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Bug 3335 - ft_version not found
| Status | CLOSED FIXED |
| Reported | 2017-08-23 14:26:00 +0200 |
| Modified | 2019-08-10 12:41:51 +0200 |
| Product: | FieldTrip |
| Component: | qsub |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P5 normal |
| Assigned to: | Robert Oostenveld |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Marcel Zwiers - 2017-08-23 14:26:34 +0200
qsubcellfun can't find ft_version.m anymore (used to work just fine). I ran qsubcellfun with just the qsub module in my matlabpath and got the following error: submitting job marzwi_dccn_c011_p16318_b1_j001... torque id 14145510.dccn-l029.dccn.nl cleaning up all scheduled and running jobs, don't worry if you see warnings from "qdel" ??? Undefined function or variable 'ft_version'. Error in ==> ft_notification at 72 [v, p] = ft_version; Error in ==> ft_warning at 58 varargout{:} = ft_notification(varargin{:}); Error in ==> qsubcellfun at 381 ws = ft_warning('off', 'FieldTrip:qsub:jobNotAvailable'); Error in ==> dd_basicproc>run_job at 1581 OK = qsubcellfun(@dd_basicproc_getsnr, stackjob(Job,'Nifti','Subj'), num2cell(1:NrSubj), LogNames, ...
Robert Oostenveld - 2017-08-23 15:17:11 +0200
it happens to be called here private/ft_notification.m:[v, p] = ft_version; and ft_notification is called by ft_warning and ft_error. See also https://github.com/fieldtrip/fieldtrip/pull/445 I will fix it... [bug3335 f2be558] added ft_version to address http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3335 1 file changed, 154 insertions(+) create mode 100644 qsub/private/ft_version.m
Robert Oostenveld - 2017-08-23 15:19:13 +0200
I solved it for now with https://github.com/fieldtrip/fieldtrip/pull/498 However, having experienced ft_error and ft_warning for some time, I am not happy with them. The ft_notify/info/debug all work fine, but for warning and error I find it confusing. So probably I will revert ft-warning to warning, and ft_error to error. But that is not part of this issue.
Marcel Zwiers - 2017-08-23 15:46:09 +0200
Mhhh, I now get: submitting job marzwi_dccn_c011_p30513_b2_j001... torque id 14146370.dccn-l029.dccn.nl cleaning up all scheduled and running jobs, don't worry if you see warnings from "qdel" Too many outputs requested. Most likely cause is missing [] around left hand side that has a comma separated list expansion. Error in ==> ft_version at 147 ftver = a.Version; Error in ==> ft_notification at 72 [v, p] = ft_version; Error in ==> ft_warning at 58 varargout{:} = ft_notification(varargin{:}); Error in ==> qsubcellfun at 381 ws = ft_warning('off', 'FieldTrip:qsub:jobNotAvailable'); Error in ==> qsubcellfun at 323 [stackargout{:}] = qsubcellfun(@cellfun, stackargin{:}, optarg{:}); Error in ==> ni_nifti_job at 365 qsubcellfun(@ni_resetdwi, DTISeriesG(Sel), repmat({false},size(DTISeriesG(Sel))), 'TimReq',60, 'MemReq',100*1024^2, 'jvm','no', 'Stack',10, 'options','-l gres=bandwidth:999');
Robert Oostenveld - 2017-08-23 15:48:49 +0200
(In reply to Marcel Zwiers from comment #3) ah, it cannot determine the fieldtrip version, since fieldtrip is not on the path. Only qsub is on the path. So I guess that the ft_warning/ft_error reverting is needed anyway...
Robert Oostenveld - 2017-08-23 15:51:40 +0200
mac011> git commit -a [bug3335 71d7f57] added a defaultId function to private and replaced ft_warning by warning(defaultId, ...). Idem for ft_error. See http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3335#c4
Marcel Zwiers - 2017-08-23 15:56:19 +0200
It is some sort of regression since having only the qsub module in the path used to work fine until recently. So this will no longer be possible?
Robert Oostenveld - 2017-08-23 18:44:27 +0200
(In reply to Marcel Zwiers from comment #6) it is indeed a regression error. It should be fixed and I will do that. Right now you know how to work around it: just add fieldtrip in total, not only ssub.
Robert Oostenveld - 2017-08-24 08:38:23 +0200
[bug3335-alt 5bcf12e] replaced ft_warning and ft_error with warning and error, only in qsub. See http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3335 25 files changed, 62 insertions(+), 619 deletions(-) delete mode 100644 qsub/private/ft_notification.m delete mode 100644 qsub/private/ft_warning.m I cerated a PR and merged it with the master https://github.com/fieldtrip/fieldtrip/pull/500 @Marcel, please verify the solution.
Robert Oostenveld - 2019-08-10 12:35:37 +0200
This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue on https://github.com/fieldtrip/fieldtrip/issues.