[BioC] bug in gcrma help CHM files?

[Patrick Aboyoun]

Jenny,
Right now the compressed HTML help files in the Windows binary package 
builds of BioC 2.2 have been a bit flaky, and we are currently looking 
into correcting the problem. For now we recommend using the plain text 
or HTML version of the help files on Windows until this issue is fixed. 
To access the plain text help files, set chmhelp = FALSE in the help 
function call. For example,

help(justGCRMA, chmhelp = FALSE)
help(rma, chmhelp = FALSE)

To access the HTML help files, set chmhelp = FALSE and htmlhelp = TRUE 
in the help function call. For example,

help(justGCRMA, chmhelp = FALSE, htmlhelp = TRUE)
help(rma, chmhelp = FALSE, htmlhelp = TRUE)


Thanks for your patience.


Patrick



Jenny Drnevich wrote:
> Hi,
>
> I'm having problems calling the help files for functions from the 
> gcrma package. I haven't had this problem with getting help files from 
> other packages (which I've done a LOT over the past week). Is it a bug?
>
> Thanks,
> Jenny
>
> > ?justGCRMA
> Error in 
> print.help_files_with_topic("C:/PROGRA~1/R/R-27~1.0/library/gcrma/chm/justGCRMA") 
> :
>   CHM file could not be displayed
> > ?gcrma
> Error in 
> print.help_files_with_topic("C:/PROGRA~1/R/R-27~1.0/library/gcrma/chm/gcrma") 
> :
>   CHM file could not be displayed
> > ?rma
> #works fine
>
> > sessionInfo()
> R version 2.7.0 (2008-04-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] canine2cdf_2.2.0     affyQCReport_1.18.0  geneplotter_1.18.0
>  [4] lattice_0.17-6       RColorBrewer_1.0-2   simpleaffy_2.16.0
>  [7] made4_1.14.0         ade4_1.4-7           affyPLM_1.16.0
> [10] affycoretools_1.12.0 annaffy_1.12.0       KEGG.db_2.1.4
> [13] gcrma_2.12.0         matchprobes_1.12.0   biomaRt_1.14.0
> [16] RCurl_0.8-1          GOstats_2.6.0        Category_2.6.0
> [19] genefilter_1.20.0    survival_2.34-1      RBGL_1.16.0
> [22] annotate_1.18.0      xtable_1.5-2         GO.db_2.1.4
> [25] AnnotationDbi_1.2.0  RSQLite_0.6-8        DBI_0.2-4
> [28] graph_1.18.0         limma_2.14.0         affy_1.18.0
> [31] preprocessCore_1.2.0 affyio_1.8.0         Biobase_2.0.0
> [34] RWinEdt_1.7-9
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.10    grid_2.7.0         KernSmooth_2.22-22 XML_1.94-0.1
> >
>
>
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
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