Installing stringr after upgrading from Ubuntu 18.04 to 20.04

Question

[tul66893]

Hi!

New to the world of bioinformatics and am looking for some help. One of the scripts my lab uses requires the stringr package to be downloaded. When I run require(stringr) i receive an error.

Loading required package: stringr
Error: package or namespace load failed for ‘stringr’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/elrodlab/R/x86_64-pc-linux-gnu-library/3.6/stringi/libs/stringi.so':
  libicui18n.so.60: cannot open shared object file: No such file or directory

Any idea how to solve this?

[Jean-Karim Heriche]

Did you re-install the stringr package after the upgrade? If not try that first. It's looking for a system library that has probably been upgraded. Re-installing the package should make it find the right library. I would be surprised if this library wasn't on your system since it provides unicode support.

[tul66893]

Thanks for the reply! When I run install.packages("stringr", repos='http://cran.us.r-project.org')

installing source package ‘stringr’ ... ** package ‘stringr’ successfully unpacked and MD5 sums checked mv: cannot move '/home/elrodlab/R/x86_64-pc-linux-gnu-library/3.6/stringr' to '/home/elrodlab/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-stringr/stringr': Permission denied ERROR: cannot remove earlier installation, is it in use?

• removing ‘/home/elrodlab/R/x86_64-pc-linux-gnu-library/3.6/stringr’ Warning in install.packages : installation of package ‘stringr’ had non-zero exit status

The downloaded source packages are in ‘/tmp/Rtmp1XIVox/downloaded_packages’ Warning message: In .rs.normalizePath(libPaths) :
path[2]="/usr/local/lib/R/site-library": No such file or directory

[Jean-Karim Heriche]

Either you have something running that still uses the package or you have a problem overwriting the old installation. Stop all running R instances (including RStudio) then delete the package directory. Also make sure that you have write permissions on the R library directory.
By the way, this is the type of question that is best asked on StackOverflow as it is not a bioinformatics question. There might also already be an answer there.