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