[R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

[Sparapani, Rodney]

Hi Jarrett:

Do the two directories exist that clang is warning you about?

'/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
'/opt/R/arm64/gfortran/lib'


--
Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
Director, Wisconsin Chapter of the American Statistical Association
Institute for Health and Equity, Division of Biostatistics
Medical College of Wisconsin, Milwaukee Campus

From: R-SIG-Mac <r-sig-mac-bounces using r-project.org> on behalf of Jarrett Phillips <phillipsjarrett1 using gmail.com>
Date: Wednesday, May 17, 2023 at 11:54 AM
To: r-sig-mac using r-project.org <r-sig-mac using r-project.org>
Subject: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()
ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

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 and how to fix the issue(s)?

Thanks!

Cheers,

Jarrett

P.S. - I've asked on the R package dev list and after trying a number of
solutions was suggested to try here as it seems to be a macOS issue.

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