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@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@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of
> Seth Falcon
> Sent: 29 March 2005 19:57
> To: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] getBioC and install.packages2 fail
>
>
> <arne.muller@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@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@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@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@stat.math.ethz.ch
> >> >
https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >
> >>
> >>
>
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>
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