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

Solution 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')

Solution 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!

Solution 3

The easiest way to avoid this issue is before installing any package run the line below

options("install.lock"=FALSE)

Then try the install.packages("name_of_package") to install the package. The 00LOCK error would not come.

Comments

[rjkunde]

This resolved the issue for me too, but I'm with @Garini, what is causing the file lock?

[Adam Lee Perelman]

deleting the file also helps

[Ale]

@rjkunde, I'm also trying to understand this issue. I see the folder 00LOCK is sometimes created when I already have the package (or a dependency) installed and there is a problem (not an error) in install.packages().

[Ale]

Sometimes unlink does not remove the folder ad it is necessary to restart the R session.

[jimmyb]

In my experience, the shared file system NFS was mostly to blame. Someone with much more knowledge of the package management file-handling will hopefully speak up and correct me, but I assumed it was related to multiple distributed R processes spread over SGE cluster trying to interact with the package index files in LIB_PATH and the latency of cleaning up lock file on NFS file system.

[Ale]

Thanks for the insight! Since my problem was that I was unable to remove the 00LOCK folder within the same R session because of a NFS file that cannot be removed, when installing a package I go through every package that will be imported (and the package itself), detach it, remove it, install it again, and attach it again. In this way it seems so far that no folder 00LOCK remains after all packages are installed. This without using INSTALL_opts = c('--no-lock').

[Thorgas]

Fixed the problem for me.

[Mohammed]

Removing the entire directory recursively worked for me

[carbocation]

Interesting, I'm hitting this issue on OS X without any NFS. But, your solution worked.

[Alperen Taciroglu]

This solution helped me through many 00Lock package installation issues. Thanks for posting this!

[Timothy M Pollington]

Note that on the command line R CMD INSTALL --no-lock <pkg> may error if you are installing over a previous installation, giving the ERROR: cannot remove earlier installation, is it in use? message followed by an autoremoval of the old installation. So just run R CMD INSTALL --no-lock <pkg> again and that should complete the installation.

[Timothy M Pollington]

Alternatively this can also be applied in the RStudio GUI using Build > Configure Build Tools > Build Tools left-hand tab > Install and Restart --- R CMD INSTALL additional options: = --no-lock This means you can then just choose Build > Install and Restart, (though twice! for the same reason as my comment above for the command line.

[MGLondon]

This is what actually worked for me. None of the other solutions worked.