提问人：Edward Lavender 提问时间：11/15/2023 最后编辑：Edward Lavender 更新时间：11/17/2023 访问量：42
R 中带有 {renv} 的库 （RcppParallel） 问题
Issue with library(RcppParallel) with {renv} in R
问：
问题：在 R 中，我可以以通常的方式运行库 （RcppParallel） 而不会出现问题，但在使用 {renv} 进行本地依赖项管理的 RStudio 项目中，运行 renv：：install（“RcppParallel”） 后，库 （RcppParallel） 失败并出现错误。我使用的是 M2 MacBook。
详：
在 R 中，我可以按照通常的方式安装和加载 {RcppParallel}，而不会出现问题：
install.packages("RcppParallel")
library(RcppParallel)
在使用 {renv} 的 RStudio 项目中，包将安装：
project <- file.path(tempdir(), "project")
dir.create(project)
setwd(project)
renv::init(settings = list(use.cache = FALSE), restart = FALSE)
writeLines("library(RcppParallel)", con = "dependencies.R")
renv::install("RcppParallel", type = "binary", prompt = FALSE)
这似乎有效：
# Downloading packages -------------------------------------------------------
- Downloading RcppParallel from CRAN ... OK [file is up to date]
Successfully downloaded 1 package in 0.64 seconds.
The following package(s) will be installed:
- RcppParallel [5.1.7]
These packages will be installed into "/private/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T/RtmpEO6paC/project/renv/library/R-4.3/aarch64-apple-darwin20".
# Installing packages --------------------------------------------------------
- Installing RcppParallel ... OK [installed binary in 0.44s]
Successfully installed 1 package in 0.45 seconds.
但是运行库（RcppParallel）失败：
source("dependencies.R")
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 '/private/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T/RtmpEO6paC/project/renv/library/R-4.3/aarch64-apple-darwin20/RcppParallel/libs/RcppParallel.so':
dlopen(/private/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T/RtmpEO6paC/project/renv/library/R-4.3/aarch64-apple-darwin20/RcppParallel/libs/RcppParallel.so, 0x0006): symbol not found in flat namespace '__ZN3tbb10interface78internal15task_arena_base24internal_max_concurrencyEPKNS0_10task_arenaE'
我认为从源代码安装 {RcppParallel} 可能是一种解决方案，但我无法让它工作，即使在 {renv} 之外：
setwd(tempdir())
install.packages("RcppParallel", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/RcppParallel_5.1.7.tar.gz'
Content type 'application/x-gzip' length 1629119 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘RcppParallel’ ...
** 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: ‘g++ (GCC) 12.2.0’
using SDK: ‘MacOSX14.0.sdk’
(tbb) Building TBB using bundled sources ...
OS: macos
arch=arm64
compiler=clang
runtime=cc15.0.0_os13.6.1
tbb_build_prefix=macos_arm64_clang_cc15.0.0_os13.6.1
work_dir=/private/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T/RtmpJxF6Aa/R.INSTALL286e431dd45c/RcppParallel/src/build/macos_arm64_clang_cc15.0.0_os13.6.1_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=cc15.0.0_os13.6.1
/usr/local/gfortran/bin/g++ -fopenmp -I../inst/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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 ../../include/tbb/tbb_stddef.h:91,
from ../../include/tbb/concurrent_hash_map.h:20,
from ../../src/tbb/concurrent_hash_map.cpp:17:
../../include/tbb/tbb_config.h:36:14: fatal error: cstddef: No such file or directory
36 | #include <cstddef>
| ^~~~~~~~~
compilation terminated.
make[2]: *** [concurrent_hash_map.o] Error 1
make[1]: *** [tbb_release] Error 2
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fPIC -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c init.cpp -o init.o
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fPIC -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c options.cpp -o options.o
In file included from ../inst/include/tthread/tinythread.h:80,
from ../inst/include/RcppParallel/TinyThread.h:9,
from ../inst/include/RcppParallel.h:6,
from options.cpp:2:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread.h:337:49: warning: this use of "defined" may not be portable [-Wexpansion-to-defined]
337 | #if !_PTHREAD_SWIFT_IMPORTER_NULLABILITY_COMPAT()
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread.h:337:49: warning: this use of "defined" may not be portable [-Wexpansion-to-defined]
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread.h:563:49: warning: this use of "defined" may not be portable [-Wexpansion-to-defined]
563 | #if !_PTHREAD_SWIFT_IMPORTER_NULLABILITY_COMPAT()
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread.h:563:49: warning: this use of "defined" may not be portable [-Wexpansion-to-defined]
/usr/local/gfortran/bin/g++ -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/gfortran/lib -Wl,-rpath,/usr/local/gfortran/lib -o RcppParallel.so init.o options.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
-macosx_version_min has been renamed to -macos_version_min
ld: warning: -multiply_defined is obsolete
ld: warning: -single_module is obsolete
ld: warning: duplicate -rpath '/usr/local/gfortran/lib' ignored
ld: warning: ignoring duplicate libraries: '-lgcc'
0 0x102cf3648 __assert_rtn + 72
1 0x102c27fac ld::AtomPlacement::findAtom(unsigned char, unsigned long long, ld::AtomPlacement::AtomLoc const*&, long long&) const + 1204
2 0x102c3d924 ld::InputFiles::SliceParser::parseObjectFile(mach_o::Header const*) const + 15164
3 0x102c4ae30 ld::InputFiles::parseAllFiles(void (ld::AtomFile const*) block_pointer)::$_7::operator()(unsigned long, ld::FileInfo const&) const + 420
4 0x1964cc440 _dispatch_client_callout2 + 20
5 0x1964e1544 _dispatch_apply_invoke_and_wait + 224
6 0x1964e084c _dispatch_apply_with_attr_f + 1180
7 0x1964e0a38 dispatch_apply + 96
8 0x102cc53b8 ld::AtomFileConsolidator::parseFiles(bool) + 292
9 0x102c66170 main + 9048
ld: Assertion failed: (resultIndex < sectData.atoms.size()), function findAtom, file Relocations.cpp, line 1336.
collect2: error: ld returned 1 exit status
make: *** [RcppParallel.so] Error 1
ERROR: compilation failed for package ‘RcppParallel’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel’
如果有帮助，则 /Users/{username}/ 的内容。R/Makevars 是：
F77 = /usr/local/bin/gfortran
FC = /usr/local/bin/gfortran
FLIBS = -L/usr/local/bin/gfortran
LOC = /usr/local/gfortran
CC=$(LOC)/bin/gcc -fopenmp
CXX=$(LOC)/bin/g++ -fopenmp
CXX11 = $(LOC)/bin/g++ -fopenmp # for fst package
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L$(LOC)/lib -Wl,-rpath,$(LOC)/lib
CPPFLAGS=-I$(LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
这是我的sessionInfo（）：
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/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: Europe/Zurich
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1 renv_1.0.3
有什么建议吗？谢谢！
答：
0赞
olybear82
11/15/2023
#1
与类似的问题作斗争。我在该主题上找到的最佳线程位于： https://community.rstudio.com/t/cant-install-packages-with-renv/96696/10
在切换到具有完全管理员的计算机后，我能够让我的 renv：：install（） - renv：：snapshot（） 正常运行。在我的工作计算机上提取代码并运行 renv：：restore（） 仍然适合我。
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0赞
Edward Lavender
11/15/2023
感谢您的回复！不幸的是，这对我没有用。我在这台计算机上具有完全管理员访问权限。
0赞
Kevin Ushey
11/17/2023
#2
此错误：
../../include/tbb/tbb_config.h:36:14: fatal error: cstddef: No such file or directory
36 | #include <cstddef>
| ^~~~~~~~~
指示编译器无法找到标准 C++ 库标头之一。鉴于您使用的是 并且而不是在 macOS 上，我认为您需要添加额外的包含路径，以便可以找到 C++ 库标头。在我的macOS机器上，我在这里看到这个：gccg++clang
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1
所以你可能需要在某个地方添加它 -- 也许是 CXXFLAGS，或类似的东西。在包含此内容时，您可能希望使用，因为它是系统标头。只需设置为编译器工具目录的根目录就足够了。看：-isystem-isysroot
https://gcc.gnu.org/onlinedocs/gcc/Directory-Options.html https://gcc.gnu.org/onlinedocs/cpp/Invocation.html
了解更多详情。
评论
0赞
Edward Lavender
11/23/2023
非常感谢您的建议！最后，我换上了 clang，这似乎为我解决了问题。我已经为其他用户发布了我的解决方案。我不确定为什么在使用 {renv} 的 RStudio 项目中从二进制文件安装仍然有问题，但至少它现在正在工作。再次感谢！
0赞
Edward Lavender
11/23/2023
#3
最后，我通过修改 Makevars 文件以使用 Apple 的 clang 而不是 gcc & g++ 从源代码解决了 {RcppParallel} 安装问题。我的完整 Makevars 文件如下：
#### Set Fortan compilers
# Define compilers for Fortan 77 & Fortran (gfortran)
F77=/usr/local/bin/gfortran
FC=/usr/local/bin/gfortran
# Define Fortran library paths (-L)
FLIBS=-L/usr/local/bin/gfortran
#### Set C/C++ compilers (clang/clang++)
# Set compilers
CC=/usr/bin/clang
CXX=/usr/bin/clang++
# Set flags to enable OpenMP
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
相关修订位于 C/C++ 部分。在使用 {renv} 的 RStudio 项目中使用 {renv} 时，从二进制文件安装成功（显然），但库 （RcppParallel） 仍然失败：
project <- file.path(tempdir(), "project")
dir.create(project)
setwd(project)
renv::init(settings = list(use.cache = FALSE), restart = FALSE)
writeLines("library(RcppParallel)", con = "dependencies.R")
renv::install("RcppParallel", type = "binary", prompt = FALSE)
source("dependencies.R")
跟
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 '/private/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T/RtmpEzGAXd/project/renv/library/R-4.3/aarch64-apple-darwin20/RcppParallel/libs/RcppParallel.so':
dlopen(/private/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T/RtmpEzGAXd/project/renv/library/R-4.3/aarch64-apple-darwin20/RcppParallel/libs/RcppParallel.so, 0x0006): symbol not found in flat namespace '__ZN3tbb10interface78internal15task_arena_base24internal_max_concurrencyEPKNS0_10task_arenaE'
但是，在重新启动 R 后（此步骤是必不可少的），重复相同的代码但从源代码安装有效：
project <- file.path(tempdir(), "project")
dir.create(project)
setwd(project)
renv::init(settings = list(use.cache = FALSE), restart = FALSE)
writeLines("library(RcppParallel)", con = "dependencies.R")
renv::install("RcppParallel", type = "source", prompt = FALSE)
source("dependencies.R")
并且似乎允许在使用 {renv} 的项目中使用 {RcppParallel}。
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