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

[Keith]

Thanks Dan for the tip. Got it too late to avoid trying to debug the 
problem, but one learns from these exercises.

This patched version of R worked as you predicted.
R version 2.15.2 Patched (2013-01-17 r61672)
Platform: x86_64-w64-mingw32/x64 (64-bit)

Only hgu95av2cdf and AnnotationDbi were installed with the 
affy:::cdfFromBioC("hgu95av2cdf")
  command.

I agree with Kasper. I still think it would be a good idea to modify 
affy and as I mentioned previously, 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.

Keith.

On 24/01/2013 3:31 PM, Kasper Daniel Hansen wrote:
> 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}}
>> _______________________________________________
>> 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
-----------------------------


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