Hi Roger,
Good to hear from you again. Given that RCurl is hosted in both the CRAN
mirrors and in the Bioconductor extra repository, it can be a little
confusing how to install it on your system. The recommended path is to
follow the steps on the Bioconductor extra home page for RCurl
http://bioconductor.org/packages/release/extra/html/RCurl.html
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R";)
biocLite("RCurl")
Patrick
Day, Roger S wrote:
Hi Patrick,
Greetings from !(sunny) Pittsburgh.
What's the scoop on RCurl on windows (XP)?
I've tried to install RCurl_0.92-0.zip and RCurl_0.9-3.zip,
with both R 2.7.2 and R 2.8.0 from the RGUI (utils:::menuInstallLocal),
and get the error
"Windows binary packages in zipfiles are not supported".
which (according to google's one and only hit) comes from a perl script.
Your suggestion (below) to use biocLite hangs the R session, at this point:
Running biocinstall version 2.3.9 with R version 2.8.0
Your version of R requires version 2.3 of Bioconductor.
trying URL
'http://bioconductor.org/packages/2.3/extra/src/contrib/RCurl_0.92-0.tar.gz'
Content type 'application/x-gzip' length 239873 bytes (234 Kb)
opened URL
downloaded 234 Kb
(In this case, R 2.7.2.)
We also tried to build RCurl from the tarballs,
in DOS window and in Cygwin window,
with a variety of problems.
Is there a current solution to installing RCurl on windows?
(I'm moving this topic to r-help from bioconductor
on suggestions seen on that list.)
Thanks for your help.
-Roger
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Patrick Aboyoun
Sent: Thursday, May 29, 2008 8:49 PM
To: Steve Lianoglou
Cc: Yan Zhou; [EMAIL PROTECTED]
Subject: Re: [BioC] Rcurl 0.8-1 update for bioconductor 2.7
Steve and Yan,
We just uploaded source, Windows binary, and MacOS X Tiger
binary packages for RCurl 0.9-3 to the Bioconductor CRAN-like
repository http://bioconductor.org/packages/2.2/extra. This
repository is make available when you use R 2.7.0 and type
source("http://bioconductor.org/biocLite.R";)
biocLite("RCurl")
Let me know if this meets your needs.
Cheers,
Patrick
Steve Lianoglou wrote:
Hi,
I'm seeking help here regarding updating the Rcurl for macOSX to a
newer version so it'll accomodate to bioconductor 2.7. The current
version of Rcurl 0.8-1 (in bioconductor 2.7 for macOSX) is
built for
bioconductor 2.6; Is there anyone who could help to put the
bioconductor 2.7 compatible version of Rcurl into the
database? So we
could use packages depending on Rcurl? Any kind help is greatly
appreciated!
When this was brought up earlier, I think the consensus was
that since
this isn't a bioconductor hosted package, you'd better
inquire over at
R-help.
That said, someone also suggested earlier to install it
straight from
the source via this incantation:
install.packages("RCurl", repos = "http://www.omegahat.org/R";)
I don't think that worked for me, and I ended up d/ling the source
package and installing it manually, by first d/ling it and
uncompressing it. You'll get an RCurl folder. At the
command line, you
can then:
$ R CMD BUILD RCurl
$ R CMD CHECK RCurl_0.9-3.tar.gz
$ R CMD INSTALL RCurl_0.9-3.tar.gz
I'm not sure if this is the best way, but I seem to have a fully
functioning RCurl again since the biomaRt package relies on
that, and
that works now.
Btw - you can get RCurl here: http://www.omegahat.org/RCurl/
HTH,
-steve
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