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

[Dan Tenenbaum]

On Wed, Jan 23, 2013 at 7:15 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> 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.
>

Starting in BioC 2.12, biocLite() just updates all installed packages.


> 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.

I could reproduce Keith's problem with R 2.15.2; however, it looks
like it has been fixed in R 2.15.2 patched (I tested 2013-01-22
r61734) and R-devel (I tested 2013-01-22 r61734).

Dan


>
> 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 at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel