Cannot run on ARM architecture chip's OS X system

[xuemingzhang]

Encountered an error while installing the Harmony package on a Mac computer with an M1 chip, the error result is as follows:

Loading required package: harmony Downloading GitHub repo immunogenomics/harmony@HEAD ── R CMD build ─────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/sl/dzs8c9n10dz8qzq29rkp07gc0000gn/T/RtmpJnSd41/remotes1355959b4ae49/immunogenomics-harmony-63ebd73/DESCRIPTION’ ... ─ preparing ‘harmony’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘harmony_0.1.1.tar.gz’

• installing source package ‘harmony’ ... using staged installation libs g++-12 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o g++-12 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c harmony.cpp -o harmony.o harmony.cpp: In member function 'void harmony::init_cluster_cpp(unsigned int)': harmony.cpp:69:18: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 69 | if (C > 0 && C < K) { | ^ harmony.cpp: In member function 'CUBETYPE harmony::moe_ridge_get_betas_cpp()': harmony.cpp:236:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 236 | for (unsigned k = 0; k < K; k++) { | ^ g++-12 -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 harmony.so RcppExports.o harmony.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/homebrew/Cellar/gcc/12.2.0 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: -undefined dynamic_lookup may not work with chained fixups installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-harmony/00new/harmony/libs R data moving datasets to lazyload DB byte-compile and prepare package for lazy loading help installing help indices * copying figures building package indices installing vignettes testing if installed package can be loaded from temporary location sh: line 1: 79470 Abort trap: 6 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/sl/dzs8c9n10dz8qzq29rkp07gc0000gn/T//RtmpQHnvqj/file136156b4bb327' ERROR: loading failed
• removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/harmony’ Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘harmony’ 2: In i.p(...) : installation of package ‘/var/folders/sl/dzs8c9n10dz8qzq29rkp07gc0000gn/T//RtmpJnSd41/file1355916eca6f4/harmony_0.1.1.tar.gz’ had non-zero exit status

[akhst7]

Arm-64 binary version of Harmony is available through a CRAN depository.

[pati-ni]

Is this still an issue? We just released a new version of the software available on CRAN, and to my knowledge, it works on M1 silicon.

[pati-ni]

Let us know if this is still an issue, closing now