Re: [galaxy-dev] histogram tool not working
I had to change the matrix to a one dimensional array: $ hg diff histogram.py diff -r ea364eb4375f tools/plotting/histogram.py --- a/tools/plotting/histogram.py Tue Feb 01 13:35:46 2011 -0500 +++ b/tools/plotting/histogram.py Tue Feb 01 16:05:42 2011 -0600 @@ -69,7 +69,8 @@ first_invalid_line = i+1 if valid: -matrix.append( row ) +# matrix.append( row ) +matrix += row if skipped_lines < i: try: I've started converting all of the tools that use rpy to rpy2 using R version 2.12.1: ( rpy2 relies less on implicit conversions, so the site configuration is less problematic ) % grep -l rpy2 `find tools -name '*.py'` tools/stats/cor.py tools/regVariation/linear_regression.py tools/plotting/scatterplot.py tools/multivariate_stats/pca.py tools/multivariate_stats/kcca.py tools/multivariate_stats/kpca.py tools/multivariate_stats/cca.py On 2/1/11 3:00 PM, Ry4an Brase wrote: On Tue, Feb 01, 2011 at 08:51:25PM +, Peter wrote: On Tue, Feb 1, 2011 at 8:06 PM, David Hoover wrote: I just updated to the most recent version of Galaxy (hg pull -u), and now the error is different: An error occurred running this job: Error in hist.default(list(8, 6, 14, 8, 10, 3, 8, 6, 3, 12, 12, 8, 8, : 'x' must be numeric What gives? David Hi, R gives the error message 'x' must be numeric, so relevant questions are what version of R do you have, what version or rpy, and what version of Python (since Galaxy's tools tends to invoke R from Python via the ryp library - certainly the histogram tool does). We had the same problem when we first installed Galaxy back in March: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-March/002199.html Looking through both our ticketing system and our local hg commits I'm not finding what JJ did to fix it, so I'm cc-ing him on this. JJ, do you recall? (Lately similar problems, which all seem to be rpy incorrectly inferring the type of its arguments, have caused us to rewrite many of the rpy using tools to use rpy2 which the rpy developers say does a lot less "guessing", but again JJ's driving the development on that and I don't know where it's at). And everyone says "what gives?". :) ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] histogram tool not working
On Tue, Feb 01, 2011 at 08:51:25PM +, Peter wrote: > On Tue, Feb 1, 2011 at 8:06 PM, David Hoover wrote: > > I just updated to the most recent version of Galaxy (hg pull -u), and now > > the error is different: > > An error occurred running this job: Error in hist.default(list(8, 6, 14, 8, > > 10, 3, 8, 6, 3, 12, 12, 8, 8, : > > 'x' must be numeric > > What gives? > > David > > Hi, > > R gives the error message 'x' must be numeric, so relevant questions > are what version of R do you have, what version or rpy, and what > version of Python (since Galaxy's tools tends to invoke R from > Python via the ryp library - certainly the histogram tool does). We had the same problem when we first installed Galaxy back in March: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-March/002199.html Looking through both our ticketing system and our local hg commits I'm not finding what JJ did to fix it, so I'm cc-ing him on this. JJ, do you recall? (Lately similar problems, which all seem to be rpy incorrectly inferring the type of its arguments, have caused us to rewrite many of the rpy using tools to use rpy2 which the rpy developers say does a lot less "guessing", but again JJ's driving the development on that and I don't know where it's at). And everyone says "what gives?". :) -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] histogram tool not working
> R gives the error message 'x' must be numeric, so relevant questions > are what version of R do you have, what version or rpy, and what > version of Python (since Galaxy's tools tends to invoke R from > Python via the ryp library - certainly the histogram tool does). python = 2.6 R = 2.10.0 rpy = 1.0.3 > P.S. Am I getting old, or is "What gives?" just regionally popular slang? What region? David ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] histogram tool not working
On Tue, Feb 1, 2011 at 8:06 PM, David Hoover wrote: > I just updated to the most recent version of Galaxy (hg pull -u), and now > the error is different: > An error occurred running this job: Error in hist.default(list(8, 6, 14, 8, > 10, 3, 8, 6, 3, 12, 12, 8, 8, : > 'x' must be numeric > What gives? > David Hi, R gives the error message 'x' must be numeric, so relevant questions are what version of R do you have, what version or rpy, and what version of Python (since Galaxy's tools tends to invoke R from Python via the ryp library - certainly the histogram tool does). Peter P.S. Am I getting old, or is "What gives?" just regionally popular slang? ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] histogram tool not working
I just updated to the most recent version of Galaxy (hg pull -u), and now the error is different: An error occurred running this job: Error in hist.default(list(8, 6, 14, 8, 10, 3, 8, 6, 3, 12, 12, 8, 8, : 'x' must be numeric What gives? David On Feb 1, 2011, at 12:28 PM, David Hoover wrote: > I think I have everything installed correctly for the histogram tool. > However, when I try to generate a histogram with a simple tabular file of > numbers, I get the following error message: > > An error occurred running this job: array() argument 1 must be char, not list > > Any ideas? > > David Hoover > Helix Systems Staff > http://helix.nih.gov > ___ > galaxy-dev mailing list > galaxy-dev@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
