[BioC] help with getBioC

[A.J. Rossini]

I'm not sure if the error is related to bugs regarding connections
mentioned as fixed, according to the release notes for 1.7.1?



best,
-tony

Gordon Smyth <smyth at wehi.edu.au> writes:

> I have never managed to use "getBioC" to install bioconductor from a
> unix machine. I have appended my latest effort below:
>
> 1. Can you tell me what stupid thing I am doing wrong?
> 2. Why does getBioC ignore my attempt to specify the destination
> directory, notice it tries to write to /usr/local/lib which I don't
> have write priveleges to. I certainly do have write priveleges to the
> directory I've specified.
> 3. Any thoughts why it takes getBioC 3-4 minutes to give me this error
> message? I can download reposTools using cvs from this machine in just
> a few seconds, so internet speed doesn't seem to be the problem.
>
> Thanks
> Gordon
>
>  > source("http://www.bioconductor.org/getBioC.R")
>  > system("pwd")
> /home/users/lab0605/smyth/gordon
>  > getBioC(libName="all",relLevel="devel",destdir="/home/users/lab0605/smyth/gordon/Rlibs")
> Running getBioC version 1.2.34....
> 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.
>
> [1] "Installing reposTools ..."
> ERROR: cannot write to or create directory '/usr/local/lib/R/library'
> Loading required package: Biobase
> Welcome to Bioconductor
>           To view some introductory material -- look at our vignettes
>           Simply type: openVignette()
>           to see the available vignettes
>           To read a vignette see the openVignette help page for details
> Creating a new generic function for "summary" in package
> Biobase
>
> Synching your local package management information ...
> Error in file(file, "wb") : unable to open connection
> In addition: Warning message:
> cannot open file `/usr/local/lib/R/library/liblisting.Rda'
>  > version
>           _
> platform i686-pc-linux-gnu
> arch     i686
> os       linux-gnu
> system   i686, linux-gnu
> status
> major    1
> minor    7.0
> year     2003
> month    04
> day      16
> language R
>
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>

-- 
A.J. Rossini  /  rossini at u.washington.edu  /  rossini at scharp.org
http://software.biostat.washington.edu/ UNTIL IT MOVES IN JULY.
Biomedical and Health Informatics, University of Washington
Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center.
FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email 

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