Trouble with subprocess.call(...) and zsh script (OSError: [Errno 8] Exec format error)

[Michael George Lerner]

Hi,

(Python 2.5, OS X 10.4.10)
I have a program called pdb2pqr on my system. It is installed so that
"pdb2pqr" is in my path and looks like:

#\!/bin/zsh -f
/sw/share/pdb2pqr/pdb2pqr.py "$@"

When I call it via this script:

#!/usr/bin/env python
import subprocess
import tempfile
args = ('/sw/bin/pdb2pqr','--help')
output_file = tempfile.Tempor aryFile(mode="w +")
print "Running",a rgs
retcode =
subprocess.call (args,stdout=ou tput_file.filen o(),stderr=subp rocess.STDOUT)
output_file.clo se()

I get this error:

localhost~/tmp$ ./x.py
Running ('/sw/bin/pdb2pqr', '--help')
Traceback (most recent call last):
File "./x.py", line 9, in <module>
retcode =
subprocess.call (args,stdout=ou tput_file.filen o(),stderr=subp rocess.STDOUT)
File "/sw/lib/python2.5/subprocess.py", line 443, in call
return Popen(*popenarg s, **kwargs).wait( )
File "/sw/lib/python2.5/subprocess.py", line 593, in __init__
errread, errwrite)
File "/sw/lib/python2.5/subprocess.py", line 1051, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error

But when I change it to directly call the script that the zsh script
calls like this:

args = ('/sw/share/pdb2pqr/pdb2pqr.py','--help')

everything works:

localhost~/tmp$ ./x.py
Running ('/sw/share/pdb2pqr/pdb2pqr.py', '--help')

This is with 2.5 on OS X 10.4.10. I'm happy to provide whatever
additional information might be useful.

Thanks,

-michael

[Rob Wolfe]

Re: Trouble with subprocess.call (...) and zsh script (OSError: [Errno 8] Exec format error)

Michael George Lerner <mglerner@gmail .comwrites:

Hi,
>
(Python 2.5, OS X 10.4.10)
I have a program called pdb2pqr on my system. It is installed so that
"pdb2pqr" is in my path and looks like:
>
#\!/bin/zsh -f

Are you sure that this shebang is correct?

I've tested that on bash and have similar error:

# t1.sh

#\!/bin/sh
echo "t1"

>>from subprocess import call
>>call(['./t1.sh'])

Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/python2.4/subprocess.py", line 413, in call
return Popen(*args, **kwargs).wait( )
File "/usr/lib/python2.4/subprocess.py", line 543, in __init__
errread, errwrite)
File "/usr/lib/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error

But running that directly through the shell works:

>>call(['./t1.sh'], shell=True)

t1
0

However this script works fine also without `shell=True` option:

# t2.sh

#!/bin/sh
echo "t2"

>>call(['./t2.sh'])

t2
0


HTH,
Rob

[Michael George Lerner]

Re: Trouble with subprocess.call (...) and zsh script (OSError: [Errno 8] Exec format error)

On Nov 11, 3:25 pm, Rob Wolfe <r...@smsnet.pl wrote:
Hi Rob,

Michael GeorgeLerner<mg ler...@gmail.co mwrites:
>

Hi,

>

(Python 2.5, OS X 10.4.10)
I have a program called pdb2pqr on my system. It is installed so that
"pdb2pqr" is in my path and looks like:

>

#\!/bin/zsh -f

>
Are you sure that this shebang is correct?

Well, it's correct in the sense that I have faithfully reproduced the
contents of the file. I didn't write it, though.

I don't know what the extra backslash is for. I suppose I'll contact
the authors and find out.

Any ideas how to make it work with the strange shebang syntax?

Thanks,

-michael

>
I've tested that on bash and have similar error:
>
# t1.sh
>
#\!/bin/sh
echo "t1"
>

>from subprocess import call
>call(['./t1.sh'])

>
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/python2.4/subprocess.py", line 413, in call
return Popen(*args, **kwargs).wait( )
File "/usr/lib/python2.4/subprocess.py", line 543, in __init__
errread, errwrite)
File "/usr/lib/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
>
But running that directly through the shell works:
>

>call(['./t1.sh'], shell=True)

>
t1
0
>
However this script works fine also without `shell=True` option:
>
# t2.sh
>
#!/bin/sh
echo "t2"
>

>call(['./t2.sh'])

>
t2
0
>
HTH,
Rob