macOS下需clang编译的R源包安装失败求助

一直使用Posit包管理器安装R二进制包，多数情况运行正常，但安装需要clang编译的源包时始终失败，怀疑与编译日志中using SDK: ''（SDK路径为空）有关。

错误示例 #

Homebrew安装的R中编译jsonlite失败 #

> install.packages("jsonlite")
Installing package into ‘/Users/r2/Library/R/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.posit.co/cran/latest/src/contrib/jsonlite_1.9.1.tar.gz'
Content type 'binary/octet-stream' length 1051291 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
using SDK: ‘’
clang -I"/opt/homebrew/Cellar/r/4.4.3_1/lib/R/include" -DNDEBUG -Iyajl/api  -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include     -fPIC  -g -O2  -c base64.c -o base64.o
clang -I"/opt/homebrew/Cellar/r/4.4.3_1/lib/R/include" -DNDEBUG -Iyajl/api  -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include     -fPIC  -g -O2  -c collapse_array.c -o collapse_array.o
...
clang -I"/opt/homebrew/Cellar/r/4.4.3_1/lib/R/include" -DNDEBUG -Iyajl/api  -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include     -fPIC  -g -O2  -c yajl/yajl_parser.c -o yajl/yajl_parser.o
clang -I"/opt/homebrew/Cellar/r/4.4.3_1/lib/R/include" -DNDEBUG -Iyajl/api  -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include     -fPIC  -g -O2  -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/opt/homebrew/Cellar/r/4.4.3_1/lib/R/lib -L/opt/homebrew/opt/gettext/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/xz/lib -L/opt/homebrew/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/opt/homebrew/Cellar/r/4.4.3_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
ld: archive member '/' not a mach-o file in '/private/var/folders/3f/0hlmq7rx34ddjqtlc1lqbxl80000gn/T/RtmpuoriDi/R.INSTALLae611eb747f2/jsonlite/src/yajl/libstatyajl.a'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [/opt/homebrew/Cellar/r/4.4.3_1/lib/R/share/make/shlib.mk:10: jsonlite.so] Error 1
ERROR: compilation failed for package ‘jsonlite’

R.app中编译jsonlite失败 #

> install.packages("jsonlite", type='source')
Installing package into ‘/Users/r2/Library/R/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.posit.co/cran/latest/src/contrib/jsonlite_1.9.1.tar.gz'
Content type 'binary/octet-stream' length 1051291 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
using SDK: ‘’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Iyajl/api  -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c base64.c -o base64.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Iyajl/api  -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c collapse_array.c -o collapse_array.o
...
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Iyajl/api  -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c yajl/yajl_parser.c -o yajl/yajl_parser.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Iyajl/api  -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -F/Library/Frameworks/R/framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: archive member '/' not a mach-o file in '/private/var/folders/3f/0hlmq7rx34ddjqtlc1lqbxl80000gn/T/RtmpVNvRR6/R.INSTALLb2f9120e3fb/jsonlite/src/yajl/libstatyajl.a'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:10: jsonlite.so] Error 1
ERROR: compilation failed for package ‘jsonlite’

环境信息 #

> R.version
               _                           
platform       aarch64-apple-darwin20      
arch           aarch64                     
os             darwin20                    
system         aarch64, darwin20           
status                                     
major          4                           
minor          4.2                         
year           2024                        
month          10                          
day            31                          
svn rev        87279                       
language       R                           
version.string R version 4.4.2 (2024-10-31)
nickname       Pile of Leaves              

Sys.which(c("gcc", "clang", "make"))
#                                          gcc 
#                               "/usr/bin/gcc" 
#                                        clang 
#                             "/usr/bin/clang" 
#                                         make 
# "/opt/homebrew/opt/make/libexec/gnubin/make"

补充信息 #

• 系统为Sequoia 15.3.2，已安装XCode 16.2 (16C5032a)
• 并非仅jsonlite存在问题，所有需要编译的R源包均无法安装（Posit包管理器的二进制包可正常安装）
• 使用R --no-site --vanilla执行仍出现错误，排除.Rprofile等配置文件影响
• 更换其他包仓库后错误相同

后续尝试 #

编辑1：XCode路径信息 #

$ xcode-select -p
/Applications/Xcode.app/Contents/Developer
$ xcrun --sdk macosx --show-sdk-path
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.2.sdk

编辑2：配置SDKROOT与调整工具链 #

未编译R本身，按照官方提示安装了gfortran*.pkg（安装前执行xattr -cr ~/Downloads/gfortran*.pkg）。此外在~/.Renviron中添加配置：

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.2.sdk

重启R后确认Sys.getenv("SDKROOT")路径正确，此时编译日志显示using SDK: ‘MacOSX.sdk’，但仍出现相同的链接错误。随后卸载Homebrew安装的make，Sys.which("make")显示路径为"/usr/bin/make"，问题仍未解决。

内容的提问来源于stack exchange，提问作者r2evans