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

[Gordon K Smyth]

Hi Jenny,

statmod is deliberately a "suggests" rather than a "depends" because only a small number of limma
functions use it.

As far I remember, there the Bioconductor install behaviour hasn't changed.  Maybe I misremember,
but I don't think biocLite() has ever installed suggested packages from CRAN.

What has changed is that the CRAN installation

  install.packages("limma")

will no longer install suggested packages whereas it did in previous versions of R.  The R 2.5.0
CHANGE file says:

  "The 'Install packages ...' menu item now only installs essential
  dependencies ('Depends' and 'Imports' but not 'Suggests'),
  using install.packages(dependencies = NA)."

Best wishes
Gordon

On Sat, April 28, 2007 7:00 am, James W. MacDonald wrote:
> 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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