[BioC] Unable to install packages

Fri Jul 8 00:06:07 CEST 2011

Thanks very much for your response,
Unfortunately I don't think I'm knowledgeable enough in the
innerworkings of R to understand what is being said by the link you
provided. I tried typing in some of the commands but I just get
messages saying "object not found" or "character(0)". Is there
somewhere I can find simple step by step instructions for R beginners
on how to fix this? How do I get the "auto fetch" as you described it,
to work?
I apologize for my lack of knowledge in this subject (my background is
biology, not computer science). Thanks so much,
~ Heather

On Wed, Jul 6, 2011 at 2:38 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> 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
>

-- 
Heather Wick
Research Coordinator
Tufts University Computer Science Department
hwick at cs.tufts.edu