Hi Paul,
Your solution seems to have done the trick! Typing 'python' on the command
line now returns the python interpreter. We have started running another
FEAT job and it appears to be successfully processing in the Post-stats
stage. We no longer see the python error.
Thank you very much for your invaluable assistance!
Jerry Chen
Doctoral Student in Clinical Psychology
Palo Alto University
[log in to unmask]
On Wed, Nov 4, 2015 at 2:12 PM, paul mccarthy <[log in to unmask]>
wrote:
> Hi Jerry,
>
> I don't quite know why your python installation is set up this way, but it
> seems to be getting caught in an infinite recursive loop when it starts up,
> while trying to load installed third party packages.
>
> Try this:
>
> 1. Open "/usr/local/lib64/python2.7/site-packages/_local.pth" in a text
> editor (you may need sudo privileges)
>
> 2. Put a '#' character at the beginning of the line (effectively
> commenting it out).
>
> 3. Try running python again. If it works (you should be presented with a
> prompt for the python interpreter), then try running FEAT again.
>
> Cheers,
>
> Paul
>
> On 4 November 2015 at 21:45, Jerry Chen <[log in to unmask]> wrote:
>
>> Hi Paul,
>>
>> Typing 'python' into a terminal window appears to return the same error
>> that we received in Feat:
>>
>> swarren@shasta:~> python
>>
>> Error processing line 1 of
>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>
>> Error processing line 1 of
>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>
>> Error processing line 1 of
>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>
>> Traceback (most recent call last):
>>
>> File "/usr/lib64/python2.7/site.py", line 152, in addpackage
>>
>> exec line
>>
>> File "<string>", line 1, in <module>
>>
>> File "/usr/lib64/python2.7/site.py", line 190, in addsitedir
>>
>> addpackage(sitedir, name, known_paths)
>>
>> File "/usr/lib64/python2.7/site.py", line 162, in addpackage
>>
>> for record in traceback.format_exception(*sys.exc_info()):
>>
>> File "/usr/lib64/python2.7/traceback.py", line 141, in
>> format_exception
>>
>> list = list + format_tb(tb, limit)
>>
>> File "/usr/lib64/python2.7/traceback.py", line 76, in format_tb
>>
>> return format_list(extract_tb(tb, limit))
>>
>> File "/usr/lib64/python2.7/traceback.py", line 101, in extract_tb
>>
>> line = linecache.getline(filename, lineno, f.f_globals)
>>
>> File "/usr/lib64/python2.7/linecache.py", line 14, in getline
>>
>> lines = getlines(filename, module_globals)
>>
>> File "/usr/lib64/python2.7/linecache.py", line 40, in getlines
>>
>> return updatecache(filename, module_globals)
>>
>> File "/usr/lib64/python2.7/linecache.py", line 127, in updatecache
>>
>> with open(fullname, 'rU') as fp:
>>
>> RuntimeError: maximum recursion depth exceeded
>>
>> Remainder of file ignored
>>
>> Python 2.7.8 (default, Sep 30 2014, 15:34:38) [GCC] on linux2
>>
>> Type "help", "copyright", "credits" or "license" for more information.
>>
>> >>>
>>
>> Any ideas or suggestions are most welcome.
>>
>> Thank you,
>> Jerry
>>
>>
>> Jerry Chen
>> Doctoral Student in Clinical Psychology
>> Palo Alto University
>> [log in to unmask]
>>
>>
>> On Wed, Nov 4, 2015 at 12:36 PM, paul mccarthy <[log in to unmask]>
>> wrote:
>>
>>> Hi Jerry,
>>>
>>> What happens when you type 'python' into a terminal?
>>>
>>> Thanks,
>>>
>>> Paul
>>>
>>> On 4 November 2015 at 03:38, Jerry Chen <[log in to unmask]> wrote:
>>>
>>>> Hi All,
>>>>
>>>> We are running into an issue when attempting to run PPI on a single
>>>> subject’s first-level analysis in FEAT. Once we run FEAT, we get the
>>>> following error in post-stats:
>>>> “Post-stats
>>>>
>>>> zstat1
>>>> Error processing line 1 of
>>>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>>>
>>>> Error processing line 1 of
>>>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>>>
>>>> Error processing line 1 of
>>>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>>>
>>>> Traceback (most recent call last):
>>>> File "/usr/lib64/python2.7/site.py", line 152, in addpackage
>>>> exec line
>>>> File "", line 1, in
>>>> File "/usr/lib64/python2.7/site.py", line 190, in addsitedir
>>>> addpackage(sitedir, name, known_paths)
>>>> File "/usr/lib64/python2.7/site.py", line 162, in addpackage
>>>> for record in traceback.format_exception(*sys.exc_info()):
>>>> File "/usr/lib64/python2.7/traceback.py", line 141, in
>>>> format_exception
>>>> list = list + format_tb(tb, limit)
>>>> File "/usr/lib64/python2.7/traceback.py", line 76, in format_tb
>>>> return format_list(extract_tb(tb, limit))
>>>> File "/usr/lib64/python2.7/traceback.py", line 101, in extract_tb
>>>> line = linecache.getline(filename, lineno, f.f_globals)
>>>> File "/usr/lib64/python2.7/linecache.py", line 14, in getline
>>>> lines = getlines(filename, module_globals)
>>>> File "/usr/lib64/python2.7/linecache.py", line 40, in getlines
>>>> return updatecache(filename, module_globals)
>>>> File "/usr/lib64/python2.7/linecache.py", line 127, in updatecache
>>>> with open(fullname, 'rU') as fp:
>>>> RuntimeError: maximum recursion depth exceeded
>>>>
>>>> Remainder of file ignored
>>>> while executing
>>>> "if { [ catch {
>>>>
>>>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>>> switch -- [ lindex $argv $argindex ] {
>>>>
>>>> -I {
>>>> incr arginde..."
>>>> (file "/usr/local/fsl/bin/feat" line 310)
>>>> Error encountered while running in main feat script, halting.
>>>> zstat1
>>>> Error processing line 1 of
>>>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>>>
>>>> Error processing line 1 of
>>>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>>>
>>>> Error processing line 1 of
>>>> /usr/local/lib64/python2.7/site-packages/_local.pth:
>>>>
>>>> Traceback (most recent call last):
>>>> File "/usr/lib64/python2.7/site.py", line 152, in addpackage
>>>> exec line
>>>> File "", line 1, in
>>>> File "/usr/lib64/python2.7/site.py", line 190, in addsitedir
>>>> addpackage(sitedir, name, known_paths)
>>>> File "/usr/lib64/python2.7/site.py", line 162, in addpackage
>>>> for record in traceback.format_exception(*sys.exc_info()):
>>>> File "/usr/lib64/python2.7/traceback.py", line 141, in
>>>> format_exception
>>>> list = list + format_tb(tb, limit)
>>>> File "/usr/lib64/python2.7/traceback.py", line 76, in format_tb
>>>> return format_list(extract_tb(tb, limit))
>>>> File "/usr/lib64/python2.7/traceback.py", line 101, in extract_tb
>>>> line = linecache.getline(filename, lineno, f.f_globals)
>>>> File "/usr/lib64/python2.7/linecache.py", line 14, in getline
>>>> lines = getlines(filename, module_globals)
>>>> File "/usr/lib64/python2.7/linecache.py", line 40, in getlines
>>>> return updatecache(filename, module_globals)
>>>> File "/usr/lib64/python2.7/linecache.py", line 127, in updatecache
>>>> with open(fullname, 'rU') as fp:
>>>> RuntimeError: maximum recursion depth exceeded
>>>>
>>>> Remainder of file ignored”
>>>>
>>>> Currently our model has a total of seven EVs. The first five are
>>>> psychological EVs (positive stimulus, negative stimulus, and cognitive load
>>>> levels 1 – 3). Our sixth EV is the physiological timecourse for our single
>>>> subject’s filtered func data. Our last EV is the interaction of a single
>>>> psychological variable with the filtered func timecourse.
>>>>
>>>> We are wondering if this error is an issue with regards to our FSL
>>>> package software version 5.0.8 (as it references Python in the error?),
>>>> rather than our actual model? We are running FSL on a Linux system with
>>>> Opensuse. Any input on this would be much appreciated!
>>>>
>>>> Best,
>>>> Jerry Chen
>>>>
>>>
>>>
>>
>
