[BioC] Unable to install packages

[Steve Lianoglou]

Hi,

On Wed, Jul 6, 2011 at 2:07 PM, Heather Wick <hwick at cs.tufts.edu> wrote:
> Hi,
> I'm trying to perform some data analysis in R using library(affyPLM)
> but I keep getting this error message when I try to use it. For
> example:
>> library(affyPLM)
>> CelData<-ReadAffy(celfile.path="~dbianc01/Lisa/TTTS/")
>> probefit<-fitPLM(CelData)
> Warning in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(),  :
>  'lib = "/usr/sup/R/lib64/R/library"' is not writable
> Error in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(),  :
>  unable to install packages

It looks like you don't have privileges to install into /usr/sup/R/*
-- still, there are ways to get it to install into a custom/home
library.

It seems that you need an R_LIBS_USER environment variable set for it
to do so, see:
http://cran.r-project.org/doc/manuals/R-admin.html#Managing-libraries

> I've done this analysis plenty of times with no problem and I can't
> figure out what is going wrong here, since I'm not doing anything
> differently than before. The staff here where I work is unfamiliar
> with R but said the following:
> "affyPLM is already installed.  The library that looks like it's
> trying to update is Biobase, which is also already installed.  (It
> might also be biocReposList, which appears to be part of Biobase, but
> I don't speak R at all, so I don't know how to check to see if that
> function is actually present in Biobase.  But given the name,
> biocReposList looks like some sort of updater, rather than a missing
> function.)

It's actually trying to install a package for the particular array you
are trying to analyze. It looks like the failing R cmd is this one:

install.packages(cdfname, lib = lib,

Where `cdfname` is the name of the package (the CDF is the
"description file" for your array -- not sure if CDF actually xlates
to "chip description file", but that's what it is in spirit).

You already have Biobase, and affyPLM installed ...

> "At a guess, it looks like Biobase is trying to automatically update
> itself, rather than just use the code that's present.  Near as I can
> tell, the version of Biobase we have is 2.8.0, which matches the
> current released version on the Bioconductor web site.  There should
> be no need for it to update.  Do you have some sort of version
> requirement in your code somewhere?  Or is this normal behavior for R,
> to auto-update libraries that don't need it on the fly?  None of us
> are R users, so we don't know what's usual for R.

Just to reiterate if it wasn't clear -- it's not trying to
auto-update, but it's trying to "auto fetch" a package which is the
"description package" for the particular array you are analyzing.

Hope that helps,

-steve

> "I'm not at all sure why it's trying to write to
> /usr/sup/R/lib64/R/library, but that directory is set read-only on
> purpose.  Nothing should be trying to write there."
>
> I also looked at the FAQ on the bioconductor website to see if I could
> update packages but I got errors with that as well:
>> source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://bioconductor.org
> Change using chooseBioCmirror().
> Warning messages:
> 1: In safeSource() : Redefining 'biocinstall'
> 2: In safeSource() : Redefining 'biocinstallPkgGroups'
> 3: In safeSource() : Redefining 'biocinstallRepos'
>> update.packages()
> Error in ret[i, ] <- c(pkgs[i], lib, desc) :
>  number of items to replace is not a multiple of replacement length
>
> As suggested in the posting guide, here is the output of sessionInfo():
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=C           LC_NUMERIC=C         LC_TIME=C
>  [4] LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C
>  [7] LC_PAPER=en_US.UTF-8 LC_NAME=C            LC_ADDRESS=C
> [10] LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] affyPLM_1.24.0        preprocessCore_1.10.0 gcrma_2.20.0
> [4] affy_1.26.1           Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.16.0 IRanges_1.6.2     affyio_1.16.0     splines_2.13.0
> [5] tools_2.13.0
>
> ...and traceback():
>> traceback()
> 5: .readPkgDesc(lib, fields)
> 4: installed.packages(lib.loc = lib.loc)
> 3: NROW(instPkgs)
> 2: old.packages(lib.loc = lib.loc, contriburl = contriburl, method = method,
>       available = available, checkBuilt = checkBuilt)
> 1: update.packages()
>
>
> What can I do to fix this? My background is not in computer science. Thanks
>
> --
> Heather Wick
> Research Coordinator
> Tufts University Computer Science Department
> hwick at cs.tufts.edu
>
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact