10

everyone! I'm trying to install Bioconductor package "cummeRbund" and constantly fail. I've tried biocLite("cummeRbund") command with BiocInstaller enabled, install.packages("cummeRbund") and their variations with specified library address. The result is always 

"Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  'lib = "/usr/lib/R/library"' is not writable"

and r keeps offering me to use personal directory. What should I do to get rid of this pesky issue ("cummeRbund" is not the only one package that keeps failing to install)?

My specs.: Ubuntu 14.04 LTS 64-bit, R version 3.2.2 (2015-08-14) -- "Fire Safety", Bioconductor version 3.2 (BiocInstaller 1.20.0)

Braiam
  • 1
  • 11
  • 47
  • 78
SirOsric
  • 189
  • 1
  • 1
  • 4
  • It means you don't have permission to install it system wide (you need `sudo` privileges). If you are the only user there is nothing really wrong with a personal directory. – cdeterman Oct 29 '15 at 12:32
  • Yes, I understand that means I have to possess root permission, and yes, I'm a solely user. But I can't call these library, if it installed in personal directory. R can't find it. – SirOsric Oct 29 '15 at 12:36
  • [How should I deal with “package 'xxx' is not available (for R version x.y.z)” warning?](http://stackoverflow.com/questions/25721884) – zx8754 Oct 29 '15 at 13:09
  • @zx8754 First double check that there are no typos. Bioconductor will not tell you the package `xXx` doesn't exists, it will tell you it's not available for your version. Copy/paste names to avoid problems. Some other problems may come too, but that's the most common – 3nrique0 Jun 15 '18 at 10:06
  • @3nrique0 I am **not** asking the question, just sharing a link to FAQ post about package issues. – zx8754 Jun 15 '18 at 10:41

2 Answers2

12

It’s normal that R’s default library path is read-only for the current user. This usually means that R was installed by a different user (most commonly a sysadmin). This isn’t a problem in itself. — Just configure R to use a different library path.

To do this, set the R_LIBS_USER environment variable. To preserve it across shell sessions, set the value in ~/.profile or similar.

export R_LIBS_USER=/path/to/your/r-library

There’s a detailed description of this solution in another answer.

Another solution is to install software for each user separately. This especially makes sense on a non-shared system. Some package managers support installing software for the local user, without super user rights.

Konrad Rudolph
  • 530,221
  • 131
  • 937
  • 1,214
0

I installed R version 3.3.0 on another OS : No ``cummeRbund´´ install issues.

Got the "3.3.0" with $ svn co https://svn.r-project.org/R/trunk/ ( svn ver. 69583 ).

Knud Larsen
  • 5,753
  • 2
  • 14
  • 19