[BioC] lumi package

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Sep 30 19:37:33 CEST 2009


Wow ... weird:

On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote:

> still not works.
> > source("http://www.bioconductor.org/biocLite.R")
> > biocLite("lumi")
> Using R version 2.9.2, biocinstall version 2.4.12.
> Installing Bioconductor version 2.4 packages:
> [1] "lumi"
> Please wait...
> Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ 
> universal/contrib/2.9/lumi_1.10.2.tgz'
> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb)
> opened URL
> ==================================================
> downloaded 6.8 Mb
> tar: Skipping to next header
> tar: Archive contains obsolescent base-64 headers
> gzip: stdin: invalid compressed data--crc error

I'm not sure why this is happening, but it looks like it can't  
uncompress the downloaded tar correctly ... installing from both  
within R (via biocLite) and from the command line is working for me.

Someone will likely have a better idea, but in the meantime, can you  
try to install the package from the command line? Like so:

1. Open Terminal.app

2. Download the package:
$ curl -O http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contrib/2.9/lumi_1.10.2.tgz

3. Install into R
$ R CMD INSTALL lumi_1.10.2.tgz

Is it still breaking? If so, continue to 4, otherwise celebrate.

4. Can you you simply uncompress that file? eg. does this uncompress  
successfully? (From within Terminal, we're not in R)
$ tar xvfz lumi_1.10.2.tgz

5. If that works, try to install the uncompressed file (it expanded to  
a "lumi" directory), but first remove the lumi*.tgz

$ rm lumi_1.10.2.tgz



Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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