Re: [galaxy-dev] Manhattan/qq plots
Hi Bjoern and Ross, thanks for your replies, we'll try to downgrade the gplot version, but we have to wait until our server admin is back from his vacation. This should be at the beginning of the next week. Best wishes, Thomas Von: Ross [mailto:ross.laza...@gmail.com] Gesendet: Dienstag, 27. August 2013 00:41 An: Bjoern Gruening Cc: Berner, Thomas; galaxy-dev@lists.bx.psu.edu Betreff: Re: [galaxy-dev] Manhattan/qq plots Hi, Thomas. There are no resources available to support that now 3 year old rgenetics code so I'm sad but not surprised to hear of this new problem. The grant ended long ago and I no longer work with SNP so have no excuse to keep fixing or working on it. Is someone using this code willing to take it over, fix these kinds of bugs and add automated installation to bring it up to speed ? I'll help all I can but without a volunteer, the code should be considered deprecated and will soon disappear from the distribution. On Tue, Aug 27, 2013 at 2:14 AM, Bjoern Gruening bjoern.gruen...@gmail.commailto:bjoern.gruen...@gmail.com wrote: Hi Thomas, I think you are running a to new version of gplot http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/ opts is now deprecated and likely causes that error. Can you downgrade the gplot version? We are working on a R dependencies mechanism but we are not done yet, sorry. Hope that helps, Bjoern Hey guys, we are running a local galaxy instance (10200:fd4113962c32)with R version 3.0.1 and want to use Manhattan/qq, but we are missing the pval manhatan.pdf, only pval qqplot.pdf is generated and we are getting the following error: Nonzero exit code = 1 [1] ### 11008 values read from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read - now running plots 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in version 0.9.1) Setting the plot title with opts(title=...) is deprecated. Use labs(title=...) or ggtitle(...) instead. (Deprecated; last used in version 0.9.1) Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. [1] ## qqplot on pval done [1] ## manhattan on pval starting 1 2 3 Error in structure(list(call = match.call(), aesthetics = aesthetics, : argument values is missing, with no default Calls: rgqqMan ... scale_colour_manual - manual_scale - discrete_scale - structure Execution halted At the galaxy-main ist working without any problems using the same input file. All the necessary packages should be installed. Any ideas? Thanks for your help. Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Manhattan/qq plots
Hey guys, we are running a local galaxy instance (10200:fd4113962c32)with R version 3.0.1 and want to use Manhattan/qq, but we are missing the pval manhatan.pdf, only pval qqplot.pdf is generated and we are getting the following error: Nonzero exit code = 1 [1] ### 11008 values read from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read - now running plots 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in version 0.9.1) Setting the plot title with opts(title=...) is deprecated. Use labs(title=...) or ggtitle(...) instead. (Deprecated; last used in version 0.9.1) Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. [1] ## qqplot on pval done [1] ## manhattan on pval starting 1 2 3 Error in structure(list(call = match.call(), aesthetics = aesthetics, : argument values is missing, with no default Calls: rgqqMan ... scale_colour_manual - manual_scale - discrete_scale - structure Execution halted At the galaxy-main ist working without any problems using the same input file. All the necessary packages should be installed. Any ideas? Thanks for your help. Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Manhattan/qq plots
Hi Thomas, I think you are running a to new version of gplot http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/ opts is now deprecated and likely causes that error. Can you downgrade the gplot version? We are working on a R dependencies mechanism but we are not done yet, sorry. Hope that helps, Bjoern Hey guys, we are running a local galaxy instance (10200:fd4113962c32)with R version 3.0.1 and want to use Manhattan/qq, but we are missing the pval manhatan.pdf, only pval qqplot.pdf is generated and we are getting the following error: Nonzero exit code = 1 [1] ### 11008 values read from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read - now running plots 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in version 0.9.1) Setting the plot title with opts(title=...) is deprecated. Use labs(title=...) or ggtitle(...) instead. (Deprecated; last used in version 0.9.1) Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. [1] ## qqplot on pval done [1] ## manhattan on pval starting 1 2 3 Error in structure(list(call = match.call(), aesthetics = aesthetics, : argument values is missing, with no default Calls: rgqqMan ... scale_colour_manual - manual_scale - discrete_scale - structure Execution halted At the galaxy-main ist working without any problems using the same input file. All the necessary packages should be installed. Any ideas? Thanks for your help. Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Manhattan/qq plots
Hi, Thomas. There are no resources available to support that now 3 year old rgenetics code so I'm sad but not surprised to hear of this new problem. The grant ended long ago and I no longer work with SNP so have no excuse to keep fixing or working on it. Is someone using this code willing to take it over, fix these kinds of bugs and add automated installation to bring it up to speed ? I'll help all I can but without a volunteer, the code should be considered deprecated and will soon disappear from the distribution. On Tue, Aug 27, 2013 at 2:14 AM, Bjoern Gruening bjoern.gruen...@gmail.comwrote: Hi Thomas, I think you are running a to new version of gplot http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/ opts is now deprecated and likely causes that error. Can you downgrade the gplot version? We are working on a R dependencies mechanism but we are not done yet, sorry. Hope that helps, Bjoern Hey guys, we are running a local galaxy instance (10200:fd4113962c32)with R version 3.0.1 and want to use Manhattan/qq, but we are missing the pval manhatan.pdf, only pval qqplot.pdf is generated and we are getting the following error: Nonzero exit code = 1 [1] ### 11008 values read from /opt/galaxy/galaxy-dist/database/files/002/dataset_2408.dat read - now running plots 'opts' is deprecated. Use 'theme' instead. (Deprecated; last used in version 0.9.1) Setting the plot title with opts(title=...) is deprecated. Use labs(title=...) or ggtitle(...) instead. (Deprecated; last used in version 0.9.1) Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. [1] ## qqplot on pval done [1] ## manhattan on pval starting 1 2 3 Error in structure(list(call = match.call(), aesthetics = aesthetics, : argument values is missing, with no default Calls: rgqqMan ... scale_colour_manual - manual_scale - discrete_scale - structure Execution halted At the galaxy-main ist working without any problems using the same input file. All the necessary packages should be installed. Any ideas? Thanks for your help. Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
