Error In Getmonograph() From Bioconductor Book.

Question

[Michael]

I am trying to load the example data from the book Bioinformatics and Computational Biology Solutions Using R and Bioconductor as described here. However, when I try to run the following commands, I get:

source("http://bioconductor.org/getMonograph.R")
Warning message:
In safeSource() : Redefining ‘biocinstall’
getMonograph()
Error in biocinstall(groupName = groupName, ...) : 
   You have an outdated biocLite() function. Run 'rm(biocLite)' and try again.

I tried rm(biocLite) but that didn't have any effect. I am using a fairly recent R 2.15. What can I do to install the monograph data?

[Martin Morgan]

This has been fixed at the source; feel free to post queries like this to the Bioconductor mailing list.

[Michael]

Nice, thank you. I normally report such things to the mailing list, and recommend to do this first. In this case somebody else had reported the problem here.

Answer 1

[Michael]

The script http://bioconductor.org/getMonograph.R uses an old version of the bioconductor installer script which doesn't work in recent R:

source("http://bioconductor.org/getBioC.R")

To install all the monograph data and other packages used in the book you can simply do:

source("http://bioconductor.org/biocLite.R")
biocLite(monograph_group())

BioC_mirror: <http://bioconductor.org>
Using R version 2.15, BiocInstaller version 1.4.7.
Warning: unable to access index for repository <http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15>
Installing package(s) 'affycomp' 'affydata' 'affypdnn' 'affyPLM' 'ALL' 'ALLMLL'
  'AmpAffyExample' 'annaffy' 'AnnBuilder' 'annotate' 'arrayQuality' 'beta7'
  'Biobase' 'bioDist' 'Biostrings' 'cMAP' 'CoCiteStats' 'convert' 'e1071' 'edd'
  'estrogen' 'exactRankTests' 'facsDorit' 'factDesign' 'gbm' 'gcrma'
  'geneplotter' 'golubEsets' 'GOstats' 'gpls' 'graph' 'hexbin' 'hgu133a'
  'hgu133atagcdf' 'hgu133acdf' 'hgu133bcdf' 'hgu2beta7' 'hgu95av2'
  'hgu95av2cdf' 'hgu95av2probe' 'hopach' 'hsahomology' 'hu6800cdf'
  'hu6800probe' 'humanLLMappings' 'ipred' 'KEGG' 'KEGGSOAP' 'kidpack' 'limma'
  'locfit' 'LogitBoost' 'matchprobes' 'mclust' 'mlbench' 'MLInterfaces'
  'multtest' 'pamr' 'prada' 'PROcess' 'ProData' 'randomForest' 'rat2302'
  'RbcBook1' 'RBGL' 'RColorBrewer' 'RCurl' 'Rgraphviz' 'rrcov' 'simpleaffy'
  'sma' 'SpikeInSubset' 'SSOAP' 'statmod' 'vsn' 'XML' 'xtable' 'YEAST'
  'yeastExpData'
Warning: unable to access ...
[...]

 Warning message:
 In monograph_group() : 'arrayMagic' package is no longer available

According to the warning, the arrayMagic package can no longer be used.