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?

Solution 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)

Solution 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.

Solution 3

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.

Solution 4

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.

View more solutions

Comments

[tcratius]

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

[Arjun Mohan]

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.