brew linkage should not fail for recommended dependencies

[mahrud]

Description of issue

Since sometime last week, tap builds started failing, apparently because brew linkage is unhappy about linkage with recommended dependencies:

==> brew linkage --test macaulay2/tap/macaulay2

==> brew linkage --cached --test --strict macaulay2/tap/macaulay2
Indirect dependencies with linkage:
  libomp
  nauty
  python@3.13
==> FAILED
Truncated linkage --cached --test --strict macaulay2/tap/macaulay2 output
  Warning:   python@3.13
  
==> brew linkage --cached macaulay2/tap/macaulay2
System libraries:
  /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
  /usr/lib/libSystem.B.dylib
  /usr/lib/libc++.1.dylib
  /usr/lib/libxml2.2.dylib
Homebrew libraries:
  /opt/homebrew/opt/bdw-gc/lib/libgc.1.dylib (bdw-gc)
  /opt/homebrew/opt/flint/lib/libflint.20.0.dylib (flint)
  /opt/homebrew/opt/gdbm/lib/libgdbm.6.dylib (gdbm)
  /opt/homebrew/opt/gmp/lib/libgmp.10.dylib (gmp)
  /opt/homebrew/opt/gmp/lib/libgmpxx.4.dylib (gmp)
  /opt/homebrew/opt/libffi/lib/libffi.8.dylib (libffi)
  /opt/homebrew/opt/libomp/lib/libomp.dylib (libomp)
  /opt/homebrew/opt/factory/lib/libfactory-4.4.1.dylib (macaulay2/tap/factory)
  /opt/homebrew/opt/givaro/lib/libgivaro.9.dylib (macaulay2/tap/givaro)
  /opt/homebrew/opt/mpsolve/lib/libmps.3.dylib (macaulay2/tap/mpsolve)
  /opt/homebrew/opt/mpfi/lib/libmpfi.0.dylib (mpfi)
  /opt/homebrew/opt/mpfr/lib/libmpfr.6.dylib (mpfr)
  /opt/homebrew/opt/nauty/lib/libnauty-2.8.9.dylib (nauty)
  /opt/homebrew/opt/ntl/lib/libntl.44.dylib (ntl)
  /opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/Python (python@3.13)
  /opt/homebrew/opt/readline/lib/libhistory.8.dylib (readline)
  /opt/homebrew/opt/readline/lib/libreadline.8.dylib (readline)
  /opt/homebrew/opt/tbb/lib/libtbb.12.dylib (tbb)
Indirect dependencies with linkage:
  libomp
  nauty
  python@3.13
Dependencies with no linkage:
  boost
  frobby

In my formula, all three of libomp nauty python@3.13 are marked with => :recommended, so I don't think this should have happened.

This should have been an issue but the "Verification" questions in the bug reporting template are strangely exclusive ...

[SMillerDev]

If the program is linking against something it's not really recommended. It's just going to break without that dependency.

[mahrud]

I don't understand. If formula X has depends_on "Y" => :recommended the bottles will be built with Y installed, but if I run brew install X --without-Y brew doesn't just install X from the bottle except without installing Y, it'll rebuild X from source without Y. No?

The point is that my formula detects whether Y is present or not, if yes it'll link against Y and otherwise not, so you can just as well build a bottle with --without-Y and it works fine.

[gromgit]

it'll rebuild X from source without Y. No?

If I'm not mistaken, --without-Y does not uninstall Y if it's already installed. That means the build configuration mechanism that the software uses can still see Y, and many projects I've seen operate on "if I can see Y, I'll build/link with Y". This is completely outside Homebrew's control.

Does your build environment already have libomp, nauty and python@3.13? If so, you'll have to remove them first, for "recommended" dependencies to mean anything.

[mahrud]

Sorry, I don't follow why whether Y is uninstalled or not is relevant. On GitHub's build environment, all recommended dependencies are installed. The option --without-python is only relevant for a user who for instance doesn't want to install python via brew, then the point is that they can install the formula from source with --without-python and everything will be fine (e.g. the compiler might find python through the system, or without python entirely if the user doesn't want anything to do with python).

However, because of this new error that brew is giving, I either have to make python a forced dependency or remove it completely. Both options are bad!

[mahrud]

Ah, actually I just realized that this error has been there previously, but didn't trigger a build failure. The build failed because of another error that came after this.

I still think the behavior of ":recommended" is unexpected, because otherwise what's the point of "depends_on "Y" => :recommended", if not to allow the following two options:

• by default, brew install X will install dependency Y, and building X from source may produce a binary linked with it.
• if desired, brew install X --without-Y will build X from source without installing Y (so the user can unlink Y before installing, or have the compiler find Y on the system).

But at least this is not blocking anything for me anymore.

[gromgit]

Sorry, commenting while on the road, got confused by brain rattling around in skull.

There definitely seems to be a bug, in that brew linkage correctly considers a recommended dependency to be "active" if the associated --without-X option was not used. However, the list of used and unused build options are not saved in the tab:

$ grep options /opt/homebrew/opt/macaulay2/INSTALL_RECEIPT.json
  "used_options": [],
  "unused_options": [],

so brew linkage thinks libomp, nauty and python must have been indirectly included by some other dependency.