Installing stringr after upgrading from Ubuntu 18.04 to 20.04

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?

18.04 20.04 stringr require error

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updated 5.2 years ago by Jean-Karim Heriche

• written 5.2 years ago by tul66893 •

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.

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written 5.2 years ago by Jean-Karim Heriche

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

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written 5.2 years ago by tul66893 •

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.

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written 5.2 years ago by Jean-Karim Heriche

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