Hello All,
I have recently deployed a local instance of Galaxy at work and while I've been able to troubleshoot problems with all other tool types, I have a persistent issue with using any tool that relies on R.
For deseq:
Traceback (most recent call last):
File "/home/adam/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 109, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/adam/galaxy-dist/lib/galaxy/jobs/__init__.py", line 999, in finish
self.sa_session.flush()
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/scoping.py", line 127, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py", line 1356, in flush
self._flush(objects)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py", line 1434, in _flush
flush_context.execute()
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute
UOWExecutor().execute(self, tasks)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
self.execute_save_steps(trans, task)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps
self.save_objects(trans, task)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects
task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj
c = connection.execute(statement.values(value_params), params)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 824, in execute
return Connection.executors[c](self, object, multiparams, params)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
return self.__execute_context(context)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 896, in __execute_context
self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.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 = ?' ['2013-05-10 06:12:01.564757', '', 'Error: Loading required package: Biobase\nLoading required package: BiocGenerics\nLoading required package: methods\nLoading required package: parallel\n\nAttaching package: \xe2\x80\x98BiocGenerics\xe2\x80\x99\n\nThe following objects are masked from \xe2\x80\x98package:parallel\xe2\x80\x99:\n\n clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n clusterExport, clusterMap, parApply, parCapply, parLapply,\n parLapplyLB, parRapply, parSapply, parSapplyLB\n\nThe following object is masked from \xe2\x80\x98package:stats\xe2\x80\x99:\n\n xtabs\n\nThe following objects are masked from \xe2\x80\x98package:base\xe2\x8
0\x99:\n\n anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval,\n Filter, Find, get, intersect, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,\n tapply, union, unique, unlist\n\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n \'browseVignettes()\'. To cite Bioconductor, see\n \'citation("Biobase")\', and for packages \'citation("pkgname")\'.\n\nLoading required package: locfit\nlocfit 1.5-9.1 \t 2013-03-22\nLoading required package: lattice\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 9 y values <= 0 omitted from logarithmic plot\nError in hclustfun(distfun(x)) : \n NA/NaN/Inf in foreign function call (arg 11)\nCalls: heatmap -> hclustfun\nExecution halted\n\n', 116]
For cummerbund:
Traceback (most recent call last):
File "/home/adam/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 109, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/adam/galaxy-dist/lib/galaxy/jobs/__init__.py", line 999, in finish
self.sa_session.flush()
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/scoping.py", line 127, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py", line 1356, in flush
self._flush(objects)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py", line 1434, in _flush
flush_context.execute()
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute
UOWExecutor().execute(self, tasks)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
self.execute_save_steps(trans, task)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps
self.save_objects(trans, task)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects
task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj
c = connection.execute(statement.values(value_params), params)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 824, in execute
return Connection.executors[c](self, object, multiparams, params)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
return self.__execute_context(context)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 896, in __execute_context
self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File "/home/adam/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.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 = ?' ['2013-05-10 04:38:55.946925', '', 'Fatal error: Exit code 1 (CummerBund Error)\nError running R script. Error in library("cummeRbund") : there is no package called \xe2\x80\x98cummeRbund\xe2\x80\x99\nExecution halted\n\n', 112]
It appears that they all fail in a similar fashion. I noticed a similar issue brought up about a year ago but deploying the fixes mentioned then (using a python wrapper to keep R messages out of stderr and telling R to run without curly quotes) has not done
anything to stop it. Any ideas would be most appreciated as several R tools are a part of my target RNA-Seq pipeline.
Thanks!
Adam
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