problem when running Histogram
We have problem to run Histogram, and the problem is the same for both python 2.4 and 2.5. Dataset 46: Histogram on data 16 Tool execution generated the following error message: Traceback (most recent call last): File "/wwwdata/galaxy-dist/tools/plotting/histogram.py", line 5, in from rpy import * File "/usr/lib64/python2.5/site-packages/rpy.py", line 248, in start_r_eventloop() File "/usr/lib64/python2.5/site-packages/rpy.py", line 238, in start_r_eventloop _r_thread.start() File "/usr/lib64/python2.5/threading.py", line 434, in start _start_new_thread(self.__bootstrap, ()) thread.error: can't start new thread Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib64/python2.5/site-packages/rpy.py", line 244, in stop_r_eventloop _r_thread.join() File "/usr/lib64/python2.5/threading.py", line 549, in join assert self.__started, "cannot join thread before it is started" AssertionError: cannot join thread before it is started Error in sys.exitfunc: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib64/python2.5/site-packages/rpy.py", line 244, in stop_r_eventloop _r_thread.join() File "/usr/lib64/python2.5/threading.py", line 549, in join assert self.__started, "cannot join thread before it is started" AssertionError: cannot join thread before it is started
The problem was for any tools using RPy. We've now solved the problem ourselves, and the causes were: 1. Something wrong with the installed RPy package. 2. Tools using RPy are run under SGE on a cluster (even if RPy is correctly installed!). On Tue, 11 May 2010, zong-pei.han@imm.ox.ac.uk wrote: Date: Tue, 11 May 2010 10:29:29 +0100 From: "zong-pei.han@imm.ox.ac.uk" <zong-pei.han@imm.ox.ac.uk> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] problem when running Histogram We have problem to run Histogram, and the problem is the same for both python 2.4 and 2.5. Dataset 46: Histogram on data 16 Tool execution generated the following error message: Traceback (most recent call last): File "/wwwdata/galaxy-dist/tools/plotting/histogram.py", line 5, in from rpy import * File "/usr/lib64/python2.5/site-packages/rpy.py", line 248, in start_r_eventloop() File "/usr/lib64/python2.5/site-packages/rpy.py", line 238, in start_r_eventloop _r_thread.start() File "/usr/lib64/python2.5/threading.py", line 434, in start _start_new_thread(self.__bootstrap, ()) thread.error: can't start new thread Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib64/python2.5/site-packages/rpy.py", line 244, in stop_r_eventloop _r_thread.join() File "/usr/lib64/python2.5/threading.py", line 549, in join assert self.__started, "cannot join thread before it is started" AssertionError: cannot join thread before it is started Error in sys.exitfunc: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib64/python2.5/site-packages/rpy.py", line 244, in stop_r_eventloop _r_thread.join() File "/usr/lib64/python2.5/threading.py", line 549, in join assert self.__started, "cannot join thread before it is started" AssertionError: cannot join thread before it is started _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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zong-pei.han＠imm.ox.ac.uk