[BioC] biocLite() fails to install all limma dependencies from CRAN

[James W. MacDonald]

Hi Jenny,

Jenny Drnevich wrote:
> Hi all,
> 
> I just installed R 2.5 today and then installed Bioconductor 2.0 
> using the recommended biocLite(). I then tried to call 
> duplicateCorrelation() from limma, but got this error:
> 
>  > corfit <- 
> duplicateCorrelation(MA.nobg.scale,design,ndups=1,block=c(1,1,2,2))
> Loading required package: statmod
> Error: could not find function "mixedModel2Fit"
> In addition: Warning message:
> there is no package called 'statmod' in: library(package, lib.loc = 
> lib.loc, character.only = TRUE, logical = TRUE,

statmod isn't a dependency for limma - it is in the Suggests field, so 
IIRC, won't be installed automatically.

Best,

Jim


> 
> 
> It appears that biocLite() didn't get the statmod package from CRAN. 
> Once I downloaded and installed statmod, everything was fine. I don't 
> remember having to do this in the past, so did something get 
> accidentally changed?
> 
> Thanks,
> Jenny
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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