[Bioc-devel] dependencies=TRUE problem, affy,gcrma,oligoClasses

Keith keith at wehi.EDU.AU
Wed Jan 23 04:44:39 CET 2013

To the Bioconductor developer group,

I emailed the author of the affy package (Rafael Irizarry) and he 
advised me to contact the Bioconductor developers with my problem.

My problem is with the affy package. My affylmGUI package depends on the 
affy package. I only noticed this problem when I tested my program on a 
fresh install of R-2.15.2. When affylmGUI normalizes data using the rma 
function in the affy package, it calls eventually the cdfFromBioC 
function (as coded in getCDFenv.R) which uses the "install.packages" 
function with the parameter "dependencies=TRUE". This worked fine up 
until R-2.15.0, but this version of R changed the meaning of the 
dependencies  parameter to include packages also mentioned in the 
"Suggests" field.

Consequently when affy installs a cdf package like "hgu95av2cdf", the 
dependency "AnnotationDbi" is installed, which is not a problem, but 
additionally all the packages in the "Suggests" field of AnnotationDbi 
are also installed. This causes the following to be installed:
'XML', 'BSgenome', 'Rsamtools', 'bitops', 'GenomicRanges', 'Biostrings',
'rtracklayer', 'biomaRt', 'RCurl', 'GenomicFeatures', 'hgu95av2.db',
'GO.db', 'org.Sc.sgd.db', 'org.At.tair.db', 'KEGG.db', 'RUnit',
'TxDb.Hsapiens.UCSC.hg19.knownGene', 'hom.Hs.inp.db', 'org.Hs.eg.db',
'seqnames.db', 'reactome.db', 'AnnotationForge', 'DBI', 'RSQLite' and

This is a 1.8GByte download which would rather destroy a lab lesson if 
it happened during a class! Of course the immediate solution is to 
install AnnotationDbi before running affylmGUI, but that may not always 

Therefore could someone please change line 102 of getCDFenv.R to 
'dependencies=c("Depends", "Imports")' to solve this problem.

It would be very helpful if you could make the change on R-2.15.2 to 
avoid the above mentioned problems.

After using Itoshi NIKAIDO's source code search engine at 
http://search.bioconductor.jp/ (Thanks for that Itoshi, it is an 
excellent tool), I suspect that 2 other packages would cause similar 
problems. Doing a code search for "dependencies=TRUE" showed that the 
gcrma package (file getPackages.R) and the oligoClasses package (file 
utils-general.R) have this parameter on the install.packages function 
call. Perhaps it would be wise to modify these packages in a similar way.


Keith Satterley
Maintainer of affylmGUI
Bioinformatics Division,
The Walter & Eliza Hall Institute
Melbourne, Australia

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