[BioC] Unable to install packages

[Heather Wick]

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

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.)

"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.

"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