symbol not found in flat namespace '___kmpc_critical'
Rodney, I don't know much about OpenMP and macOS, but note that these days https://mac.r-project.org/tools/ says "Additional information on the OpenMP page is available for those interested in OpenMP support which is not supported by Apple, but still possible with additional libraries." and links to https://mac.r-project.org/openmp/ I _believe_ that this requires the _user_ (or the check/build system) of the package on macOS to install one of the custom clang compilers listed on the page. For this reason, I don't think it is trivial to get the package through CRAN or distribute the package if it links / uses OpenMP. I could be wrong of course, since it is not something I follow. I am guessing the best solution (which could be complicated) is to have a configure script which checks at build time whether the system supports OpenMP. This feels like something someone has thought about. Best, Kasper On Sat, Apr 29, 2023 at 6:32?PM Sparapani, Rodney via R-SIG-Mac <
r-sig-mac at r-project.org> wrote:
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-bounces at r-project.org> on behalf of Sparapani, Rodney via R-SIG-Mac <r-sig-mac at r-project.org> Date: Saturday, April 29, 2023 at 4:18 PM To: r-sig-mac at r-project.org <r-sig-mac at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Best, Kasper [[alternative HTML version deleted]]