The error seems to be a BioC problem[*] and associated with having a
package installed with an empty DESCRIPTION file. So please take a
look at your installed packages and remove any such.
The following R code may help:
for(lib in .libPaths()) {
descs <- Sys.glob(file.path(lib, "*", "DESCRIPTION"))
sizes <- file.info(descs)$size
names(sizes) <- descs
print(sizes[sizes < 100])
}
[*] They don't know how they did it, but reported this symptom on
R-devel recently.
On Mon, 15 Nov 2010, Dick Beyer wrote:
Hi,
I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are the
relevant lines:
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
source("http://www.bioconductor.org/biocLite.R";)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite("Biobase")
Using R version 2.12.0, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] "Biobase"
Please wait...
Error: subscript out of bounds
traceback()
7: .readPkgDesc(lib, fields)
6: installed.packages(lib.loc = libpath, fields = c("Package", "Version"))
5: getDependencies(pkgs, dependencies, available, lib)
4: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
dependencies = dependencies, libs_only = libs_only, ...)
3: install.packages(pkgs = pkgs, repos = repos, ...) at biocinstall.R#205
2: biocinstall(pkgs = pkgs, groupName = groupName, ...) at biocLite.R#5
1: biocLite("Biobase")
It doesn't matter if I use biocLite, or just install.packages(), I get the same
error. I did a re-install of R, but that didn't help. I'm hoping someone else
has seen this error and might have a suggestion.
Thanks very much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
