"Error: Homebrew/Science was deprecated" error message after "brew upgrade"


#1

I’m facing an issue that I can’t seem to resolve or find a relevant solution. Basically, every time I issue the brew upgrade command to upgrade my current homebrew installation, I receive the error message

Error: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated.

Here is an example output with some context to help show what I’m experiencing:

$ brew upgrade
==> Upgrading 17 outdated packages, with result:
wget 1.19.4_1 -> 1.19.5, flann 1.9.1_3 -> 1.9.1_4, arpack 3.5.0_1 -> 3.5.0_2, gnuplot 5.2.2_1 -> 5.2.3, boost 1.67.0 -> 1.67.0_1, bdw-gc 7.6.4 -> 7.6.6, netpbm 10.73.18 -> 10.73.19, graphicsmagick 1.3.28_1 -> 1.3.29, lz4 1.8.1.2 -> 1.8.2, numpy 1.14.2 -> 1.14.3_1, openexr 2.2.0 -> 2.2.0_1, fig2dev 3.2.7 -> 3.2.7a, opencv 3.4.1_2 -> 3.4.1_5, gperftools 2.6.3 -> 2.7, octave 4.2.2_1 -> 4.4.0, vtk 8.1.0_1 -> 8.1.0_2, bazel 0.12.0 -> 0.13.0
==> Upgrading bazel 
==> Downloading https://homebrew.bintray.com/bottles/bazel-0.13.0.high_sierra.bottle.tar.gz
######################################################################## 100.0%
==> Pouring bazel-0.13.0.high_sierra.bottle.tar.gz
==> Caveats
Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

zsh completions have been installed to:
  /usr/local/share/zsh/site-functions
==> Summary
🍺  /usr/local/Cellar/bazel/0.13.0: 12 files, 107.7MB
Error: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated.

I’ve checked to see if any log files were present for the last package that was installed/built (for instance, under ~/Library/Logs/Homebrew/bazel) after issuing an upgrade, but none are present. My upgrade process has now become quite cumbersome because I now have to keep issuing the brew upgrade command to cycle through all of my packages that need to be upgraded.

Has anyone run into this issue that may be able to shed some insight to point me in the right direction for a resolution?


(Eduard Rozenberg) #2

That tap no longer exists. Once you figure out which scientific packages were installed using that tap, you may need to uninstall them, then install them again using the homebrew formulas instead of the tapped science formulas.

For example:

brew uninstall some_pkg1_installed_from_homebrew_science
brew uninstall some_pkg2_installed_from_homebrew_science
brew uninstall some_pkg3_installed_from_homebrew_science

brew untap homebrew/science

brew update

brew install some_pkg1
brew install some_pkg2
brew install some_pkg3

Note that some options may have changed in the migrated science formulas, so when you reinstall the packages they may not be built the same exact way as the older ones.

If you want to make 100% sure it will all work before blowing away your old installed packages, you could set up homebrew on another Mac (if one is available), and install those packages with brew install and make sure everything works as you need it to.


#3

Thanks, @edrozenberg for your response! I don’t have another mac available to make sure the method works, but I’m going to go ahead to proceed as you instructed on my current mac.

Is there any way to install packages from a list similar to the requirements.txt file for pip install?


#4

Is there any way to install packages from a list similar to the requirements.txt file for pip install?

Looks like I found the answer to my question with brew bundle dump/install