[BioC] getBioC and install.packages2 fail

Wed Mar 30 12:21:12 CEST 2005

Thanks,

When doing getBioC(libName='proteomics')

I don't get any error message at all:

> 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 
>

The "install.packages" command prints an error, for some reason the proxy authentification failed!

> install.packages(pkgs=c("gpls", "PROcess"), CRAN=biocUrl,dependencies=TRUE, me
thod="wget")
--12:07:56--  http://www.bioconductor.org/packages/bioc/stable/src/contrib/PACKA
GES
           => `/tmp/RtmpEi1pKG/file74b0dc51'
Resolving firewall... done.
Connecting to firewall[XXX.XXX.XXX.XXX]:XX... connected.
Proxy request sent, awaiting response... 407 Proxy Authentication Required
12:07:56 ERROR 407: Proxy Authentication Required.

dependencies 'gpls''PROcess' are not available

Warning message:
Download had nonzero exit status in: download.file(url = paste(contriburl, "PACK
AGES", sep = "/"),
>

However, when I connect to the web via mozilla (linux RH 7.3) and *then* run the install.packages the packages get downaloaded and installed properly.

I guess this means there's something wrong with my proxy authentification.

By the way, when running

> source("http://www.bioconductor.org/getBioC.R") 
> getBioC(libName='proteomics')

under w2k (using R --internet2) the installation works straight away ... 

Another hint that my proxy authentification under linux may be screwed up.

	kind regards,

	Arne

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of 
> Seth Falcon
> Sent: 29 March 2005 19:57
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] getBioC and install.packages2 fail
> 
> 
> <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
> >> > 
> >> 
> >>
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>