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 ----------------------------- ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
