Re: (no subject)

-----Original Message-----
From: Greg Ewing [mailto:[email protected]] =

Sent: Monday, February 10, 2014 7:06 PM
To: [email protected]
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 fro=
m the answers, but my mail client is unfortunately not very smart about tha=
t 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 =3D 1)

How exactly did you install Pyrex 0.9.9?

I suspect that you have more than one version of Python installed, and what=
ever 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 directo=
ry so generated, and then running " python setup.py install | tee kc_log.tx=
t", 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/Compi=
ler
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/Compi=
ler
copying Pyrex/Compiler/Filenames.py -> build/lib.linux-x86_64-2.7/Pyrex/Com=
piler
copying Pyrex/Compiler/CmdLine.py -> build/lib.linux-x86_64-2.7/Pyrex/Compi=
ler
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/Co=
mpiler
copying Pyrex/Compiler/__init__.py -> build/lib.linux-x86_64-2.7/Pyrex/Comp=
iler
copying Pyrex/Compiler/ModuleNode.py -> build/lib.linux-x86_64-2.7/Pyrex/Co=
mpiler
copying Pyrex/Compiler/Version.py -> build/lib.linux-x86_64-2.7/Pyrex/Compi=
ler
copying Pyrex/Compiler/PyrexTypes.py -> build/lib.linux-x86_64-2.7/Pyrex/Co=
mpiler
copying Pyrex/Compiler/Naming.py -> build/lib.linux-x86_64-2.7/Pyrex/Compil=
er
copying Pyrex/Compiler/ExprNodes.py -> build/lib.linux-x86_64-2.7/Pyrex/Com=
piler
copying Pyrex/Compiler/Scanning.py -> build/lib.linux-x86_64-2.7/Pyrex/Comp=
iler
copying Pyrex/Compiler/Errors.py -> build/lib.linux-x86_64-2.7/Pyrex/Compil=
er
copying Pyrex/Compiler/Symtab.py -> build/lib.linux-x86_64-2.7/Pyrex/Compil=
er
copying Pyrex/Compiler/Options.py -> build/lib.linux-x86_64-2.7/Pyrex/Compi=
ler
copying Pyrex/Compiler/TypeSlots.py -> build/lib.linux-x86_64-2.7/Pyrex/Com=
piler
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/Compi=
ler
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/Dis=
tutils
copying Pyrex/Distutils/extension.py -> build/lib.linux-x86_64-2.7/Pyrex/Di=
stutils
copying Pyrex/Distutils/build_ext.py -> build/lib.linux-x86_64-2.7/Pyrex/Di=
stutils
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/pyre=
xc -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 erro=
r 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 o=
f 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 part=
icular point in the process. =