RcppParallel
RcppParallel copied to clipboard
RcppCore
Mac ARM installation failed
HI I have trouble to install qs2 from @traversc in https://github.com/qsbase/qs2/issues/3
He suggested me to ask you help.
When I install RcppParallel I got :
> remotes::install_github("RcppCore/RcppParallel",force = T)
Downloading GitHub repo RcppCore/RcppParallel@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/k7/pk9ppb456l7c_qx99rf0sqhh0000gn/T/RtmpYjP1YW/remotes1af72d54dc10/RcppCore-RcppParallel-b478b62/DESCRIPTION’ ...
─ preparing ‘RcppParallel’:
✔ checking DESCRIPTION meta-information
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (432ms)
─ checking for empty or unneeded directories
─ building ‘RcppParallel_5.1.9.9000.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: ‘Apple clang version 16.0.0 (clang-1600.0.26.3)’
using SDK: ‘MacOSX15.0.sdk’
(tbb) Building TBB using bundled sources ...
OS: macos
arch=arm64
compiler=clang
runtime=cc16.0.0_os15.0.1
tbb_build_prefix=macos_arm64_clang_cc16.0.0_os15.0.1
work_dir=/private/var/folders/k7/pk9ppb456l7c_qx99rf0sqhh0000gn/T/RtmpAcWiLW/R.INSTALL38ac364dd4fa/RcppParallel/src/build/macos_arm64_clang_cc16.0.0_os15.0.1_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=cc16.0.0_os15.0.1
clang++ -arch arm64 -I../inst/include -I/opt/homebrew/include -I/opt/R/arm64/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 -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1 -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
In file included from ../../src/tbb/concurrent_hash_map.cpp:17:
In file included from /opt/homebrew/include/tbb/concurrent_hash_map.h:17:
In file included from /opt/homebrew/include/tbb/../oneapi/tbb/concurrent_hash_map.h:21:
In file included from /opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:25:
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_config.h:440:13: warning: TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least. [-W#pragma-messages]
440 | #pragma message("TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least.")
| ^
In file included from ../../src/tbb/concurrent_hash_map.cpp:17:
In file included from /opt/homebrew/include/tbb/concurrent_hash_map.h:17:
In file included from /opt/homebrew/include/tbb/../oneapi/tbb/concurrent_hash_map.h:21:
In file included from /opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:27:
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:58:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
58 | inline namespace d0 {
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:129:1: error: unknown type name 'constexpr'
129 | constexpr std::uintptr_t number_of_bits() {
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:129:16: error: cannot define or redeclare 'uintptr_t' here because namespace 'd0' does not enclose namespace 'std'
129 | constexpr std::uintptr_t number_of_bits() {
| ~~~~~^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:129:16: warning: variable templates are a C++14 extension [-Wc++14-extensions]
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:129:25: error: expected ';' at end of declaration
129 | constexpr std::uintptr_t number_of_bits() {
| ^
| ;
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:129:26: error: a type specifier is required for all declarations
129 | constexpr std::uintptr_t number_of_bits() {
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:130:19: error: use of undeclared identifier 'T'
130 | return sizeof(T) * CHAR_BIT;
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:137:39: error: expected '(' for function-style cast or type construction
137 | return (number_of_bits<decltype(x)>() - 1) ^ gnu_builtins::clz(x);
| ~~~~~~~~~~~^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_machine.h:137:41: error: expected expression
137 | return (number_of_bits<decltype(x)>() - 1) ^ gnu_builtins::clz(x);
| ^
In file included from ../../src/tbb/concurrent_hash_map.cpp:17:
In file included from /opt/homebrew/include/tbb/concurrent_hash_map.h:17:
In file included from /opt/homebrew/include/tbb/../oneapi/tbb/concurrent_hash_map.h:21:
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:31:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
31 | inline namespace d0 {
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:34:18: warning: variadic templates are a C++11 extension [-Wc++11-extensions]
34 | template<typename... T> void suppress_unused_warning(T&&...) {}
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:34:55: warning: rvalue references are a C++11 extension [-Wc++11-extensions]
34 | template<typename... T> void suppress_unused_warning(T&&...) {}
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:40:1: error: unknown type name 'constexpr'
40 | constexpr size_t max_nfs_size = 128;
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:40:17: error: expected ';' after top level declarator
40 | constexpr size_t max_nfs_size = 128;
| ^
| ;
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:41:1: error: unknown type name 'constexpr'
41 | constexpr std::size_t max_nfs_size_exp = 7;
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:41:16: error: cannot define or redeclare 'size_t' here because namespace 'd0' does not enclose namespace 'std'
41 | constexpr std::size_t max_nfs_size_exp = 7;
| ~~~~~^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:41:22: error: expected ';' after top level declarator
41 | constexpr std::size_t max_nfs_size_exp = 7;
| ^
| ;
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:42:20: error: use of undeclared identifier 'max_nfs_size_exp'
42 | static_assert(1 << max_nfs_size_exp == max_nfs_size, "max_nfs_size_exp must be a log2(max_nfs_size)");
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:42:40: error: use of undeclared identifier 'max_nfs_size'
42 | static_assert(1 << max_nfs_size_exp == max_nfs_size, "max_nfs_size_exp must be a log2(max_nfs_size)");
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:49:12: error: unknown type name 'constexpr'
49 | static constexpr std::int32_t LOOPS_BEFORE_YIELD = 16;
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:49:27: error: non-friend class member 'int32_t' cannot have a qualified name
49 | static constexpr std::int32_t LOOPS_BEFORE_YIELD = 16;
| ~~~~~^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:49:34: error: expected ';' at end of declaration list
49 | static constexpr std::int32_t LOOPS_BEFORE_YIELD = 16;
| ^
| ;
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:61:45: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
61 | atomic_backoff(const atomic_backoff&) = delete;
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:62:56: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
62 | atomic_backoff& operator=(const atomic_backoff&) = delete;
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:66:22: error: use of undeclared identifier 'LOOPS_BEFORE_YIELD'
66 | if (count <= LOOPS_BEFORE_YIELD) {
| ^
/opt/homebrew/include/tbb/../oneapi/tbb/detail/_utils.h:79:21: error: use of undeclared identifier 'LOOPS_BEFORE_YIELD'
79 | if (count < LOOPS_BEFORE_YIELD) {
| ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
8 warnings and 20 errors generated.
make[2]: *** [concurrent_hash_map.o] Error 1
make[1]: *** [tbb_release] Error 2
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I/opt/homebrew/include -I/opt/R/arm64/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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I/opt/homebrew/include -I/opt/R/arm64/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 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RcppParallel.so init.o options.o -Ltbb/build/lib_release -ltbb -Wl,-rpath,@loader_path/../lib -L/opt/homebrew/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/RcppParallel’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel’
Warning messages:
1: In readLines(old_path) :
incomplete final line found on '/Users/benjamin/.R/Makevars'
2: In i.p(...) :
installation of package ‘/var/folders/k7/pk9ppb456l7c_qx99rf0sqhh0000gn/T//RtmpYjP1YW/file1af71e3bb5b0/RcppParallel_5.1.9.9000.tar.gz’ had non-zero exit status
How can I do ? thanks in advance
Works fine on my machine with the same version of Apple Clang.
$ clang --version
Apple clang version 16.0.0 (clang-1600.0.26.3)
Target: arm64-apple-darwin24.0.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
1: In readLines(old_path) :
incomplete final line found on '/Users/benjamin/.R/Makevars'
There's probably something in their ~/.R/Makevars that's causing trouble here.
Works fine on my machine with the same version of Apple Clang.
$ clang --version Apple clang version 16.0.0 (clang-1600.0.26.3) Target: arm64-apple-darwin24.0.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin1: In readLines(old_path) : incomplete final line found on '/Users/benjamin/.R/Makevars'There's probably something in their
~/.R/Makevarsthat's causing trouble here.
Hi ! Can you show your Makevars ?
https://github.com/RcppCore/RcppParallel/commit/69d50f65fa6cfc8163cccf09c6a500e55f1e24a7 may fix this for you.
This is still a problem: the reason is that you cannot use bundled oneTBB if it is already installed in the system since the headers will clash. The error will vary by cause, but below is another example that makes it more clear (here the system TBB is more recent so the conflict is more apparent). It seems that the bug is likely in the detection whether to use the bundled version as it should not use it when a system version is already present.
* installing *source* package ‘RcppParallel’ ...
** this is package ‘RcppParallel’ version ‘5.1.11-1’
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** 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: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using SDK: ‘MacOSX26.0.sdk’
(tbb) Building TBB using bundled sources ...
OS: macos
arch=arm64
compiler=clang
runtime=cc17.0.0_os26.0.1
tbb_build_prefix=macos_arm64_clang_cc17.0.0_os26.0.1
work_dir=/private/var/folders/fy/phsn55195339nxll0q_frr4r0000gn/T/RtmpAIK6JL/R.INSTALL1295a7340fb19/RcppParallel/src/build/macos_arm64_clang_cc17.0.0_os26.0.1_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=cc17.0.0_os26.0.1
clang++ -arch arm64 -I../inst/include -I/opt/R/arm64/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 -std=gnu++11 -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 -I/opt/R/arm64/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 -std=gnu++11 -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 -I/opt/R/arm64/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 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -DTBB_NO_LEGACY=1 -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_vector.cpp
In file included from ../../src/tbb/concurrent_vector.cpp:25:
In file included from ../../include/tbb/tbb_exception.h:20:
../../include/tbb/tbb_stddef.h:21:9: warning: 'TBB_VERSION_MAJOR' macro redefined [-Wmacro-redefined]
21 | #define TBB_VERSION_MAJOR 2019
| ^
/opt/R/arm64/include/tbb/../oneapi/tbb/version.h:30:9: note: previous definition is here
30 | #define TBB_VERSION_MAJOR 2022
| ^
In file included from ../../src/tbb/concurrent_vector.cpp:25:
In file included from ../../include/tbb/tbb_exception.h:20:
../../include/tbb/tbb_stddef.h:22:9: warning: 'TBB_VERSION_MINOR' macro redefined [-Wmacro-redefined]
22 | #define TBB_VERSION_MINOR 0
| ^
/opt/R/arm64/include/tbb/../oneapi/tbb/version.h:32:9: note: previous definition is here
32 | #define TBB_VERSION_MINOR 2
| ^
In file included from ../../src/tbb/concurrent_vector.cpp:25:
In file included from ../../include/tbb/tbb_exception.h:20:
../../include/tbb/tbb_stddef.h:25:9: warning: 'TBB_INTERFACE_VERSION' macro redefined [-Wmacro-redefined]
25 | #define TBB_INTERFACE_VERSION 11008
| ^
/opt/R/arm64/include/tbb/../oneapi/tbb/version.h:47:9: note: previous definition is here
47 | #define TBB_INTERFACE_VERSION 12160
| ^
[...]
