[BioC] Bioconductor installation problem on Mac

Debashis Bhattacharya bhattach at simbiosys-biowares.com
Tue Aug 29 20:20:39 CEST 2006


I have posted this problem earlier, but there was no response. Hence, 
I'm posting this again.

I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo 
iMac).

When I try to install bioconductor -- following instructions, using 
biocLite() -- it downloads
the packages mentioned on the install page. However, the instatllation 
does not complete.

I get the following message after the downloads are complete:

------
The downloaded packages are in
   /tmp/RtmpJdBYlA/downloaded_packages
Warning messages:
1: number of rows of result
   is not a multiple of vector length (arg 2) in: cbind(1, res0, 
Repository = repos)
2: cannot create HTML package index in: make.packages.html()
------

I have tried installation with only one package (affy), and still face 
the same problem. The entire log
for affy is as follows:

--------
 > source("http://www.bioconductor.org/biocLite.R")
 > biocLite(c("affy"))
Running getBioC version 0.1.6 with R version 2.3.1
Running biocinstall version 1.8.4 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying URL 
'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/contrib/2.3/affy_1.10.0.tgz' 

Content type 'application/x-gzip' length 1733585 bytes
opened URL
==================================================
downloaded 1692Kb


The downloaded packages are in
   /tmp/RtmpJdBYlA/downloaded_packages
Warning messages:
1: number of rows of result
   is not a multiple of vector length (arg 2) in: cbind(1, res0, 
Repository = repos)
2: cannot create HTML package index in: make.packages.html()
---------

Please help.



Debashis Bhattacharya.



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