在带有 Apple M1 芯片的 MacBook 上安装 gfortran 以在 R 中使用答案

【问题标题】：Installing gfortran on MacBook with Apple M1 chip for use in R在带有 Apple M1 芯片的 MacBook 上安装 gfortran 以在 R 中使用
【发布时间】：2022-05-11 19:20:12
【问题描述】：

我使用的是配备 Apple M1 芯片的 MacBook Air，使用的是 macOS 11.6 Big Sur。我在 R 4.1.1 上。我安装了 Xtools 和 gfortran for the Apple M1：

markwhite@marks-air ~ % which xcode-select
/usr/bin/xcode-select
markwhite@marks-air ~ % which gfortran
/usr/local/bin/gfortran

我能够成功安装和运行 R，但安装一些软件包给我带来了麻烦：

> install.packages("mvtnorm")

  There is a binary version available but the source version is later:
        binary source needs_compilation
mvtnorm  1.1-2  1.1-3              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘mvtnorm’

trying URL 'https://cran.rstudio.com/src/contrib/mvtnorm_1.1-3.tar.gz'
Content type 'application/x-gzip' length 166421 bytes (162 KB)
==================================================
downloaded 162 KB

* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c miwa.c -o miwa.o
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c mvt.f -o mvt.o
make: /opt/R/arm64/bin/gfortran: No such file or directory
make: *** [mvt.o] Error 1
ERROR: compilation failed for package ‘mvtnorm’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/mvtnorm’
Warning in install.packages :
  installation of package ‘mvtnorm’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/fx/f46lfqf56_df59fvzgqhcbyr0000gn/T/RtmpfGZUAF/downloaded_packages’
>

我认为关键是：make: /opt/R/arm64/bin/gfortran: No such file or directory 它正在寻找 gfortran 的错误位置。

确认它不存在：

markwhite@marks-air ~ % cd /opt/R/arm64/
markwhite@marks-air arm64 % ls -la
total 0
drwxrwxr-x   8 root  wheel  256 Oct 18 11:04 .
drwxrwxr-x   3 root  wheel   96 May 13 20:40 ..
drwxrwxr-x  14 root  wheel  448 Oct 19 21:34 bin
drwxrwxr-x  29 root  wheel  928 May 13 20:47 include
drwxrwxr-x  20 root  wheel  640 May 14 18:50 lib
drwxrwxr-x   5 root  wheel  160 May 13 20:40 man
drwxr-xr-x   3 root  wheel   96 May 14 18:28 pkg
drwxrwxr-x   5 root  wheel  160 Oct 18 11:04 share
markwhite@marks-air arm64 %

所以，我只是将 gfortran 从原来的位置移动到 R 想要的位置：

markwhite@marks-air gfortran % sudo mv /usr/local/bin/gfortran /opt/R/arm64/bin
Password:
markwhite@marks-air gfortran %

然后，我重新启动 R 并重试：

> install.packages("mvtnorm")

  There is a binary version available but the source version is later:
        binary source needs_compilation
mvtnorm  1.1-2  1.1-3              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘mvtnorm’

trying URL 'https://cran.rstudio.com/src/contrib/mvtnorm_1.1-3.tar.gz'
Content type 'application/x-gzip' length 166421 bytes (162 KB)
==================================================
downloaded 162 KB

* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c miwa.c -o miwa.o
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c mvt.f -o mvt.o
mvt.f:861:11:

  861 |       hs = sign( one, dh - r*dk )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:862:11:

  862 |       ks = sign( one, dk - r*dh )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:1155:16:

 1155 |             K = MOD( C(NP, MIN(NDIM-1,KLIM-1))*DBLE(K), DBLE(P(NP)) )
      |                1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:1215:17:

 1215 |             JP = 1 + J*R(J)
      |                 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:94:39:

   94 |       DOUBLE PRECISION COV(NL*(NL+1)/2), A(NL), B(NL), DL(NL), Y(NL)
      |                                       1
Warning: Array ‘cov’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider using ‘-frecursive’, or increase the ‘-fmax-stack-var-size=’ limit, or change the code to use an ALLOCATABLE array. [-Wsurprising]
mvt.f:86:33:

   86 |       SUBROUTINE MVSUBR( N, W, NF, F )
      |                                 1
Warning: Unused dummy argument ‘nf’ at (1) [-Wunused-dummy-argument]
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c mvtnorm-init.c -o mvtnorm-init.o
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c tvpack.f -o tvpack.o
tvpack.f:395:14:

  395 |          HS = SIGN( ONE, DH - R*DK )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:396:14:

  396 |          KS = SIGN( ONE, DK - R*DH )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:60:52:

   60 |       DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT, TVTL
      |                                                    1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
tvpack.f:60:45:

   60 |       DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT, TVTL
      |                                             1
Warning: Unused variable ‘zros’ declared at (1) [-Wunused-variable]
tvpack.f:220:72:

  220 |       END
      |                                                                        ^
Warning: ‘fin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
tvpack.f:196:58:

  196 |       DOUBLE PRECISION EI(NL), AI(NL), BI(NL), FI(NL), FIN, ERR, KRNRDT
      |                                                          ^
note: ‘fin’ was declared here
clang -arch arm64 -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 mvtnorm.so C_FORTRAN_interface.o miwa.o mvt.o mvtnorm-init.o tvpack.o -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: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
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: *** [mvtnorm.so] Error 1
ERROR: compilation failed for package ‘mvtnorm’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/mvtnorm’
Warning in install.packages :
  installation of package ‘mvtnorm’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/fx/f46lfqf56_df59fvzgqhcbyr0000gn/T/RtmpmlhiE8/downloaded_packages’
>

看起来它仍然与目录路径混淆，或者 mv 实际上并没有移动它需要移动的东西。

如何将 R 指向正确的目录或将 gfortran 安装在正确的目录中？

我知道这个问题现在一团糟，我查看了other threads，但无法完全得到任何人建议的工作。

【问题讨论】：

对于其他在这里找到自己的方式的人：我已经编写了适用于 Big Sur 和 Monterey here 的说明。蒙特雷的细节并没有根本不同，但有一些复杂性。

标签： r macos gfortran apple-m1

【解决方案1】：

我删除了所有与 gfortran 相关的内容并重新开始。

我使用浏览器下载了 .tar.xz 文件 here，该文件将文件转储到了我的下载文件夹中。我双击打开它。

我将该目录移动到 R 想要的位置：

markwhite@marks-air ~ % sudo mv Downloads/gfortran /opt/R/arm64/

然后我重新启动 R 并再次尝试。它向我抛出了一些 Fortran 编译消息——我不会在这里假装理解——但它成功安装了：

> install.packages("mvtnorm")

  There is a binary version available but the source version is later:
        binary source needs_compilation
mvtnorm  1.1-2  1.1-3              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘mvtnorm’

trying URL 'https://cran.rstudio.com/src/contrib/mvtnorm_1.1-3.tar.gz'
Content type 'application/x-gzip' length 166421 bytes (162 KB)
==================================================
downloaded 162 KB

* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c miwa.c -o miwa.o
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c mvt.f -o mvt.o
mvt.f:861:11:

  861 |       hs = sign( one, dh - r*dk )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:862:11:

  862 |       ks = sign( one, dk - r*dh )
      |           1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:1155:16:

 1155 |             K = MOD( C(NP, MIN(NDIM-1,KLIM-1))*DBLE(K), DBLE(P(NP)) )
      |                1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:1215:17:

 1215 |             JP = 1 + J*R(J)
      |                 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
mvt.f:94:39:

   94 |       DOUBLE PRECISION COV(NL*(NL+1)/2), A(NL), B(NL), DL(NL), Y(NL)
      |                                       1
Warning: Array ‘cov’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider using ‘-frecursive’, or increase the ‘-fmax-stack-var-size=’ limit, or change the code to use an ALLOCATABLE array. [-Wsurprising]
mvt.f:86:33:

   86 |       SUBROUTINE MVSUBR( N, W, NF, F )
      |                                 1
Warning: Unused dummy argument ‘nf’ at (1) [-Wunused-dummy-argument]
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c mvtnorm-init.c -o mvtnorm-init.o
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c tvpack.f -o tvpack.o
tvpack.f:395:14:

  395 |          HS = SIGN( ONE, DH - R*DK )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:396:14:

  396 |          KS = SIGN( ONE, DK - R*DH )
      |              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
tvpack.f:60:52:

   60 |       DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT, TVTL
      |                                                    1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
tvpack.f:60:45:

   60 |       DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT, TVTL
      |                                             1
Warning: Unused variable ‘zros’ declared at (1) [-Wunused-variable]
tvpack.f:220:72:

  220 |       END
      |                                                                        ^
Warning: ‘fin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
tvpack.f:196:58:

  196 |       DOUBLE PRECISION EI(NL), AI(NL), BI(NL), FI(NL), FIN, ERR, KRNRDT
      |                                                          ^
note: ‘fin’ was declared here
clang -arch arm64 -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 mvtnorm.so C_FORTRAN_interface.o miwa.o mvt.o mvtnorm-init.o tvpack.o -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: could not create compact unwind for _mvkrsv_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _mvkbrv_: stack size is too large for frameless function
ld: warning: could not create compact unwind for _mvstdt_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _mvbvtl_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _pntgnd_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _mvbvu_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _tvtmfn_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _krnrdt_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _mvbvn_: registers 21 and 22 not saved contiguously in frame
ld: warning: could not create compact unwind for _bvnd_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _bvtl_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _tvtlrcall_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _mvbvt_: registers 21 and 22 not saved contiguously in frame
ld: warning: could not create compact unwind for _mvspcl_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _mvsort_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _mvvlsb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _mvtdst_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _mvbvtc_: register 73 saved somewhere other than in frame
installing to /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-mvtnorm/00new/mvtnorm/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mvtnorm)

The downloaded source packages are in
    ‘/private/var/folders/fx/f46lfqf56_df59fvzgqhcbyr0000gn/T/RtmptXzvKK/downloaded_packages’

【讨论】：

这对我有用（谢谢！），但必须进入 Mac 安全设置（两次）才能批准 fortran 运行。

【解决方案2】：

您是否尝试对问题回答“否”：

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

除非您确实需要尝试下载的软件包的最新版本，否则它似乎可以正常工作，而无需像您那样在指定的文件夹中安装 gfortran。

【讨论】：

【解决方案3】：

我在安装其他软件包时遇到了类似的问题，但我尝试做以下选择，它允许我继续：

Update all/some/none? [a/s/n]: 
n

【讨论】：

【解决方案4】：

我在尝试从源代码安装软件包时遇到了类似的问题。我的解决方案是

安装 Homebrew 版本的 gcc（包括 gfortran）

brew 安装 gcc
告诉 R 它应该在哪里寻找 gfortran 此信息存储在文件“Makeconf”中，在我的例子中可以在这里找到： /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/etc/Makeconf

在“Makeconf”中改行

FLIBS =  -L/Volumes/Builds/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/Volumes/Builds/opt/R/arm64/gfortran/lib/gcc -L/Volumes/Builds/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm

到

FLIBS =  -L/opt/homebrew/Cellar/gcc/11.3.0/lib/gcc/11/gcc/aarch64-apple-darwin21/11 -L/opt/homebrew/Cellar/gcc/11.3.0/lib/gcc/11 -lgfortran -lquadmath -lm

您可能需要根据系统上安装的 gcc 版本调整路径。

重启R

【讨论】：