[Bioc-devel] dependencies=TRUE problem, affy, gcrma, oligoClasses
Dan Tenenbaum
dtenenba at fhcrc.org
Thu Jan 24 05:09:53 CET 2013
Hi Keith,
On Wed, Jan 23, 2013 at 6:28 PM, Keith <keith at wehi.edu.au> wrote:
> Hi Jim,
>
> thanks very much for testing this. However I get a different outcome to you.
>
> I've done this twice with similar results. I did a fresh R-2.15.2 install,
> sourced biocLite, ran biocLite(), deleted AnnotationDbi from the library
> directory.
>
> I then used biocLite to install the affy package. I loaded the affy package
> and then ran the command "affy:::cdfFromBioC("hgu95av2cdf")". This installed
> dependency "AnnotationDbi" and then reported
> :
> also installing the dependencies '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'
>
> The help for install.packages command says that with the dependencies
> parameter,
> "|TRUE| means (as from *R* 2.15.0) to use |c("Depends", "Imports",
> "LinkingTo", "Suggests")| for |pkgs| and |c("Depends", "Imports",
> "LinkingTo")| for added dependencies".
>
> One would think that added dependencies (like AnnotationDbi) would be
> installed with dependencies of |c("Depends", "Imports", "LinkingTo"),
> |
> This was not the case. With my limited ability to debug these things, I
> think that install.packages call utils:::getDependencies with dependencies
> set to TRUE and pkgs="hgu95av2cdf", which seems to result in dependencies
> being set by the getDependencies line:
> if (depends && is.logical(dependencies)) {
> dependencies <- c("Depends", "Imports", "LinkingTo",
> "Suggests")
> The call also sets pkgs to "AnnotationDbi" "hgu95av2cdf", which seems
> reasonable.
>
> Later on install.packages calls utils:::.install.winbinary with a pkgs =
> "AnnotationDbi" "hgu95av2cdf" and dependencies=TRUE. The .install.winbinary
> function then calls utils:::getDependencies with dependencies set to TRUE,
> which sets dependencies to c("Depends", "Imports", "LinkingTo",
> "Suggests") again.
>
> Consequently the Suggested packages are being installed.
>
> I'm not very sure of my ground here and would appreciate some help from the
> experts.
>
> I have included a summarized copy of my R session, with a sessionInfo() at
> the bottom of it.
>
> I can only think that changing the dependencies value in the cdfFromBioC
> function will fix this.
>
I think this issue is fixed in R-2.15.2-patched and R-devel. Can you
try one of those?
Thanks,
Dan
> Appreciate your response,
>
> Keith
> ************************
> R version 2.15.2 (2012-10-26) -- "Trick or Treat"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>>source("http://bioconductor.org/biocLite.R")
> ...
> package 'BiocInstaller' successfully unpacked and MD5 sums checked
> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>> biocLite()
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
> also installing the dependencies 'BiocGenerics', 'DBI', 'RSQLite'
> ...
> package 'BiocGenerics' successfully unpacked and MD5 sums checked
> package 'DBI' successfully unpacked and MD5 sums checked
> package 'RSQLite' successfully unpacked and MD5 sums checked
> package 'Biobase' successfully unpacked and MD5 sums checked
> package 'IRanges' successfully unpacked and MD5 sums checked
> package 'AnnotationDbi' successfully unpacked and MD5 sums checked
> ...
> Old packages: 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart',
> 'survival'
> Update all/some/none? [a/s/n]: n
>
>> 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] 3
>> biocLite("affy")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'affy'
> also installing the dependencies 'affyio', 'preprocessCore', 'zlibbioc'
> ...
> package 'affyio' successfully unpacked and MD5 sums checked
> package 'preprocessCore' successfully unpacked and MD5 sums checked
> package 'zlibbioc' successfully unpacked and MD5 sums checked
> package 'affy' successfully unpacked and MD5 sums checked
> ...
>
>> sum(x %in% .packages(all.available = TRUE))
> [1] 3
>
>> 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:
> C:/RTest2/R-2.15.2/library. Now searching the internet repository."
>
> [1] "Checking to see if your internet connection works ..."
> also installing the dependency 'AnnotationDbi'
>
> also installing the dependencies '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'
> ...
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=C
> LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] affy_1.36.0 Biobase_2.18.0 BiocGenerics_0.4.0
> BiocInstaller_1.8.3
> loaded via a namespace (and not attached):
> [1] affyio_1.26.0 preprocessCore_1.20.0 tools_2.15.2
> zlibbioc_1.4.0
>>
> ************************
>
>
>
>
> On 24/01/2013 2:15 AM, James W. MacDonald 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.
>>
>> 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 at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
> --
> cheers,
>
> Keith
> ------------------------------
> Keith Satterley
> Bioinformatics Division,
> The Walter & Eliza Hall Institute
> Melbourne, Australia
> e:keith at wehi.edu.au
>
> -----------------------------
>
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:6}}
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