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

Thu Jan 24 05:31:17 CET 2013

Many people will use a standard 2.15.2 and not the patched version.

For this particular case - the automatic download of CDF packages - I
believe Keith has made a very good point, that it is not sensible to
download suggested packages.  I see no reason why the function cannot
be changed in a defensive manner to explicitly state what the depends
argument is, instead of using the default.  I am happy to take
responsibility for changing it.

On a side note, I don't understand why the CDF packages depends on
AnnotationDbi.  I don't see the data structures using anything in
AnnotationDbi and nothing is imported in the NAMESPACE and nothing
seems to used in the R code.

Kasper

On Wed, Jan 23, 2013 at 11:09 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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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