Not able to install rstanarm on Ubuntu 18.04 LTS

Question

I'm not able to install rstanarm on R 3.5.3 running on Ubuntu 18.04 LTS. I used the following commands:

install.packages("rstanarm")

and

devtools::install_github("stan-dev/rstanarm", build_vignettes = FALSE)

and both throws the following error:

Execution halted
Makevars:17: recipe for target 'stan_files/lm.cc' failed
make: *** [stan_files/lm.cc] Error 1
ERROR: compilation failed for package ‘rstanarm’

sessionInfo

sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] usethis_1.5.0  devtools_2.0.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        ps_1.3.0          prettyunits_1.0.2 rprojroot_1.3-2  
 [5] digest_0.6.18     crayon_1.3.4      withr_2.1.2       assertthat_0.2.1 
 [9] R6_2.4.0          backports_1.1.3   magrittr_1.5      rlang_0.3.4      
[13] cli_1.1.0         curl_3.3          fs_1.2.7          remotes_2.0.2    
[17] testthat_2.0.1    callr_3.2.0       desc_1.2.0        tools_3.5.3      
[21] glue_1.3.1        pkgload_1.0.2     compiler_3.5.3    processx_3.3.0   
[25] pkgbuild_1.0.3    sessioninfo_1.1.1 tcltk_3.5.3       memoise_1.1.0    
> 

Kuebbing

Do you have everything from github.com/stan-dev/rstan/wiki/… ? – Management

Since you are using a newer Ubuntu, it's unlikely, but worth checking g++ version. – Guibert

Thanks @BenGoodrich for your comment. I've already attempted all this but still it is not working. Any thoughts. Thanks – Kuebbing

What is shown before the words Execution halted? – Billyebilobate

@duckmayr: "/usr/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan Error: (converted from warning) S3 methods 'print.stanfit', 'as.array.stanfit', 'as.matrix.stanfit', 'as.data.frame.stanfit', 'is.array.stanfit', 'dim.stanfit', 'dimnames.stanfit', 'names.stanfit', 'names<-.stanfit', 'pairs.stanfit', 'loo.stanfit' were declared in NAMESPACE but not found – Kuebbing

@Kuebbing Have you tried (from the terminal) sudo apt update then sudo apt install r-cran-rstan? – Billyebilobate

@duckmayr: Yes, I've alread tried sudo apt update and then sudo apt install r-cran-rstan which throws the error: ` E: Unable to locate package r-cran-rstan`. Any thoughts – Kuebbing

@Kuebbing Sorry, I forgot to add that you need to add the PPAs first: sudo add-apt-repository -y "ppa:marutter/rrutter" and sudo add-apt-repository -y "ppa:marutter/c2d4u" – Billyebilobate

@duckmayr: I also added the PPAs – Kuebbing

Let us continue this discussion in chat. – Billyebilobate

do you have a .RProfile file either in you home directory or in R directory , if you do ,then please can you share the content of it here or add it to your question ? – Accursed

Answer 1

On Ubuntu 18.04 + R 3.5.3, you can install rstanarm via the following:

sudo add-apt-repository -y "ppa:marutter/rrutter"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
sudo apt update
sudo apt install r-cran-rstanarm

Some background info on why you may have had trouble previously:

The RStan installation guide for Ubuntu is out of date for those using R 3.5.x.

Ben Goodrich linked in the comments to the RStan GitHub Guide to Installing RStan on Linux. There they advise the following for Ubuntu:

# Add marutter's c2d4u repository, (and rrutter for CRAN builds too)
sudo add-apt-repository -y "ppa:marutter/rrutter"
sudo add-apt-repository -y "ppa:marutter/c2d4u"
sudo apt-get update
sudo apt-get install r-cran-rstan

However, for newer versions of R, you need to instead do the following

# Add marutter's c2d4u repository, (and rrutter for CRAN builds too)
sudo add-apt-repository -y "ppa:marutter/rrutter"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
sudo apt-get update
sudo apt-get install r-cran-rstan

This should install RStan for you just fine on Ubuntu 18.04 + R 3.5.3.

Billyebilobate

Got installed. However, library(rstanarm) throws the following Error: package or namespace load failed for ‘rstanarm’ in library.dynam(lib, package, package.lib): shared object ‘rstanarm.so’ not found. Any thoughts, please. – Kuebbing

@Kuebbing Does running find . -name 00LOCK-rstan* from the terminal (from your home directory) return anything? – Billyebilobate

Did not find anything. – Kuebbing

Answer 2

First time when this error occured and assuming that you have a .RProfile in your R root directory you will most likely find a line where it says : setwd("~/R") ,go ahead and comment this line and restart R and get a new session , then run again : install.packages("rstanarm") you should be able to install rstanarm successfully , don't forget to uncomment setwd("~/R") after the installation , the reason of the this error to occur is that rstanarm install script assumes that the working directory is the root of the package directory which not the case when you call setwd() in .Rprofile if you want to give this a try .. please remove the rstanarm that you installed using PPA

Accursed