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orthofinder and MCL (markov clustering) does not compile on M1 #1698

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stephrom opened this issue Jun 3, 2024 · 0 comments
Open
3 tasks

orthofinder and MCL (markov clustering) does not compile on M1 #1698

stephrom opened this issue Jun 3, 2024 · 0 comments

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@stephrom
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stephrom commented Jun 3, 2024

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

If reporting this issue please do so at (not Homebrew/brew or Homebrew/homebrew-core):
https://github.com/brewsci/homebrew-bio/issues

  • What you expected to happen
  • Step-by-step reproduction instructions (by running brew install commands)

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 See config.log' for more details

Formula 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

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