[BioC] getBioC and install.packages2 fail

[Seth Falcon]

<Arne.Muller at sanofi-aventis.com> writes:
> I forgot to mentione the OS (linux RH 7.3), wget 1.8.1 and
> reposTools 1.5.2. I'm behind a firewall that requires
> authentification (it's a web-procy, too), but the code below
> (download.file) works, so I guess it's a problem with the existing
> installation. Well, or maybe it is a proxy probelm?

I suspect that it is a proxy problem.

> ps: install.packages2("gpls") from the R prompt does not work either
> :-(

And by "does not work", you mean it hangs?  Prints an error message?
Help me out here.

In your original post, you wanted to install the proteomics related
packages: gpls, PROcess, and apComplex.

apComplex is missing from the release1.5 repository and I'm looking
into why.  The other two are present.  

If gpls and PROcess would be of use to you, please try the following:

>From an R session enter:

biocUrl <- "http://www.bioconductor.org/packages/bioc/stable"
install.packages(pkgs=c("gpls", "PROcess"), CRAN=biocUrl,
                 dependencies=TRUE, method="wget")

And let us know if it works (and if not, send us the error output ;-)

+ seth






>
>> -----Original Message-----
>> From: Adaikalavan Ramasamy [mailto:ramasamy at cancer.org.uk]
>> Sent: 29 March 2005 17:28
>> To: Muller, Arne PH/FR
>> Cc: BioConductor mailing list
>> Subject: Re: [BioC] getBioC and install.packages2 fail
>> 
>> 
>> What OS ? Are you able to do this successfully ?
>> 
>> download.file( 
>> "http://www.bioconductor.org/repository/release1.5/package/Sou
>> rce/gpls_1.0.6.tar.gz", destfile="/tmp/junk" )
>> 
>> If yes, that should rule out any firewall problem. If no, 
>> then see help
>> (download.file) or search the R-help archives for solution.
>> 
>> If you are able to download successfully,then it might be some problem
>> with installation.
>> 
>> Since proteomics comprises only 3 packages, it might be worth to just
>> download them manually and install it.
>> 
>> Regards, Adai
>> 
>> 
>> 
>> On Tue, 2005-03-29 at 17:00 +0200, 
>> Arne.Muller at sanofi-aventis.com wrote:
>> > Hello,
>> > 
>> > I've an installation problem. I'm running R 2.0.1 and BioC 
>> 1.5. . I'd like to install the 'proteomics' package. Getting 
>> the most  recent getBioC fucntion works fine (I'm behind a 
>> firewall). ReposTools and tools get loaded automatically and 
>> then the script terminates without any error message and 
>> withour installing the proteomics package:
>> > 
>> > > getBioC(libNam='proteomics', method='wget')
>> > Running getBioC version 1.2.69....
>> > If you encounter problems, first make sure that
>> > you are running the latest version of getBioC()
>> > which can be found at: www.bioconductor.org/getBioC.R
>> > 
>> > Please direct any concerns or questions to 
>> bioconductor at stat.math.ethz.ch.
>> > 
>> > Loading required package: reposTools 
>> > Loading required package: tools 
>> > 
>> > When running install.packages2('gpls')
>> > 
>> > nothing happens either, no error, no output no instllation :-(
>> > 
>> > Any ideas what goes wrong?
>> > 
>> > 	thanks a lot for your help,
>> > 
>> > 	Arne
>> > 
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > 
>> 
>>