mskcc
MacOS installation error | clang (LLVM option parsing): Unknown command line argument '-x86-pad-for-align=false'
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!
Same issue here, would appreciate pointers. I have also updated gfortran. This issue also seems related https://github.com/mskcc/facets/issues/180
