我用的是苹果M1芯片的MacBook Air，使用的是macOS 11.6 Big Sur。我用的是R 4.1.1。我已经为Apple M1安装了Xtools和gfortran:
markwhite@marks-air ~ % which xcode-select
/usr/bin/xcode-select
markwhite@marks-air ~ % which gfortran
/usr/local/bin/gfortran
我能够成功安装并运行r -但是安装一些包给我麻烦:
> 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’
>
我认为关键行是:make: /opt/R/arm64/bin/gfortran: No such file or directory，它在错误的位置寻找gfortran。
确认不存在:
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 %
我把gfortran从原来的位置移到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并再次尝试:
> 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实际上没有移动它需要移动的内容。
如何将R指向正确的目录或在正确的目录中安装gfortran ?
我知道这个问题现在是一团糟，我已经看了其他线程，但不能得到任何人建议的任何工作。
以下是我在Mac OS M1系统上使用的方法。R版本4.2.1(从这里的解决方案修改，可能适用于英特尔mac电脑)
-
安装包含gfortran和
brew install gcc的gcc -
创建一个文件
~/.R/Makevars(如果它还不存在)。 -
将以下行添加到
~/.R/Makevars
FC = /opt/homebrew/Cellar/gcc/11.3.0_2/bin/gfortranF77 = /opt/homebrew/Cellar/gcc/11.3.0_2/bin/gfortranFLIBS = -L/opt/homebrew/Cellar/gcc/11.3.0_2/lib/gcc/11
请注意，您可能必须将gcc版本11.3.0_2更改为您的gcc版本。
我删除了所有与gfortran相关的内容，重新开始。
我下载了。tar。xz文件在这里使用浏览器，它转储到我的下载文件夹。我双击它打开它。
我把这个目录移到了R想要的地方:
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—我在这里不会假装理解—但是它成功安装了:
> 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’
我在尝试从源代码安装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 install gcc
-
告诉R应该在哪里查找gfortran此信息存储在文件"Makeconf"在我的情况下，可以在这里找到:/图书馆/框架/R.framework/版本/4.1 -arm64/资源/etc/Makeconf
在"Makeconf"更改
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
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
你有没有试着回答"没有";对于问题:
Do you want to install from sources the package which needs compilation? (Yes/no/cancel)
?
除非你真的需要最新版本的软件包，否则它似乎可以正常工作，而不必像你那样在指定的文件夹中安装gfortran。
我在安装其他软件包时遇到了类似的问题，但我试图做以下选择，它允许我继续:
Update all/some/none? [a/s/n]:
n
我按照本教程中的说明操作，它成功了:https://www.cynkra.com/blog/2021-03-16-gfortran-macos/
创建了一个文件~/.R/Makevars
，然后按照教程，键入以下行(使用我自己的gfortran目录):
FC = /usr/local/bin/gfortran
F77 = /usr/local/bin/gfortran
FLIBS = -L/usr/local/bin/gfortran/lib
使用Makevars文件的修复(如在SO帖子中建议的，R中的错误信息链接到)不适合我，但修改这里的其他答案之一(https://stackoverflow.com/a/72200132/7449737)有效。
对于上下文:我使用MacBook Pro 2023 M2 Max, macOS Ventura 13.5.2, R 4.3.1, gfortran安装了homebrew和Xcode。
- 以防万一，备份你的
Makeconf，如Makeconf.bak - 在编辑器中打开
Makeconf - 你可能会看到很多东西。再往下，在
C和C++部分下面，你应该找到Fortran部分，它可能看起来像这样:
## Fortran
FC = /opt/gfortran/bin/gfortran -arch arm64
FCFLAGS = -Wall -g -O2 $(LTO_FC)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -Wall -g -O2 $(LTO_FC)
FLIBS = -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath
FPICFLAGS = -fPIC
FPIEFLAGS = -fPIE
F_VISIBILITY =
- 您需要在这里更改
FC和FLIBS的两行，如下所示: - 对于
FC:通过运行which gfortran来查找从终端访问gfortran的位置 - 对于
FLIBS:运行brew info gfortran来查找安装的gfortran版本，并找到需要放在版本前面的位置以完成正确的路径 - 在
Makeconf中，用以下信息编辑FC和FLIBS行
作为比较，下面是Makeconf中的两行代码:
FC = /opt/homebrew/bin/gfortran -arch arm64
FLIBS = -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13 -L/opt/homebrew/lib -lgfortran -lemutls_w -lquadmath
我希望这能进一步阐明这个问题，并帮助那些对Makevars修复不适合他们感到沮丧的人。