R语言harmony包安装失败求助：编译报错及多种尝试无效

尝试安装harmony包始终失败，已尝试安装二进制版本、手动从归档下载安装，均未成功。以下是安装源码版本时的报错信息：

> install.packages("harmony")

  There is a binary version available but the source version is later:
        binary source needs_compilation
harmony  0.1.0  0.1.1              TRUE


Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes


installing the source package ‘harmony’

trying URL 'https://cran.rstudio.com/src/contrib/harmony_0.1.1.tar.gz'
Content type 'application/x-gzip' length 1351250 bytes (1.3 MB)
==================================================

downloaded 1.3 MB


* installing *source* package ‘harmony’ ...
** package ‘harmony’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./harmony_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c harmony.cpp -o harmony.o
In file included from harmony.cpp:1:
In file included from ./harmony.h:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning 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 harmony.so RcppExports.o harmony.o -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R/framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [harmony.so] Error 1
ERROR: compilation failed for package ‘harmony’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/harmony’
Warning in install.packages :
  installation of package ‘harmony’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/vv/kfqy3z8d70z_7w2t399bt80w0000gn/T/RtmpzuHWlG/downloaded_packages’

问题原因 #

报错核心是ld: library not found for -lgfortran，说明系统缺少gfortran编译器，而harmony依赖的RcppArmadillo包需要Fortran编译环境才能完成源码编译。同时日志中找不到gfortran的目录，进一步确认编译环境缺失。

解决步骤 #

• 安装gfortran编译环境：
  对于Apple Silicon（arm64）架构的Mac，可通过Homebrew安装gcc（包含gfortran）：

  brew install gcc
  

  安装完成后，在终端执行which gfortran验证路径是否存在，确保环境被正确识别。

• 重新安装harmony包：
  优先尝试预编译的二进制版本：

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

  若二进制版本仍无法安装，确认gfortran环境就绪后，再尝试源码安装：

  install.packages("harmony", type = "source")
  

• 备选方案：
  如果上述方法无效，可尝试安装GitHub上的最新版本（需先安装devtools包）：

  install.packages("devtools")
  devtools::install_github("immunogenomics/harmony")
  

内容的提问来源于stack exchange，提问作者Sinatra