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
'IRanges'.
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
happen.
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.
cheers,
Keith
------------------------------
Keith Satterley
Maintainer of affylmGUI
Bioinformatics Division,
The Walter & Eliza Hall Institute
Melbourne, Australia
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