gfortran: command not found on macos-latest

[paulmueller]

Description

The command "gfortran" is not available in the latest macOS builds. Calling gfortran --version fails with the following error on macos-latest:

/Users/runner/work/_temp/b20baed3-9e90-42e3-a7d3-dcacff880807.sh: line 2: gfortran: command not found
Error: Process completed with exit code 127.

Area for Triage: Apple

Question, Bug, or Feature?: Bug

Virtual environments affected

• Ubuntu 16.04
• Ubuntu 18.04
• Ubuntu 20.04
• macOS 10.15.7 (macos-latest)
• macOS 11.0
• Windows Server 2016 R2
• Windows Server 2019

Image version: 20210503.2

Image version where you are experiencing the issue.

Expected behavior
gfortran --version should print the version of gfortran

Actual behavior
command not found

Repro steps
CI job:
https://github.com/ZELLMECHANIK-DRESDEN/dclab/runs/2567423623?check_suite_focus=true

relevant line in yml:
https://github.com/ZELLMECHANIK-DRESDEN/dclab/blob/master/.github/workflows/check.yml#L27

[miketimofeev]

Hi @paulmueller!
You need to specify gfortran major version as it is described in the docs:

We don't have the gfortran alias intentionally, please take a look at this comment:
#1280 (comment)

[paulmueller]

The problem is that I intend to install the R package statmodel which somehow needs gfortran to build. I am not in control. Is there a way to manually add a global alias gfortran -> gfortran-8?

[paulmueller]

I manually added the symlink ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran (found it in the thread you mentioned). Will close this issue if it works.

[paulmueller]

The yaml entry I used:

    - name: symlink gfortran (macOS)
      if: runner.os == 'macOS'
      run: |
        # make sure gfortran is available
        ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran
        gfortran --version

[paulmueller]

Sorry, I have to reopen. Building the statmodel package fails. Could you please help me with this thing:

https://github.com/ZELLMECHANIK-DRESDEN/dclab/runs/2568138465?check_suite_focus=true

----------------------------- Captured stdout call -----------------------------
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c gaussq2.f -o gaussq2.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -mmacosx-version-min=10.13 -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 statmod.so gaussq2.o init.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
----------------------------- Captured stderr call -----------------------------
* installing *source* package ‘statmod’ ...
** package ‘statmod’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [statmod.so] Error 1
ERROR: compilation failed for package ‘statmod’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/statmod’

Do I also have to update a library path or so? I don't know how things work on macOS.

[miketimofeev]

@paulmueller could you please file another issue and provide all the details there?

[miketimofeev]

@paulmueller looks like we already had pretty the same issue. Could you take a look here, please?
#2524

[paulmueller]

Thanks for your help, that worked:

    - name: Symlink gfortran (macOS)
      if: runner.os == 'macOS'
      run: |
        # make sure gfortran is available
        # https://github.com/actions/virtual-environments/issues/2524
        # https://github.com/cbg-ethz/dce/blob/master/.github/workflows/pkgdown.yaml
        sudo ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran
        sudo mkdir /usr/local/gfortran
        sudo ln -s /usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9 /usr/local/gfortran/lib
        gfortran --version

[miketimofeev]

@paulmueller Creating a symbolic link for gcc10 not working? I'm asking since you prefer gfortran 10, but link libs from version 9

    - name: Symlink gfortran (macOS)
      if: runner.os == 'macOS'
      run: |
        # make sure gfortran is available
        # https://github.com/actions/virtual-environments/issues/2524
        # https://github.com/cbg-ethz/dce/blob/master/.github/workflows/pkgdown.yaml
        sudo ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran
        sudo mkdir /usr/local/gfortran
        sudo ln -s /usr/local/Cellar/gcc@10/*/lib/gcc/10 /usr/local/gfortran/lib
        gfortran --version

[paulmueller]

Thanks for that!

[paulmueller]

For the new macOS 12 image:

    - name: Symlink gfortran (macOS)
      if: runner.os == 'macOS'
      run: |
        # make sure gfortran is available
        # https://github.com/actions/virtual-environments/issues/2524
        # https://github.com/cbg-ethz/dce/blob/master/.github/workflows/pkgdown.yaml
        sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
        sudo mkdir /usr/local/gfortran
        sudo ln -s /usr/local/Cellar/gcc@11/*/lib/gcc/11 /usr/local/gfortran/lib
        gfortran --version

[manlaya]

Thanks for the solution. It worked for me, until MacOS14 image.
For anyone wondering, here is the updated paths for MacOS14 that worked for me:

jobs:
  my_job_name:
  
  ...

    env:
      FC: gfortran
      GCC_V: 12

    steps:
  
    ... 
    
      - name: Symlink gfortran (macOS)
        if: runner.os == 'macOS'
        run: |
          # make sure gfortran is available
          # https://github.com/actions/runner-images/blob/main/images/macos/macos-15-Readme.md
          # https://github.com/actions/runner-images/issues/3371
          # ln version - new path 'MacOS14'
          sudo ln -fs /opt/homebrew/bin/gfortran-${GCC_V} /usr/local/bin/gfortran
          sudo mkdir -p /usr/local/gfortran
          sudo ln -sf /opt/homebrew/Cellar/gcc@${GCC_V}/*/lib/gcc/${GCC_V} /usr/local/gfortran/lib