Oh, that was totally self-inflicted. I had commented out PKG_LIBS in Makevars.in That does work on Linux with OpenMP somehow. However, it does NOT with macOS. Thanks
-- 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-boun...@r-project.org> on behalf of Sparapani, Rodney via R-SIG-Mac <r-sig-mac@r-project.org> Date: Saturday, April 29, 2023 at 4:18 PM To: r-sig-mac@r-project.org <r-sig-mac@r-project.org> Subject: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical' ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hi Gang: After hours of debugging, I�m stuck and hoping that someone has an idea of what the issue is here. Any hints/tips/etc. are greatly appreciated! I�m getting this error from my CRAN package, nftbart. Right now, I�m preparing for a new release: v1.6. However, I�m stumped by this error message that I get when installing with OpenMP. Without OpenMP, everything is fine; however, the package benefits greatly from OpenMP. I am getting the same results for R 4.2.3 and 4.3.0 RC. The source code is on github at https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$<https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$> So, to demonstrate, you just need to do something like this� $ git clone https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$<https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$> DIR $ cd DIR $ R CMD build nftbart $ R CMD INSTALL nftbart_1.6.tar.gz * installing to library �/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library� * installing *source* package �nftbart� ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes checking for clang++ -arch x86_64 -std=gnu++17 option to support OpenMP... -lomp -Xclang -fopenmp configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: �Apple clang version 14.0.3 (clang-1403.0.22.14.1)� using C++ compiler: �Apple clang version 14.0.3 (clang-1403.0.22.14.1)� using SDK: �� clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp -Xclang -fopenmp -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp -Xclang -fopenmp -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nftbart.cpp -o nftbart.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o nftbart.so init.o nftbart.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs ** R ** data ** demo ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for �nftbart� in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so': dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so, 0x0006): symbol not found in flat namespace '___kmpc_critical' Error: loading failed Execution halted ERROR: loading failed * removing �/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart� * restoring previous �/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart� > sessionInfo() R version 4.3.0 Patched (2023-04-27 r84338) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.2.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/Chicago tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.3.0 > OpenMP Build: LLVM 14.0.6 $ codesign -d -vv /usr/local/lib/libomp.dylib Executable=/usr/local/lib/libomp.dylib Identifier=libomp Format=Mach-O universal (x86_64 arm64) CodeDirectory v=20400 size=6506 flags=0x0(none) hashes=198+2 location=embedded Signature size=8977 Authority=Developer ID Application: Simon Urbanek (VZLD955F6P) Authority=Developer ID Certification Authority Authority=Apple Root CA Timestamp=Feb 5, 2023 at 4:26:54 PM Info.plist=not bound TeamIdentifier=VZLD955F6P Sealed Resources=none Internal requirements count=1 size=168 -- 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 [[alternative HTML version deleted]] [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
