Can't access User Library in R - "Non-Zero Exit Status" warning

Question

When I tried to install packages on my work laptop, I got an error. I've been told that I have full privileges with the laptop, so there should be no blocks.

I think it might be something to do with the file path to the library where installed packages go? I'm using both the latest version of R and R Studio, 64-bit, and using Canada's U of T CRAN mirror site.

Here is what comes up when I try to install plyr with

install.packages("plyr")

also installing the dependency ‘Rcpp’ Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘Rcpp’ ‘plyr’

And when I try to install ggplot2, here is the long error message:

ERROR: dependency 'stringi' is not available for package 'stringr' * removing 'C:/RPackages/R-3.2.3/library/stringr' Warning in install.packages : running command '"C:/RPACKA~1/R-32~1.3/bin/x64/R" CMD INSTALL -l "C:\RPackages\R-3.2.3\library" C:\Users\MICHAE~1.COL\AppData\Local\Temp\RtmpGs24zA/downloaded_packages/stringr_1.0.0.tar.gz' had status 1 Warning in install.packages : installation of package ‘stringr’ had non-zero exit status ERROR: dependency 'colorspace' is not available for package 'munsell' * removing 'C:/RPackages/R-3.2.3/library/munsell' Warning in install.packages : running command '"C:/RPACKA~1/R-32~1.3/bin/x64/R" CMD INSTALL -l "C:\RPackages\R-3.2.3\library" C:\Users\MICHAE~1.COL\AppData\Local\Temp\RtmpGs24zA/downloaded_packages/munsell_0.4.3.tar.gz' had status 1 Warning in install.packages : installation of package ‘munsell’ had non-zero exit status ERROR: dependencies 'digest', 'plyr', 'reshape2', 'scales' are not available for package 'ggplot2' * removing 'C:/RPackages/R-3.2.3/library/ggplot2' Warning in install.packages : running command '"C:/RPACKA~1/R-32~1.3/bin/x64/R" CMD INSTALL -l "C:\RPackages\R-3.2.3\library" C:\Users\MICHAE~1.COL\AppData\Local\Temp\RtmpGs24zA/downloaded_packages/ggplot2_2.0.0.tar.gz' had status 1 Warning in install.packages : installation of package ‘ggplot2’ had non-zero exit status The downloaded source packages are in ‘C:\Users\michael.colangelo\AppData\Local\Temp\RtmpGs24zA\downloaded_packages’

What does "non-zero exit status" mean? Is it trying to find a library for the installation?> The appData file mentioned in the code doesn't seem to exist or I cannot access it. How do I change it to another local folder?

Janayjanaya

A non-zero exit status means in this case that the system failed to install the package. Try to disentangle the problem by installing one package after the other. In this case you could start with install.packages("stringi", dependencies=TRUE), then do the same with stringr, Rcpp, plyr, dlpyr, reshape2, digest,scales and finally ggplot2. At the moment there seem to be too many unresolved interdependencies. – Chastise

Thannks so much! All I had to do was add "dependencies=TRUE" and everything worked. I'm no longer frustrated :) I'm still new to Stack Overflow, is there a way to accept your response so you get credit for it? – Janayjanaya

Thank you @Mike, I'm glad that I could help. I'll add an answer which, if you like, you can accept by clicking on the tick on the left. Then the question can be considered as closed. – Chastise

Answer 1

A non-zero exit status means in this case that the system failed to install the package. There seem to be a number of unresolved dependencies in the installation process. You could try to resolve this by attempting to install the package using the option dependencies=TRUE; like this:

install.packages("ggplot2", dependencies=TRUE)

Chastise

Answer 2

i was struggling with the same problem, for a long time and mikes solution didnt help me either. I tried everything upto reinstalling R. Still didnt work. However the solution is quite simple in my case. In the Terminal dont run R as R but use:

sudo -i R

or change ownership of the r package folders, becaues if its owned by root you are not allowed to read or write in it.

Rives

This solved my problem on Debian on GCP – Containment

Answer 3

Several of my students have been having problems like this with R3.3.3 (Mac) and R3.5.0 (all). We found that installing devtools and loading packages from github helped get beyond the odd "non zero exit status" problems, e.g. to get the C50 package at https://github.com/topepo/C5.0:

require("devtools")
install_github("topepo/C5.0")

We tried all of the solutions listed on this page prior to this method finally working.

Hullo

oddly worked on windows 10 as well, thank you. Was trying to install library ModelMetrics. – Noll

I'm having a similar issue, but I'm not even able to install devtools, I keep getting the 'had non-zero exit status', even when I added dependencies=TRUE. Unsure what's really going on, I also get the warning that Rtools isn't installed either, but I already did install that in Documents/R/win-library/3.5, with the .Renviron file added to the Documents fodler so unclear what the issue is. – Senzer

Answer 4

RCpp must be compiled by Rtools. You should check the path of your Rtools.

By the way, on my computer (WIN10, R-3.5.1), Rtools must be installed at C:\Rtools. If I change the install location, R will not find it.

Schiffman

Answer 5

Hello I got the same problem, I uninstalled R, Rtools, and Rstuido then I downloaded and run as administrator 1)R 2)Rtools and 3)Rstuido, the order is important, then everything worked fine.

Criseldacrisey

i just ran into this same issue - non-zero exit status but no further info. i followed this suggestion (starting from scratch on a different workstation in my office), and it solved the problem. thanks! – Novellanovello

Answer 6

My problem was fixed by giving me ownership permissions over the Resources/library folder.

The way I solved it, was to go to Recovery Mode (Press Command + R when booting), then go to Utilities > Terminal.

I temporarily disabled the Configuring System Integrity Protection with (WARNING: REMEMBER TO ENABLE IT AFTERWARDS):

csrutil disable

Went back to macOS, right click on the library folder > Get Info > Sharing & Permissions > Click on the lock and enter your admin password > and added myself to read/write.

Restart the mac, enter Recovery Mode again, go to the terminal, and enable the Integrity Protection

csrutil enable

Hope it helps, and please, remember to re-enable the csrutil, your system is very vulnerable in that state, so if you suspect you have some kind of malware, don't use this solution.

Cathrin

Answer 7

Installing all of the tidyverse packages was the only thing that worked for me.

install.packages("tidyverse")

Soulsearching

Answer 8

I had the same problem and solved it by install g++ compiler

$ sudo apt install g++

Toxicosis