macOS更新后无法从源码安装R包的问题求助

问题背景 #

已安装Xcode命令行工具，按官方指引安装了gfortran，取消了RStudio包设置里的唯一HTTPS勾选，但安装estimatr等需要源码编译的R包时仍报错，核心问题是链接器找不到gfortran库。

错误日志 #

22 warnings generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o estimatr.so RcppExports.o horvitz_thompson_variance.o lm_robust_helper.o naomit.o
    -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R/framework/.. -framework R -Wl,-framework -Wl,CoreFoundation 
ld: warning: -single_module is obsolete 
ld: warning: -multiply_defined is obsolete 
ld: warning: search path '/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0' not found 
ld: warning: search path '/opt/R/arm64/gfortran/lib' not found 
ld: library 'gfortran' not found 
clang: error: linker command failed with exit code 1 (use -v to see invocation) 
make: *** [estimatr.so] Error 1 ERROR: compilation failed for package ‘estimatr’
* removing ‘/Users/myname/Library/R/arm64/4.1/library/estimatr’

Session信息 #

R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.0

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_2.4.2 usethis_2.2.2 

loaded via a namespace (and not attached):
 [1] prettyunits_1.2.0 ps_1.7.5          crayon_1.5.2      R6_2.5.1          lifecycle_1.0.3   magrittr_2.0.3   
 [7] rlang_1.1.1       cachem_1.0.6      cli_3.6.1         remotes_2.4.2.1   rstudioapi_0.13   fs_1.6.3         
[13] callr_3.7.3       vctrs_0.6.4       ellipsis_0.3.2    tools_4.1.1       glue_1.6.2        purrr_1.0.2      
[19] pkgload_1.3.3     processx_3.8.2    fastmap_1.1.0     compiler_4.1.1    pkgbuild_1.4.2    sessioninfo_1.2.2
[25] memoise_2.0.1  

可尝试的解决方法 #

• 匹配gfortran安装路径
  打开终端执行which gfortran查看实际安装路径，如果不是R期望的/opt/R/arm64/gfortran/bin/gfortran，手动创建软链接：

  sudo mkdir -p /opt/R/arm64/gfortran/lib
  sudo ln -s /usr/local/gfortran/lib/* /opt/R/arm64/gfortran/lib/
  sudo ln -s /usr/local/gfortran/lib/gcc/aarch64-apple-darwin20/11.0.0 /opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0
  

  注：如果你的gfortran安装在其他路径，替换上述命令中的/usr/local/gfortran为实际路径。

• 设置R编译环境变量
  终端执行以下命令临时配置链接路径：

  export LDFLAGS="-L/usr/local/gfortran/lib -lgfortran"
  export CPPFLAGS="-I/usr/local/gfortran/include"
  

  重启R/RStudio后再尝试安装包。若要永久生效，将这两行添加到~/.zshrc或~/.bash_profile（取决于你使用的shell）。

• 升级R版本
  当前使用的R 4.1.1版本较旧，与macOS 14.0兼容性可能存在问题，建议升级到最新的ARM版R，新版本对Apple Silicon的支持更完善，可能自动解决路径匹配问题。

• 优先安装二进制包
  在R中执行以下命令，跳过源码编译直接安装预编译包：

  install.packages("estimatr", type = "binary")
  

• 重装Xcode命令行工具
  执行xcode-select --install重新安装命令行工具，确保clang等编译工具完整且为最新版本。

内容的提问来源于stack exchange，提问作者canIchangethis