MacOS installation error | clang (LLVM option parsing): Unknown command line argument '-x86-pad-for-align=false'

[oliverartz]

Dear developers,

Thank you for creating facets, a great tool widely used by the community. I would like to implement facets in our pipeline to determine CNVs in tumor-only samples. Unfortunately, I am running into issues during the installation process.

I am running remotes::install_github("mskcc/facets", build_vignettes = TRUE), which throws the following error message:

Downloading GitHub repo mskcc/facets@HEAD
✔  checking for file ‘/private/var/folders/bc/k7ngxkf93nl2p6ln5w5s_fs1dk8ynz/T/RtmpDd7zrX/remotes16eb4293f493/mskcc-facets-f3c93ee/DESCRIPTION’ ...
─  preparing ‘facets’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to process help pages
         -----------------------------------
─  installing *source* package ‘facets’ ...
   ** using staged installation
   ** libs
   clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c 000.init.c -o 000.init.o
   gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c cbs2rank.f -o cbs2rank.o
   cbs2rank.f:24:45:

      24 |      1     psmax2, psdiff2, rn, zstat, hijinv, dnhet, xm1, xm2
         |                                             1
   Warning: Unused variable 'hijinv' declared at (1) [-Wunused-variable]
   cbs2rank.f:24:57:

      24 |      1     psmax2, psdiff2, rn, zstat, hijinv, dnhet, xm1, xm2
         |                                                         1
   Warning: Unused variable 'xm1' declared at (1) [-Wunused-variable]
   cbs2rank.f:24:62:

      24 |      1     psmax2, psdiff2, rn, zstat, hijinv, dnhet, xm1, xm2
         |                                                              1
   Warning: Unused variable 'xm2' declared at (1) [-Wunused-variable]
   clang (LLVM option parsing): Unknown command line argument '-x86-pad-for-align=false'.  Try: 'clang (LLVM option parsing) --help'
   clang (LLVM option parsing): Did you mean '--x86-slh-loads=false'?
   make: *** [cbs2rank.o] Error 1
   ERROR: compilation failed for package ‘facets’
─  removing ‘/private/var/folders/bc/k7ngxkf93nl2p6ln5w5s_fs1dk8ynz/T/RtmpUlYPEe/Rinst22313af7ea3/facets’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'facets' from GitHub:
  ! System command 'R' failed

I suspected issues with clang or gfortran, so I updated both on my system, but this did not solve the problem.

This is the sessionInfo()

R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2  xfun_0.32         remotes_2.4.2     purrr_0.3.4       vctrs_0.4.1       generics_0.1.3    miniUI_0.1.1.1    htmltools_0.5.3   usethis_2.1.6     yaml_2.3.5       
[11] utf8_1.2.2        rlang_1.0.5       pkgbuild_1.3.1    later_1.3.0       pillar_1.8.1      urlchecker_1.0.1  withr_2.5.0       glue_1.6.2        DBI_1.1.3         sessioninfo_1.2.2
[21] lifecycle_1.0.1   stringr_1.4.1     devtools_2.4.4    htmlwidgets_1.5.4 memoise_2.0.1     evaluate_0.16     knitr_1.40        callr_3.7.2       fastmap_1.1.0     httpuv_1.6.5     
[31] ps_1.7.1          curl_4.3.2        fansi_1.0.3       Rcpp_1.0.9        xtable_1.8-4      promises_1.2.0.1  cachem_1.0.6      pkgload_1.3.0     mime_0.12         fs_1.5.2         
[41] digest_0.6.29     stringi_1.7.8     processx_3.7.0    dplyr_1.0.10      shiny_1.7.2       rprojroot_2.0.3   cli_3.4.0         tools_4.1.3       magrittr_2.0.3    tibble_3.1.8     
[51] pacman_0.5.1      profvis_0.3.7     crayon_1.5.1      pkgconfig_2.0.3   ellipsis_0.3.2    prettyunits_1.1.1 assertthat_0.2.1  rmarkdown_2.16    rstudioapi_0.14   R6_2.5.1         
[61] compiler_4.1.3   

I would appreciate any pointers. Thank you very much!

[danwiththeplan]

Same issue here, would appreciate pointers. I have also updated gfortran. This issue also seems related https://github.com/mskcc/facets/issues/180

[eholdmore]

Ran into similar issues with install on Mac (Ventura, M1) and was able to resolve it using macrtools.