$ R /usr/bin/R: line 238: /usr/lib64/R/etc/ldpaths: Permission denied $ rpm -q R R-3.2.3-2.fc23.x86_64 That /usr/bin/R#L238 is: . "${R_HOME}/etc${R_ARCH}/ldpaths" I noticed the error began bursting shortly after I ran dnf update. An excerpt from dnf's transaction logs: $ dnf history info <ID> Upgraded setroubleshoot-3.3.5-2.fc23.x86_64 @updates Upgrade 3.3.5-3.fc23.x86_64 @updates Upgraded setroubleshoot-server-3.3.5-2.fc23.x86_64 @updates Upgrade 3.3.5-3.fc23.x86_64 @updates The missing part in the above logs is about a kernel update. May the_"Permission denied"_ error be related to SELinux ? Here're the contexts for R and ldpaths: $ ls -lhZ /usr/bin/R /usr/lib64/R/etc/ldpaths system_u:object_r:bin_t:s0 8.6K /usr/bin/R unconfined_u:object_r:lib_t:s0 574 /usr/lib64/R/etc/ldpaths Something weird is that RStudio keeps running as it used to do earlier when R on the command line was still _allowed_ to run. The root's shell gives no error, too. # R --version R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" The only R-related environment variable that is set is R_LIBS. I'd appreciate any help on this one.