Hi, Nikhil,
In my experience, R chatters to stderr in an unhelpful way such as to let
you know a package got loaded or a function got masked...
That's the main reason I've given up trying to execute R as a command
directly - I find myself writing python wrappers (usually to call Rscript
using subprocess) - so I can deal with this in a controlled way.
It sure looks like there are lots of what look like unicode thingys in the
error - eg
"The following object(s) are masked from
\xe2\x80\x98package:methods\xe2\x80\x99:\n\n getClass, getClasses,
getMethods\n\nThe following object(s) are masked from
\xe2\x80\x98package:base\xe2\x80\x99:\n\n attach, detach,
environment, gc, load, save\n\naroma.light v1.22.0 (2011-10-31)
successfully loaded. See ?aroma.light for help.\n', 1345]"
<untested>
If you don't want to write a wrapper to control R's bad habits, you could
maybe try sink() in your R script to divert all messages to a file which
you can then leave in the history for posterity - or not...depending on
whether it matters.
</untested>
On Wed, Feb 22, 2012 at 2:24 PM, Nikhil Joshi <najo...@ucdavis.edu> wrote:
> Hi all,
>
> I have been writing an R script to run as a tool in galaxy and it
> seems to work just fine. I needed to add some fine-grained error
> detection in the script and I wanted it to produce a "red X" if the
> error occurred. In order to do this I wrote to the stderr handle.
> Before I had put in the error code, I had redirected stderr to
> /dev/null in the xml, but I took that out so that galaxy could see the
> errors I wrote to the stderr handle. For some reason if I do not
> redirect stderr to /dev/null, I get this error:
>
> Traceback (most recent call last):
> File "/opt/Bio/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
> 125, in run_job
> job_wrapper.finish( stdout, stderr )
> File "/opt/Bio/galaxy-dist/lib/galaxy/jobs/__init__.py", line 643, in
> finish
> self.sa_session.flush()
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py",
> line 127, in do
> return getattr(self.registry(), name)(*args, **kwargs)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 1356, in flush
> self._flush(objects)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
> line 1434, in _flush
> flush_context.execute()
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py",
> line 261, in execute
> UOWExecutor().execute(self, tasks)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py",
> line 753, in execute
> self.execute_save_steps(trans, task)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py",
> line 768, in execute_save_steps
> self.save_objects(trans, task)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py",
> line 759, in save_objects
> task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
>
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py",
> line 1413, in _save_obj
> c = connection.execute(statement.values(value_params), params)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 824, in execute
> return Connection.executors[c](self, object, multiparams, params)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 874, in _execute_clauseelement
> return self.__execute_context(context)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 896, in __execute_context
> self._cursor_execute(context.cursor, context.statement,
> context.parameters[0], context=context)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 950, in _cursor_execute
> self._handle_dbapi_exception(e, statement, parameters, cursor, context)
> File
> "/opt/Bio/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
> line 931, in _handle_dbapi_exception
> raise exc.DBAPIError.instance(statement, parameters, e,
> connection_invalidated=is_disconnect)
> ProgrammingError: (ProgrammingError) You must not use 8-bit
> bytestrings unless you use a text_factory that can interpret 8-bit
> bytestrings (like text_factory = str). It is highly recommended that
> you instead just switch your application to Unicode strings. u'UPDATE
> job SET update_time=?, stdout=?, stderr=? WHERE job.id = ?'
> ['2012-02-22 02:50:49.979136', 'locfit 1.5-6 \t 2010-01-20 \nnull
> device \n 1 \nnull device \n 1 \nnull device \n
> 1 \nnull device \n 1 \n\n Inf -Inf NaN \n 924 447 1710
> 0 \nnull device \n 1 \nnull device \n 1 \nnull
> device \n 1 \n', 'Loading required package:
> Biobase\n\nWelcome to Bioconductor\n\n Vignettes contain introductory
> material. To view, type\n \'browseVignettes()\'. To cite
> Bioconductor, see\n \'citation("Biobase")\' and for packages
> \'citation("pkgname")\'.\n\nLoading required package: locfit\nLoading
> required package: akima\nLoading required package: lattice\nWarning
> messages:\n1: In xy.coords(x, y, xlabel, ylabel, log) :\n 1710 x
> values <= 0 omitted from logarithmic plot\n2: In xy.coords(x, y,
> xlabel, ylabel, log) :\n 2880 y values <= 0 omitted from logarithmic
> plot\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n
> 1710 x values <= 0 omitted from logarithmic plot\nLoading required
> package: R.methodsS3\nR.methodsS3 v1.2.1 (2010-09-18) successfully
> loaded. See ?R.methodsS3 for help.\nLoading required package:
> R.oo\nR.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for
> help.\n\nAttaching package: \xe2\x80\x98R.oo\xe2\x80\x99\n\nThe
> following object(s) are masked from
> \xe2\x80\x98package:R.methodsS3\xe2\x80\x99:\n\n
> throw.default\n\nThe following object(s) are masked from
> \xe2\x80\x98package:methods\xe2\x80\x99:\n\n getClass, getClasses,
> getMethods\n\nThe following object(s) are masked from
> \xe2\x80\x98package:base\xe2\x80\x99:\n\n attach, detach,
> environment, gc, load, save\n\naroma.light v1.22.0 (2011-10-31)
> successfully loaded. See ?aroma.light for help.\n', 1345]
>
> It seems that R produces some output on stdout that I can't get rid of
> yet, but it doesn't seem to affect the outcome... it doesn't explain
> why this error happens... Any ideas? Is R using some sort of weird
> encoding that the python can't get?
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Programmer
> UC Davis Genome Center
> Davis, CA
> ___________________________________________________________
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>
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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