I am running Ubuntu 18.04 on Windows 10 WSL. I originally installed R 3.6 following this guide: R-CRAN-Linux-Ubuntu-Installation. This question is related to: Permission denied while installing R package. I am writing a new question instead of commenting on the former because I don't have sufficient reputation. I tried to follow the instructions in the only answer in that post, however uninstalling R 3.6 and installing R 3.4 from default ubuntu repositories results in a similar error (below).

Finally, I cannot install ps from apt using the same pattern as r-cran-xml2, as no such package (r-cran-ps) exists on bionic. r-cran-ps is available on disco. I am trying to install ps because it is a dependency of rlib TSclust.

I can run R 3.6 on Windows without any problem so I expect this is related to WSL Ubuntu. Any advice or references from others who are familiar with this error is appreciated.

> ~/code/real-estate-lab/R$ sudo -E R

R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

> install.packages("ps") Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/ps_1.3.0.tar.gz' Content type 'application/x-gzip' length 261887 bytes (255 KB) ================================================== downloaded 255 KB

* installing source package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall px.c -o px
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-common.c -o api-common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.c -o common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extra.c -o extra.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dummy.c -o dummy.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c posix.c -o posix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-posix.c -o api-posix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c linux.c -o linux.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-linux.c -o api-linux.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ps.so init.o api-common.o common.o extra.o dummy.o posix.o api-posix.o linux.o api-linux.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /usr/local/lib/R/site-library/00LOCK-ps/00new/ps ** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries mv: cannot move '/usr/local/lib/R/site-library/00LOCK-ps/00new/ps' to '/usr/local/lib/R/site-library/ps': Permission denied ERROR: moving to final location failed

The downloaded source packages are in ‘/tmp/RtmpG1GgKd/downloaded_packages’ Warning message: In install.packages("ps") : installation of package ‘ps’ had non-zero
exit status
> q()


Have you tried the other solution given to the related question you mentioned?

install.packages("ps", dependencies=TRUE, INSTALL_opts = c('--no-lock'))

Note that using sudo for installing packages, although a quick workaround, will trap you into having to quit and restart R every time you want to remove or update your packages created in a sudo R session.

  • Thank you. I think this error is related to machine-specific constraints. Was an engineering laptop built for corporate environment. I continued to have serious challenges with WSL and stopped using it entirely. Using R on Windows itself turned out fine for my case as I just needed to do data analysis. Dec 23 '19 at 16:34

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.