R session aborded package raster - r

Question

Hello stackoverflow community,
I upgraded to the latest version of R and R studio this week, and have my R sessions encountering fatal error whenever I try to load the package raster.
I tried looking at the dependencies of the package, and re-installed all of them just to be sure.
# Install dependencies
db <- available.packages()
(deps <- tools::package_dependencies("raster", db)$raster)
# [1] "sp" "Rcpp" "methods"
install.packages(deps)
Any ideas?
Below are my session infos.
devtools::session_info("raster")
─ Session info ───────────────────────────────────────────────────────────────────
setting value
version R version 3.6.3 (2020-02-29)
os macOS Mojave 10.14.6
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-04-17
─ Packages ───────────────────────────────────────────────────────────────────────
package * version date lib source
lattice * 0.20-41 2020-04-02 [1] CRAN (R 3.6.2)
raster 3.0-12 2020-01-30 [1] CRAN (R 3.6.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.3)
sp 1.4-1 2020-02-28 [1] CRAN (R 3.6.0)
[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
While looking for a solution, I also found out that my Makevars file is incomplete. I used the solution described in here, which asks RStudio to ensure it always saves files with a trailing newline, but it doesn't work here.
Problem is I don't know if I have had this issue for a long time, or whether it is related to the raster issue.
I tried loading >50 other packages, and the error seems to be tied to the raster library.
> writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
##CC=clang
##CXX=clang++
CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
CC = gcc
CXX=/usr/local/bin/g++-9
CXX1X=/usr/local/clang6/bin/clang++
CXX98=/usr/local/clang6/bin/clang++
CXX11=/usr/local/clang6/bin/clang++
CXX14=/usr/local/clang6/bin/clang++
CXX17=/usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib
Warning message:
In readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")) :
incomplete final line found on '/Users/Rosalie/.R/Makevars'
Thanks a lot in advance for any help you may be able to provide. I really have no idea what to test next!
Best,
Rosalie

Answer 1

The issue was with clang.
I first updated to macOS Catalina 10.15.4, then uninstalled the R development toolchain I had for previous version using this code. Then, I used some here:
In the terminal, I used the code xcode-select --install, that open a pop-up window. Press "Install", and follow the steps to install xcode.
Verify installation by taping in gcc --version.
Then, download and install the appropriate gfortran binary find correct version here.
In R, I re-installed Rcpp and raster install.packages("Rcpp", "raster").
I am now able to load the raster without the session abording!