Yes when running in command line I get:

bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R

Error in value[[3L]](cond) :

  failed to read experimental design data: cannot open the connection

Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>

In addition: Warning message:

In file(file, "rt") : cannot open file 'NA': No such file or directory

Execution halted


On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> > On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
> >>
> >> The initial error now seems to be taken care of and now am getting this
> >> message on attempting to run tool:
> >>
> >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> >> line 153, in prepare_job
> >>      job_wrapper.runner_command_line = self.build_command_line(
> >> job_wrapper, include_metadata=include_metadata,
> >> include_work_dir_outputs=include_work_dir_outputs )
> >>    File
> "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> >> line 176, in build_command_line
> >>      return build_command( self, job_wrapper,
> >> include_metadata=include_metadata,
> >> include_work_dir_outputs=include_work_dir_outputs )
> >>    File
> "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
> >> line 19, in build_command
> >>      commands_builder = CommandsBuilder(job_wrapper.get_command_line())
> >>    File
> "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
> >> line 109, in __init__
> >>      commands = initial_command.rstrip("; ")
> >> AttributeError: 'NoneType' object has no attribute 'rstrip'
> >>
>
> This is still breaking inside Galaxy, before ever trying to run your
> scripts. There is likely still a problem in your XML.
>
> On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
> > again, have you tried running your Rscript outside of Galaxy called by
> > Rscript_wrapper.sh ?
> >
>
> This is an important question :)
>
> Also, please remember to CC the mailing list and not just reply
> to the previous email's sender only.
>
> Thanks,
>
> Peter
>
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