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: drnev...@illinois.edu
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