[英]Installing gfortran on MacBook with Apple M1 chip for use in R
I'm on a MacBook Air with an Apple M1 chip, using macOS 11.6 Big Sur.我在一台装有 Apple M1 芯片的 MacBook Air 上,使用 macOS 11.6 Big Sur。 I'm on R 4.1.1.
我在 R 4.1.1 上。 I have Xtools and gfortran for the Apple M1 installed:
我为 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
I am able to successfully install and run R—but installing some packages is giving me trouble: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’
>
I believe the key line is: make: /opt/R/arm64/bin/gfortran: No such file or directory
where it is looking in the wrong location for gfortran.我相信关键是:
make: /opt/R/arm64/bin/gfortran: No such file or directory
,它在错误的位置寻找 gfortran。
Confirming it is not there: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 %
So, I just move gfortran from where it is to where R wants it to be:所以,我只是将 gfortran 从它所在的位置移动到 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 %
Then, I restart R and try again: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’
>
It looks like it is still getting confused with directory paths, or mv
didn't actually move what it needed to move.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。
How can I point R to the correct directory or install gfortran in the correct directory?如何将 R 指向正确的目录或将 gfortran 安装在正确的目录中?
I know this problem is a mess right now, I've looked at other threads , but can't quite get anything anyone suggests to work.我知道这个问题现在很混乱,我查看了其他线程,但无法完全得到任何人建议的工作。
I deleted everything gfortran related and started over.我删除了所有与 gfortran 相关的内容并重新开始。
I downloaded the .tar.xz file here using the browser, which dumped the file into my Downloads folder.我使用浏览器在此处下载了 .tar.xz 文件,该浏览器将文件转储到了我的下载文件夹中。 I double-clicked it to unpack it.
我双击它来解压它。
I moved that directory to where R wanted it:我将该目录移动到 R 想要的位置:
markwhite@marks-air ~ % sudo mv Downloads/gfortran /opt/R/arm64/
Then I restarted R and tried again.然后我重新启动 R 并再次尝试。 It threw me some Fortran compilation messages—which I will not pretend to comprehend here—but it successfully installed:
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’
Have you tried to answer "no" to the question: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)
? ?
Except if you really need the latest version of the package you are trying to download, it seems to be working without having to install gfortran in the specified folder like you did.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。
I have met the similar problem when installing other packages but I tried to do the following choice and it allowed me to go on: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
I came across a similar problem when trying to install a package from source.尝试从源代码安装软件包时遇到了类似的问题。 My solution was
我的解决方案是
Install the Homebrew version of gcc (this includes gfortran)安装 gcc 的 Homebrew 版本(包括 gfortran)
brew install gcc酿造安装 gcc
Tell R where it should look for gfortran This information is stored in the file "Makeconf" which in my case can be found here: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/etc/Makeconf告诉 R 它应该在哪里查找 gfortran 此信息存储在文件“Makeconf”中,在我的情况下可以在此处找到:/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/etc/Makeconf
In "Makeconf" change the line在“Makeconf”中更改该行
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
to至
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
You may need to adapt the path according to the gcc version installed on your system.您可能需要根据系统上安装的 gcc 版本来调整路径。
Here is what has worked for me on a Mac OS M1 system.这是在 Mac OS M1 系统上对我有用的方法。 R version 4.2.1 (modified from the solution here which will probably work for Intel Macs)
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)
Install gcc which includes gfortran with brew install gcc
使用
brew install gcc
Create a file ~/.R/Makevars
(if it does not exist yet).创建一个文件
~/.R/Makevars
(如果它还不存在)。 See for example here .例如,请参见此处。
Add the following lines to ~/.R/Makevars
将以下行添加到
~/.R/Makevars
FC = /opt/homebrew/Cellar/gcc/11.3.0_2/bin/gfortran
F77 = /opt/homebrew/Cellar/gcc/11.3.0_2/bin/gfortran
FLIBS = -L/opt/homebrew/Cellar/gcc/11.3.0_2/lib/gcc/11
Note that you might have to change gcc version 11.3.0_2
to whatever your gcc version is.请注意,您可能必须将 gcc 版本
11.3.0_2
更改为您的 gcc 版本。
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