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
Prof Brian Ripley
2010-Nov-16 07:52 UTC
[R] Cannot install packages in R 2.12.0 on Windows 7
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, ripley at 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