [Pyrex] (no subject)

Kevin Conway wrote:
> Is it OK to just respond to your email, or should I be responding to 
> the list explicitly somehow?

Sorry, I hadn't noticed that the original message was from the list, and I think I may have just replied to you.
Normally I answer list questions on the list so that others can benefit from the answers, but my mail client is unfortunately not very smart about that sort of thing.
I'm putting it back on the list now.

>    And here is the version 0.9.8.6 pyrexc from our newer machine:
> 
> cat /usr/local/bin/pyrexc
> 
> #!/usr/bin/python
> 
> #
> #   Pyrex -- Main Program, Unix
> #
> 
> from Pyrex.Compiler.Main import main
> main(command_line = 1)

How exactly did you install Pyrex 0.9.9?

I suspect that you have more than one version of Python installed, and whatever method you used resulted in Pyrex getting put into a different Python from the one that /usr/bin/python runs.

--
Greg

   Hi, Greg.
   I installed Pyrex 0.9.9 by extracting the tarball, cd'ing to the directory so generated, and then running " python setup.py install | tee kc_log.txt", which produced this output:

running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/Pyrex
copying Pyrex/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex
copying Pyrex/Utils.py -> build/lib.linux-x86_64-2.7/Pyrex
copying Pyrex/Debugging.py -> build/lib.linux-x86_64-2.7/Pyrex
creating build/lib.linux-x86_64-2.7/Pyrex/Mac
copying Pyrex/Mac/MacSystem.py -> build/lib.linux-x86_64-2.7/Pyrex/Mac
copying Pyrex/Mac/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex/Mac
copying Pyrex/Mac/DarwinSystem.py -> build/lib.linux-x86_64-2.7/Pyrex/Mac
copying Pyrex/Mac/TS_Misc_Suite.py -> build/lib.linux-x86_64-2.7/Pyrex/Mac
copying Pyrex/Mac/setup.py -> build/lib.linux-x86_64-2.7/Pyrex/Mac
copying Pyrex/Mac/MacUtils.py -> build/lib.linux-x86_64-2.7/Pyrex/Mac
creating build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/test_tm.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Machines.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Lexicons.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Actions.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Regexps.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Timing.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Traditional.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/DFA.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Errors.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Transitions.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
copying Pyrex/Plex/Scanners.py -> build/lib.linux-x86_64-2.7/Pyrex/Plex
creating build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Builtin.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Nodes.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Parsing.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Filenames.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/CmdLine.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Main.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/DebugFlags.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/ModuleNode.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Version.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/PyrexTypes.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Naming.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/ExprNodes.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Scanning.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Errors.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Symtab.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Options.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/TypeSlots.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Code.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
copying Pyrex/Compiler/Lexicon.py -> build/lib.linux-x86_64-2.7/Pyrex/Compiler
creating build/lib.linux-x86_64-2.7/Pyrex/Unix
copying Pyrex/Unix/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex/Unix
copying Pyrex/Unix/LinuxSystem.py -> build/lib.linux-x86_64-2.7/Pyrex/Unix
creating build/lib.linux-x86_64-2.7/Pyrex/DistutilsOld
copying Pyrex/DistutilsOld/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex/DistutilsOld
copying Pyrex/DistutilsOld/build_ext.py -> build/lib.linux-x86_64-2.7/Pyrex/DistutilsOld
creating build/lib.linux-x86_64-2.7/Pyrex/Distutils
copying Pyrex/Distutils/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex/Distutils
copying Pyrex/Distutils/extension.py -> build/lib.linux-x86_64-2.7/Pyrex/Distutils
copying Pyrex/Distutils/build_ext.py -> build/lib.linux-x86_64-2.7/Pyrex/Distutils
running build_scripts
creating build/scripts-2.7
copying and adjusting bin/pyrexc -> build/scripts-2.7
changing mode of build/scripts-2.7/pyrexc from 644 to 755
running install_lib
running install_scripts
copying build/scripts-2.7/pyrexc -> /usr/local/bin
changing mode of /usr/local/bin/pyrexc to 755
running install_data
running install_egg_info
Removing /usr/local/lib/python2.7/dist-packages/Pyrex-0.9.9.egg-info
Writing /usr/local/lib/python2.7/dist-packages/Pyrex-0.9.9.egg-info

   The version of pyrexc remains 0.9.8.6, according to "/usr/local/bin/pyrexc -v":

      Pyrex version 0.9.8.6

   I can run the build for RSeQC, but it eventually produces this error:

...
running build_ext
pyrexc lib/bx/bitset.pyx --> lib/bx/bitset.c
/home/####/to-be-installed/RSeQC-2.3.7/lib/bx/bitset.pyx:75:12: Syntax error in C variable declaration
...

   And ultimately fails with:

lib/bx/bitset.c:1:2: error: #error Do not use this file, it is the result of a failed Pyrex compilation.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

   We do have at least two versions of python installed (2.7 and 3.3):

locate python | grep bin\/ | grep -v anaconda
/home/ubuntu/.virtualenvs/CM/bin/python
/home/ubuntu/.virtualenvs/CM/bin/python2
/home/ubuntu/.virtualenvs/CM/bin/python2.7
/usr/bin/dh_python
/usr/bin/dh_python2
/usr/bin/dh_python3
/usr/bin/pvtkpython
/usr/bin/python
/usr/bin/python-config
/usr/bin/python-mkdebian
/usr/bin/python2
/usr/bin/python2-config
/usr/bin/python2.7
/usr/bin/python2.7-config
/usr/bin/python3
/usr/bin/python3-config
/usr/bin/python3.3
/usr/bin/python3.3-config
/usr/bin/python3.3m
/usr/bin/python3.3m-config
/usr/bin/python3m
/usr/bin/python3m-config
/usr/bin/vtkpython
/usr/bin/x86_64-linux-gnu-python-config
/usr/bin/x86_64-linux-gnu-python2.7-config
/usr/bin/x86_64-linux-gnu-python3-config
/usr/bin/x86_64-linux-gnu-python3.3-config
/usr/bin/x86_64-linux-gnu-python3.3m-config
/usr/bin/x86_64-linux-gnu-python3m-config
/usr/sbin/update-python-modules
/usr/share/doc/python-twisted-bin/changelog.Debian.gz
/usr/share/doc/python-twisted-bin/copyright

   However, I have no idea how to control which version is used at any particular point in the process.