[R] change in default behavior of ?functionname in R 2.10?

[Uwe Ligges]

[Going through some old and from what I see unanswered messages

This was a bug in the installer that nobody reported during the test 
phases (alpha / beta / release candidate). So please try out new R 
releases in order to help finding such bugs before release.

The installer cannot be tested easily in the regular regression tests.

Best wishes,
Uwe Ligges



Jenny Drnevich wrote:
> Hi everyone,
> 
> I just installed R 2.10 using the Windows binary. At some point in 
> the past using the Windows binary installation, the default behavior 
> of ?functionname changed from plain text to a nice html interface. 
> Now with R 2.10, the default behavior has changed back to the plain 
> text help. I assume this has some thing to do with these changes 
> listed for R 2.10, but I don't quite understand what it's saying or 
> how to change my system back to the html-style help:
> 
> 
> Package help is now converted from Rd by the R-based converters
>          that were first introduced in 2.9.0.  This means
> 
>          - Packages that were installed by R-devel after 2009-08-09
>            should not be used with earlier versions of R, and most
>            aspects of package help (including the runnable examples)
>            will be missing if they are so used.
> 
>          - Text, HTML and latex help and examples for packages
>            installed under the new system are converted on-demand from
>            stored parsed Rd files.  (Conversions stored in packages
>            installed under R < 2.10.0 are used if no parsed Rd files
>            are found.  It is recommended that such packages be
>            re-installed.)
> 
> 
>      o   HTML help is now generated dynamically using an HTTP server
>          running in the R process and listening on the loopback
>          interface.
> 
>          - Those worried about security implications of such a server
>            can disable it by setting the environment variable
>            R_DISABLE_HTTPD to a non-empty value.  This disables
>            help.start() and HTML help (so text help is shown instead).
> 
>          - The Java/Javascript search engine has been replaced by an
>            HTML interface to help.search().  help.start() no longer has
>            an argument 'searchEngine' as it is no longer needed.
> 
>          - The HTML help can now locate cross-references of the form
>            \link[pkg]{foo} and \link[pkg:foo]{bar} where 'foo' is an
>            alias in the package, rather than the documented (basename
>            of a) filename (since the documentation has been much
>            ignored).
> 
> 
> I'd appreciate any help, as the html-style help is so much more convenient!
> 
> Thanks,
> Jenny
> 
>  > sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices datasets  utils     methods
> [8] base
> 
> other attached packages:
>   [1] ath1121501cdf_2.5.0  limma_3.2.1          affyQCReport_1.24.0
>   [4] lattice_0.17-26      xtable_1.5-5         simpleaffy_2.22.0
>   [7] genefilter_1.28.0    made4_1.20.0         scatterplot3d_0.3-29
> [10] gplots_2.7.3         caTools_1.10         bitops_1.0-4.1
> [13] gdata_2.6.1          gtools_2.6.1         RColorBrewer_1.0-2
> [16] ade4_1.4-11          affyPLM_1.22.0       preprocessCore_1.8.0
> [19] gcrma_2.18.0         affycoretools_1.18.0 KEGG.db_2.3.5
> [22] GO.db_2.3.5          RSQLite_0.7-3        DBI_0.2-4
> [25] AnnotationDbi_1.8.0  affy_1.24.0          Biobase_2.6.0
> [28] RWinEdt_1.8-1
> 
> loaded via a namespace (and not attached):
>   [1] affyio_1.14.0     annaffy_1.18.0    annotate_1.24.0   biomaRt_2.2.0
>   [5] Biostrings_2.14.0 Category_2.12.0   GOstats_2.12.0    graph_1.24.0
>   [9] GSEABase_1.8.0    IRanges_1.4.0     RBGL_1.20.0       RCurl_1.2-1
> [13] splines_2.10.0    survival_2.35-7   tools_2.10.0      XML_2.6-0
>  >
> 
> 
> 
> 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 illinois.edu 
> 	[[alternative HTML version deleted]]
> 
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