[BioC] installation problems of affy package

James MacDonald jmacdon at med.umich.edu
Thu May 6 16:01:18 CEST 2004

Francesco Falciano gave a fix in a recent post:




James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Toralf Kirsten <tkirsten at izbi.uni-leipzig.de> 05/06/04 06:57AM >>>
we use R 1.9.0 on a x86 machine with Fedore Linux and want to install 
the bioc package by calling the installation script getBioC() directly

within R as described on R-Project homepage.
But the affy package installation terminates when the install routine 
tries to install the help documents.

The same error occurs when I try it manually by calling
 > a <- CRAN.packages(CRAN=getOption("BIOC"))
 > install.packages("affy", .libPaths()[1], available=a, 

error message:

   normalize.contrast                text    html    latex   example
   normalize.invariantset            text    html    latex

ERROR: command (e.g. \url) inside \link
ERROR: building help failed for package 'affy'
** Removing '/usr/lib/R/library/affy'

Unfortunately, I couldn't find something in the mailing list archive.
Is anybody out there who knows what I can do?


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