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

James W. MacDonald jmacdon at uw.edu
Wed Jan 23 16:15:16 CET 2013

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


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 
[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.



> '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
> -----------------------------
> ______________________________________________________________________
> The information in this email is confidential and intend...{{dropped:4}}
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

More information about the Bioc-devel mailing list