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

Hi Keith,


On 1/22/2013 10:44 PM, Keith wrote:

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:

There are two problems here. First, a normal BioC installation will already
have AnnotationDbi installed, as this is one of only three core packages
that are installed by

biocLite()

which is the first step in a 'regular' BioC installation procedure.

Second, if I install BioC and then strip out all of the packages you say
will be installed, I can't reproduce what you are seeing:

x <- c('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' ,'IRanges', 'AnnotationDbi')
sum(x %in% .packages(all.available = TRUE))

[1] 0

So I don't have any of these packages installed, including AnnotationDbi.

library(affy)
affy:::cdfFromBioC("hgu95av2cdf")

[1] "Attempting to obtain hgu95av2cdf from Bioconductor website"
[1] "Checking to see if package hgu95av2cdf is already installed"
[1] "The environment hgu95av2cdf was not found in these directories:
/misc/staff/jmacdon/R-devel/library.  Now searching the internet
repository."
[1] "Checking to see if your internet connection works ..."
also installing the dependencies DBI, RSQLite, IRanges, AnnotationDbi

So I end up installing the cdf, and four other packages.

I think the problem lies elsewhere.

Best,

Jim

'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
-----------------------------

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099