R help - Dec 2008 - [BioC] Rcurl 0.8-1 update for bioconductor 2.7

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: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Patrick Aboyoun
> Sent: Thursday, May 29, 2008 8:49 PM
> To: Steve Lianoglou
> Cc: Yan Zhou; bioconductor at stat.math.ethz.ch
> 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: 
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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: bioconductor-bounces at stat.math.ethz.ch 
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
>> Patrick Aboyoun
>> Sent: Thursday, May 29, 2008 8:49 PM
>> To: Steve Lianoglou
>> Cc: Yan Zhou; bioconductor at stat.math.ethz.ch
>> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: 
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>       
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>