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symbol(s) not found for architecture arm64#218
@joshua-zh

Description

@joshua-zh
joshua-zh
opened on May 28, 2024

Hi, anybody could help me dealt with these errors?
I have installed RcppParelle from github previously. However, perhaps after I upgrade the llvm, the issue appeared.

remotes::install_github("RcppCore/RcppParallel")
Downloading GitHub repo RcppCore/RcppParallel@HEAD
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T/RtmpHcmCE0/remotes36e41d717cf/RcppCore-RcppParallel-3756f5b/DESCRIPTION’ ...
─  preparing ‘RcppParallel’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (1.1s)
─  checking for empty or unneeded directories
─  building ‘RcppParallel_5.1.7-9001.tar.gz’
   
* installing *source* package ‘RcppParallel’ ...
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'R/tbb-autodetected.R.in' => 'R/tbb-autodetected.R'
*** configured file: 'src/Makevars.in' => 'src/Makevars'
*** configured file: 'src/install.libs.R.in' => 'src/install.libs.R'
** finished configure for package 'RcppParallel'
** libs
using C++ compiler: ‘Homebrew clang version 18.1.6’
using SDK: ‘MacOSX14.4.sdk’
(tbb) Building TBB using bundled sources ...
OS: macos
arch=arm64
compiler=clang
runtime=ccHomebrew clang version 18.1.6_os14.5
tbb_build_prefix=macos_arm64_clang_ccHomebrew clang version 18.1.6_os14.5
work_dir=/private/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T/RtmpGMLICG/R.INSTALL44c57b5f424/RcppParallel/src/build/macos_arm64_clang_ccHomebrew /private/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T/RtmpGMLICG/R.INSTALL44c57b5f424/RcppParallel/src/tbb/src/clang /private/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T/RtmpGMLICG/R.INSTALL44c57b5f424/RcppParallel/src/tbb/src/version /private/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T/RtmpGMLICG/R.INSTALL44c57b5f424/RcppParallel/src/tbb/src/18.1.6_os14.5_release
Created ../build/lib_release directory
make -C "../build/lib_release"  -r -f ../../build/Makefile.tbb cfg=release
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=arm64 compiler=clang target=macos runtime=ccHomebrew clang version 18.1.6_os14.5
clang++ -arch arm64 -I../inst/include  -o concurrent_hash_map.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
clang++ -arch arm64 -I../inst/include  -o concurrent_queue.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_queue.cpp
clang++ -arch arm64 -I../inst/include  -o concurrent_vector.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_vector.cpp
clang++ -arch arm64 -I../inst/include  -o dynamic_link.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/dynamic_link.cpp
clang++ -arch arm64 -I../inst/include  -o itt_notify.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/itt_notify.cpp
clang++ -arch arm64 -I../inst/include  -o cache_aligned_allocator.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/cache_aligned_allocator.cpp
clang++ -arch arm64 -I../inst/include  -o pipeline.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/pipeline.cpp
clang++ -arch arm64 -I../inst/include  -o queuing_mutex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/queuing_mutex.cpp
clang++ -arch arm64 -I../inst/include  -o queuing_rw_mutex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/queuing_rw_mutex.cpp
clang++ -arch arm64 -I../inst/include  -o reader_writer_lock.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/reader_writer_lock.cpp
clang++ -arch arm64 -I../inst/include  -o spin_rw_mutex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/spin_rw_mutex.cpp
clang++ -arch arm64 -I../inst/include  -o x86_rtm_rw_mutex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/x86_rtm_rw_mutex.cpp
clang++ -arch arm64 -I../inst/include  -o spin_mutex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/spin_mutex.cpp
clang++ -arch arm64 -I../inst/include  -o critical_section.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/critical_section.cpp
clang++ -arch arm64 -I../inst/include  -o mutex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/mutex.cpp
clang++ -arch arm64 -I../inst/include  -o recursive_mutex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/recursive_mutex.cpp
clang++ -arch arm64 -I../inst/include  -o condition_variable.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/condition_variable.cpp
clang++ -arch arm64 -I../inst/include  -o tbb_thread.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_thread.cpp
clang++ -arch arm64 -I../inst/include  -o concurrent_monitor.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_monitor.cpp
clang++ -arch arm64 -I../inst/include  -o semaphore.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/semaphore.cpp
clang++ -arch arm64 -I../inst/include  -o private_server.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/private_server.cpp
clang++ -arch arm64 -I../inst/include  -o rml_tbb.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/rml/client/rml_tbb.cpp
sh ../../build/version_info_macos.sh clang++ -arch arm64 -I../inst/include  -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1  -I../../src -I../../src/rml/include -I../../include -I. >version_string.ver
clang++ -arch arm64 -I../inst/include  -o tbb_misc_ex.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_misc_ex.cpp
clang++ -arch arm64 -I../inst/include  -o task.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/task.cpp
clang++ -arch arm64 -I../inst/include  -o task_group_context.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/task_group_context.cpp
clang++ -arch arm64 -I../inst/include  -o governor.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/governor.cpp
clang++ -arch arm64 -I../inst/include  -o market.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/market.cpp
clang++ -arch arm64 -I../inst/include  -o arena.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/arena.cpp
clang++ -arch arm64 -I../inst/include  -o scheduler.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/scheduler.cpp
clang++ -arch arm64 -I../inst/include  -o observer_proxy.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/observer_proxy.cpp
clang++ -arch arm64 -I../inst/include  -o tbb_statistics.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_statistics.cpp
clang++ -arch arm64 -I../inst/include  -o tbb_main.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_main.cpp
sh ../../build/generate_tbbvars.sh DY
clang++ -arch arm64 -I../inst/include  -E -x c++ ../../src/tbb/mac64-tbb-export.def -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1 -I../../src -I../../src/rml/include -I../../include > tbb.def
../../src/tbb/arena.cpp:261:14: warning: variable 'drained' set but not used [-Wunused-but-set-variable]
  261 |     intptr_t drained = 0;
      |              ^
clang++ -arch arm64 -I../inst/include  -o tbb_misc.o -c -MMD -O2 -DUSE_PTHREAD  -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -fPIC  -D__TBB_BUILD=1 -Wall -Wno-non-virtual-dtor -Wno-dangling-else -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include -I. ../../src/tbb/tbb_misc.cpp
1 warning generated.
clang++ -arch arm64 -I../inst/include  -fPIC -o libtbb.dylib concurrent_hash_map.o concurrent_queue.o concurrent_vector.o dynamic_link.o itt_notify.o cache_aligned_allocator.o pipeline.o queuing_mutex.o queuing_rw_mutex.o reader_writer_lock.o spin_rw_mutex.o x86_rtm_rw_mutex.o spin_mutex.o critical_section.o mutex.o recursive_mutex.o condition_variable.o tbb_thread.o concurrent_monitor.o semaphore.o private_server.o rml_tbb.o tbb_misc.o tbb_misc_ex.o task.o task_group_context.o governor.o market.o arena.o scheduler.o observer_proxy.o tbb_statistics.o tbb_main.o    -ldl -lpthread -dynamiclib -install_name @rpath/libtbb.dylib -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -Wl,-exported_symbols_list,tbb.def
Undefined symbols for architecture arm64:
  "std::exception_ptr::__from_native_exception_pointer(void*)", referenced from:
      tbb::internal::tbb_exception_ptr::tbb_exception_ptr(tbb::captured_exception const&) in task_group_context.o
  "___cxa_init_primary_exception", referenced from:
      tbb::internal::tbb_exception_ptr::tbb_exception_ptr(tbb::captured_exception const&) in task_group_context.o
ld: symbol(s) not found for architecture arm64
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libtbb.dylib] Error 1
make[1]: *** [tbb_release] Error 2
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include  -I/opt/homebrew/include   -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c init.cpp -o init.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include  -I/opt/homebrew/include   -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c options.cpp -o options.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/homebrew/lib -o RcppParallel.so init.o options.o -Ltbb/build/lib_release -ltbb -Wl,-rpath,@loader_path/../lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: reexported library with install name '/opt/homebrew/opt/llvm/lib/libunwind.1.dylib' found at '/opt/homebrew/Cellar/llvm/18.1.6/lib/libunwind.1.0.dylib' couldn't be matched with any parent library and will be linked directly
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-RcppParallel/00new/RcppParallel
** R
** inst
** 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 ‘RcppParallel’:
 .onLoad failed in loadNamespace() for 'RcppParallel', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so, 0x0006): symbol not found in flat namespace '__ZN3tbb10interface78internal15task_arena_base24internal_max_concurrencyEPKNS0_10task_arenaE'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T//RtmpHcmCE0/file36e30d4d9a6/RcppParallel_5.1.7-9001.tar.gz’ had non-zero exit status

Activity

kevinushey

kevinushey commented on May 28, 2024

@kevinushey
kevinushey
on May 28, 2024
Contributor

It works for me using the default macOS toolchain. How have you configured R to use your custom LLVM toolchain?

joshua-zh

joshua-zh commented on May 29, 2024

@joshua-zh
joshua-zh
on May 29, 2024
Author

This is my zprofile file:

##Run these two commands in your terminal to add Homebrew to your PATH:
  eval "$(/opt/homebrew/bin/brew shellenv)"
  eval "$(/usr/libexec/path_helper)"

##If you need to have llvm first in your PATH, run:
  export PATH="/opt/homebrew/opt/llvm/bin:$PATH"

##For compilers to find homebrew installation
  export LDFLAGS="-L/opt/homebrew/lib"
  export CPPFLAGS="-I/opt/homebrew/include"


##To use the bundled libc++ please add the following LDFLAGS:
  export LDFLAGS="-L/opt/homebrew/opt/llvm/lib/c++ -Wl,-rpath,/opt/homebrew/opt/llvm/lib/c++"


##For compilers to find llvm you may need to set:
  export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"
  export CPPFLAGS="-I/opt/homebrew/opt/llvm/include"

and the makeconf file:

## C++ compilers
CXX = clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp
CXXFLAGS = -falign-functions=64 -Wall -g -O2 $(LTO)
CXXPICFLAGS = -fPIC
CXX11 = clang++ -arch arm64
CXX11FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO)
CXX11PICFLAGS = -fPIC
CXX11STD = -std=gnu++11
CXX14 = clang++ -arch arm64
CXX14FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO)
CXX14PICFLAGS = -fPIC
CXX14STD = -std=gnu++14
CXX17 = clang++ -arch arm64
CXX17FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO)
CXX17PICFLAGS = -fPIC
CXX17STD = -std=gnu++17
CXX20 = clang++ -arch arm64
CXX20FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO)
CXX20PICFLAGS = -fPIC
CXX20STD = -std=gnu++20
CXX23 = clang++ -arch arm64
CXX23FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO)
CXX23PICFLAGS = -fPIC
CXX23STD = -std=gnu++2b
CXX_VISIBILITY =
kevinushey

kevinushey commented on May 29, 2024

@kevinushey
kevinushey
on May 29, 2024
Contributor
clang++ -arch arm64 -I../inst/include  -fPIC -o libtbb.dylib concurrent_hash_map.o concurrent_queue.o concurrent_vector.o dynamic_link.o itt_notify.o cache_aligned_allocator.o pipeline.o queuing_mutex.o queuing_rw_mutex.o reader_writer_lock.o spin_rw_mutex.o x86_rtm_rw_mutex.o spin_mutex.o critical_section.o mutex.o recursive_mutex.o condition_variable.o tbb_thread.o concurrent_monitor.o semaphore.o private_server.o rml_tbb.o tbb_misc.o tbb_misc_ex.o task.o task_group_context.o governor.o market.o arena.o scheduler.o observer_proxy.o tbb_statistics.o tbb_main.o    -ldl -lpthread -dynamiclib -install_name @rpath/libtbb.dylib -stdlib=libc++ -arch arm64 -mmacosx-version-min=10.11  -Wl,-exported_symbols_list,tbb.def
Undefined symbols for architecture arm64:
  "std::exception_ptr::__from_native_exception_pointer(void*)", referenced from:
      tbb::internal::tbb_exception_ptr::tbb_exception_ptr(tbb::captured_exception const&) in task_group_context.o
  "___cxa_init_primary_exception", referenced from:
      tbb::internal::tbb_exception_ptr::tbb_exception_ptr(tbb::captured_exception const&) in task_group_context.o
ld: symbol(s) not found for architecture arm64
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libtbb.dylib] Error 1
make[1]: *** [tbb_release] Error 2

Sounds like this is could be an issue with your LLVM installation. See e.g.

llvm/llvm-project#86077
llvm/llvm-project#77653

And also:

Homebrew/homebrew-core#169820 (comment)

kevinushey
closed this as completedon May 29, 2024
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      symbol(s) not found for architecture arm64 · Issue #218 · RcppCore/RcppParallel