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.
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 intend...{{dropped:4}}