[x] Confirmed this is a problem with brew installing one, specific formula and not every time you run brew? If it's a general brew problem please file this issue at https://github.com/Homebrew/brew/issues/new.
[x] Ran brew update and retried your prior step?
[x] Ran brew doctor, fixed all issues and retried your prior step?
[x] Ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
[x] If brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?
brew config and brew doctor outputs
giulio@giulio:/tmp/cacaca$ brew config
HOMEBREW_VERSION: 4.4.3
ORIGIN: https://github.com/Homebrew/brew
HEAD: 91f3671b16fe62121364c465c14e0dfd088d7ead
Last commit: 2 days ago
Core tap JSON: 29 Oct 09:24 UTC
HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: :1
HOMEBREW_MAKE_JOBS: 20
Homebrew Ruby: 3.3.5 => /home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.5/bin/ruby
CPU: 20-core 64-bit unknown_0x6_0x9a
Clang: 14.0.0
Git: 2.34.1 => /bin/git
Curl: 7.81.0 => /bin/curl
Kernel: Linux 6.8.0-47-generic x86_64 GNU/Linux
OS: Ubuntu 22.04.4 LTS (jammy)
Host glibc: 2.35
/usr/bin/gcc: 11.4.0
/usr/bin/ruby: N/A
glibc: N/A
gcc@11: N/A
gcc: N/A
xorg: N/A
giulio@giulio:/tmp/cacaca$ brew doctor
Your system is ready to brew.
Issue
Installing prokka fails in the post install step with the following error:
==> Installing brewsci/bio/prokka
==> Pouring prokka--1.14.6_1.x86_64_linux.bottle.tar.gz
==> /home/linuxbrew/.linuxbrew/Cellar/prokka/1.14.6_1/bin/prokka --setupdb
Last 15 lines from /home/giulio/.cache/Homebrew/Logs/prokka/post_install.01.prokka:
2024-10-29 11:12:48 +0200
/home/linuxbrew/.linuxbrew/Cellar/prokka/1.14.6_1/bin/prokka
--setupdb
Clone.c: loadable library and perl binaries are mismatched (got first handshake key 0xf380080, needed 0xeb80080)
Warning: The post-install step did not complete successfully
You can try again using:
brew postinstall brewsci/bio/prokka
==> Caveats
This formula doesn't contain tbl2asn because it is deprecated now.
See https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ for details.
==> Summary
🍺 /home/linuxbrew/.linuxbrew/Cellar/prokka/1.14.6_1: 44 files, 202.3MB
==> Running `brew cleanup prokka`...
Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
==> Caveats
==> prokka
This formula doesn't contain tbl2asn because it is deprecated now.
See https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ for details.
brew installing one, specific formula and not every time you runbrew? If it's a generalbrewproblem please file this issue at https://github.com/Homebrew/brew/issues/new.brew updateand retried your prior step?brew doctor, fixed all issues and retried your prior step?brew gist-logs <formula>(where<formula>is the name of the formula that failed) and included the output link?brew gist-logsdidn't work: ranbrew configandbrew doctorand included their output with your issue?brew configandbrew doctoroutputsIssue
Installing prokka fails in the post install step with the following error:
I think it happens only when perl is in the latest version or it is installed as part of the prokka install, because of the update that was made to the perl formula one week ago. See https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/p/perl.rb