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
<najoshi@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;