R library contains no packages

Question

My installation of R seems to be faulty. I tried using several packages using library() , and was told they could not be found. I then tried just running library() with no arguments, and it said Warning message: In library() : library '/usr/local/lib/R/site-library' contains no packages . The output of .libpaths is

[1] "/home/username/R/x86_64-pc-linux-gnu-library/3.2"
[2] "/usr/local/lib/R/site-library"                       
[3] "/usr/lib/R/site-library"                             
[4] "/usr/lib/R/library"

The output of sessionInfo() is

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.3

locale:
 [1] LC_CTYPE=en_AU.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8       
 [4] LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8   
 [6] LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8
[12] LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

loaded via a namespace (and not attached):
[1] tools_3.2.3

I have not been able to find any information on this error online. Everyone else seems to have a problem with not finding specific packages. I have not seen anyone complain about having no packages whatsoever.

These are the error messages I have received when attempting to install "tidyverse" from RStudio using install.packages("tidyverse") :

Installing package into ‘/home/username/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependencies

...

* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c colorspace.c -o colorspace.o
colorspace.c:2:19: fatal error: ctype.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'colorspace.o' failed
make: *** [colorspace.o] Error 1
ERROR: compilation failed for package ‘colorspace’
* removing ‘/home/dylanus-zwei/R/x86_64-pc-linux-gnu-library/3.4/colorspace’
Warning in install.packages :
  installation of package ‘colorspace’ had non-zero exit status

This repeats for a while, followed by:

Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------

The same error arises for openssl. I installed libcurl this morning, so I'm not sure what it's expecting here.

checking for gcc... gcc -std=gnu99
checking whether the C compiler works... no

The C compiler definitely works. I have used it many times. The other messages all seem to be the same kind of thing.

Answer 1

This could be a similar problem, due to permissions: Library is not writable

What's the error message when you try installing packages? And what does the site-packages directory look like when you navigate to it using a shell? Is there anything in there? What are the permissions?

To summarize, we've now learned that the current permissions for the directory that is supposed to hold the packages are: drwxr_xr_x , if you copied the line for the correct directory ( /usr/local/lib/R/site-library ). I'm clarifying because it looks like you may have copy pasted the permissions for the first package in your site-directory, abind . If you did, then it means there are packages in site-directory and we have a different problem (possibly also a permissions problem, but read rather than write).

So if the output of ls -ld /usr/local/lib/R/site_library starts with drwxr-sr-x 6 root staff the answer, by Manual Va , from that question that should resolve things. It wouldn't hurt to add yourself to staff, in general, but that by itself won't solve your problem. Here's the modified answer for you

Do:

$ cd /usr/local/lib/R
$ sudo chmod go+w site-library
$ ls -l

The printed line should look like this:

drwxrwsrwx 2 root staff 0000 Mar 31 00:00 site-library