[R-pkg-devel] Problems with devtools::build() in R

[Duncan Murdoch]

On 16/05/2023 12:07 p.m., Jarrett Phillips wrote:
> Hi All,
> 
> I'm trying to generate a `tar.gz` file on a Mac for R package submission to
> CRAN but am having issues.
> 
> I'm using `devtools`, specifically `build()` and `install()`.
> 
> My package relies on compiled code via `Rcpp/RcppArmadillo`.
> 
>      build("HACSim_OO")
>      ── R CMD build
> ─────────────────────────────────────────────────────────────────
>      ✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
> simulation/HACSim_OO/DESCRIPTION’ ...
>      ─  preparing ‘HACSim’:
>      ✔  checking DESCRIPTION meta-information ...
>      ─  cleaning src
>      ─  installing the package to process help pages
>           -----------------------------------
>      ─  installing *source* package ‘HACSim’ ...
>         ** using staged installation
>         ** libs
>         clang++ -arch arm64 -std=gnu++11 -
> I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>   -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
> -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall
> -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
>         clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>   -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
> -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall
> -pedantic -fdiagnostics-color=always -c accumulate.cpp -o accumulate.o
>         clang++ -arch arm64 -std=gnu++11 -dynamiclib
> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
> -L/opt/R/arm64/lib -o HACSim.so RcppExports.o accumulate.o
> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
> -L/Library/Frameworks/R.framework/Resources/lib -lRblas
> -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
> -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
>         ld: warning: directory not found for option
> '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
>         ld: warning: directory not found for option
> '-L/opt/R/arm64/gfortran/lib'
>         ld: library not found for -lgfortran
>         clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
>         make: *** [HACSim.so] Error 1
>         ERROR: compilation failed for package ‘HACSim’
>      ─  removing
> ‘/private/var/folders/r4/xm5blbcd2tn06tjv00lm1c780000gn/T/RtmpN4uaYR/Rinstdf4219594de/HACSim’
>           -----------------------------------
>      ERROR: package installation failed
>      Error in `(function (command = NULL, args = character(),
> error_on_status = TRUE, …`:
>      ! System command 'R' failed
>       ---
>       Exit status: 1
>       stdout & stderr: <printed>
>       ---
>      Type .Last.error to see the more details.
> 
> `clang` is installed (since I am able to run the code within my package)
> and I've verified by typing `gcc` in the Mac Terminal. I've also installed
> `Homebrew` and `gfortran`, verifying via typing in the Terminal.
> 
> Any idea on what's going on how to fix the issue(s)?

You don't say how you installed gfortran, but it sounds as though you 
installed Homebrew's build of it.  You should install the tools as 
available from https://mac.r-project.org/tools/.

Duncan Murdoch