Please fill out the issue checklist below, and provide all of the requested information.
Please always follow these steps:
[ 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?
[ ] Ran brew doctor, fixed all issues and retried your prior step?
[ ] Ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
[ ] If brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?
To help us debug your issue please explain:
What you were trying to do (and why)
I'm trying to install orthofinder locally on a Macbook pro M1. All dependencies (diamond, fastme) if installed separately works fine, except MCL. The diamond and fastme that were installed with orthofinder were pre-compiled executables that didn't work. Creating softlinks pointing to the pre-installed, independently, solved the issue. Except for mcl.
What happened (include command output)
brew install mcl
==> Downloading https://formulae.brew.sh/api/formula.jws.json
########################################################################################################################################### 100.0%
==> Downloading https://formulae.brew.sh/api/cask.jws.json
########################################################################################################################################### 100.0%
==> Fetching brewsci/bio/mcl
==> Downloading https://micans.org/mcl/src/mcl-14-137.tar.gz
Already downloaded: /Users/strom/Library/Caches/Homebrew/downloads/2270c1e35b168dd765d6a0cec7fcbe7de4f6a0f971073bf1caa3e3d44737d6cb--mcl-14-137.tar.gz
==> Installing mcl from brewsci/bio
==> ./configure --enable-blast
Last 15 lines from /Users/strom/Library/Logs/Homebrew/mcl/01.configure:
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking build system type... configure: error: /bin/sh autofoo/config.sub -apple-darwin23.5.0 failed
configure: WARNING: cache variable ac_cv_build contains a newline
./configure
checking for a BSD-compatible install... /opt/local/bin/ginstall -c
checking whether build environment is sane... yes
/Users/strom/Downloads/mcl-22-282/autofoo/missing: Unknown --is-lightweight' option Try/Users/strom/Downloads/mcl-22-282/autofoo/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /opt/local/bin/gmkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make supports the include directive... yes (GNU style)
checking for gcc... /opt/homebrew/bin/gcc
checking whether the C compiler works... no
configure: error: in /Users/strom/Downloads/mcl-22-282': configure: error: C compiler cannot create executables Seeconfig.log' for more details
Formula additions or changes
There is an issue compiling the code. I guess the same happens when installing from brew
Please fill out the issue checklist below, and provide all of the requested information.
Please always follow these steps:
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?To help us debug your issue please explain:
If reporting this issue please do so at (not Homebrew/brew or Homebrew/homebrew-core): https://github.com/brewsci/homebrew-bio/issues
brew installcommands)downloading the original : wget https://www.micans.org/mcl/src/mcl-22-282.tar.gz setenv CC /opt/homebrew/bin/gcc setenv CPATH /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
./configure checking for a BSD-compatible install... /opt/local/bin/ginstall -c checking whether build environment is sane... yes /Users/strom/Downloads/mcl-22-282/autofoo/missing: Unknown
--is-lightweight' option Try/Users/strom/Downloads/mcl-22-282/autofoo/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /opt/local/bin/gmkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking whether make supports the include directive... yes (GNU style) checking for gcc... /opt/homebrew/bin/gcc checking whether the C compiler works... no configure: error: in/Users/strom/Downloads/mcl-22-282': configure: error: C compiler cannot create executables Seeconfig.log' for more detailsFormula additions or changes
There is an issue compiling the code. I guess the same happens when installing from brew
To get formulae added or changed in Brewsci/bio please file a Pull Request. config.log