cynkra

gfortran support for R on macOS

From the Blog
R
DevOps
Patrick Schratz

Author(s)

Patrick Schratz

Published

For a long time, gfortran support on macOS could be achieved by installing the homebrew cask gfortran via brew cask install gfortran.

As of 2021, both the brew cask command and the cask gfortran are deprecated. Users who have installed this cask already, will not notice since things will continue to work as normal. Only new users who want to install gfortran this way, will get the message that the cask is “not available”. The cask was removed in December 2020 and merged into the gcc formula (which can be installed via brew install gcc). Now, one could go to https://github.com/fxcoudert/gfortran-for-macOS/releases and manually install the respective .dmg file. However, this is not a long-term approach, and usually, one would like to do this via brew, the most popular package manager for macOS.

Unfortunately, this change did not result in a smooth experience for R users who want to compile packages from source that require a functional gfortran compiler. This requirement does not occur very often, as most users install R package binaries on macOS. These do not require a working gfortran installation.

However, in some cases, when calling install.packages(), a working gfortran installation is needed. And if type = "source" is used, it needs to be there.

The issue after the integration of gfortran into the gcc formula is that the official R binary installer for macOS expects the gfortran installation at /usr/local/gfortran. This was fulfilled by the old gfortran cask but is not by the new gcc integration. Hence, trying to install the “cluster” package via install.packages("cluster", type = "source") will fail and gfortran will not be found:

* installing *source* package ‘cluster’ ...
** package ‘cluster’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c clara.c -o clara.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c daisy.f -o daisy.o
make: gfortran: No such file or directory
make: *** [/Library/Frameworks/R.framework/Resources/etc/Makeconf:196: daisy.o] Error 127
ERROR: compilation failed for package ‘cluster’

There was a discussion about these changes in the homebrew PR, but the comments that highlighted potential issues seem to have gone unnoticed. Also, some workarounds posted in the thread do not work.

So how does one now install gfortran on macOS these days?

It is likely that one will not need the workaround presented below in the future since it will probably be fixed in the R installer at some point (hopefully). In the meantime, the following helps:

  1. Create a file ~/.R/Makevars (if it does not exist yet)

  2. Add the following to ~/.R/Makevars

    FC      = usr/local/opt/gcc/bin/gfortran
F77     = /usr/local/opt/gcc/bin/gfortran
FLIBS   = -L/usr/local/opt/gcc/lib

  3. Restart R

  4. Test the changes by calling install.packages("cluster", type = "source")

The output should look like this

* installing *source* package ‘cluster’ ...
** package ‘cluster’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c clara.c -o clara.o
/usr/local/opt/gcc/bin/gfortran -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c daisy.f -o daisy.o
/usr/local/opt/gcc/bin/gfortran -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c dysta.f -o dysta.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fanny.c -o fanny.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mona.c -o mona.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pam.c -o pam.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sildist.c -o sildist.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c spannel.c -o spannel.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c twins.c -o twins.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -L/usr/local/opt/gcc/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: object file (daisy.o) was built for newer macOS version (11.2) than being linked (11.0)
ld: warning: object file (dysta.o) was built for newer macOS version (11.2) than being linked (11.0)
installing to /Users/pjs/Library/R/4.0/library/00LOCK-cluster/00new/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (cluster)

Caution: After using this approach for a few days, I have seen issues with certain packages (e.g. hsdar). It is unclear if the issues trace back to the packages or the new way of using gfortran. You might want to re-think using this proposed approach and eventually manually install the linked standalone gfortran binary shown earlier in this post.

Notes

  • I am not sure about the ld: warning: object file (dysta.o) was built for newer macOS version (11.2) than being linked (11.0) warning, but it does not seem to have a practical impact.
  • This approach was tested with R 4.0.4, macOS 11.2.3 in March 2021.
  • If you still have the old gfortran cask installed, you may want to switch to the new approach as the cask is no longer being updated. Hence, you will run a very outdated gfortran at some point without noticing. You can remove the old cask with brew remove – cask gfortran.