R install.packages returns "failed to create lock directory"

Question

I get this error when downloading the Rcpp package:

> install.packages("Rcpp", dependencies=TRUE) Installing package(s) into ‘/home/me/src/Rlibs’ (as ‘lib’ is unspecified) trying URL 'http://cran.us.r-project.org/src/contrib/Rcpp_0.10.2.tar.gz' Content type 'application/x-gzip' length 2380089 bytes (2.3 Mb) ... Warning in dir.create(lockdir, recursive = TRUE) :   cannot create dir '/home', reason 'Permission denied' ERROR: failed to create lock directory ‘/home/me/src/Rlibs/00LOCK-Rcpp’ ... 

As my machine is on a computer cluster, I've tried it on different nodes, and I was careful to delete the temporary files downloaded in /tmp. What is strange is that I have rights to write in /home/me/src/Rlibs/. So my questions are:

1. why does R want to have writing rights in /home while it only needs writing rights in /home/me/?
2. how can I fix the error?

---

> sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-redhat-linux-gnu (64-bit) locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  [7] LC_PAPER=C                 LC_NAME=C  [9] LC_ADDRESS=C               LC_TELEPHONE=C  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base loaded via a namespace (and not attached): [1] tools_2.15.2 

Answer 1

On NFS file systems it is sometimes not obvious what things you have to close.

The best way to avoid this is to use the --no-lock argument on the command line, i.e.:

R CMD INSTALL --no-lock <pkg> 

From within R, you can do this from within your command using:

install.packages("Rcpp", dependencies = TRUE, INSTALL_opts = '--no-lock') 

Answer 2

This happens when your last package installation has interrupted abnormally. to fix this you should remove the locked file. For example Execute this command in R console:

unlink("/home/me/src/Rlibs/00LOCK-Rcpp", recursive = TRUE) 

Hope this helps!