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Cannot install tRNAscan-SE #1593

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4 of 5 tasks
lmrodriguezr opened this issue Nov 28, 2022 · 0 comments
Open
4 of 5 tasks

Cannot install tRNAscan-SE #1593

lmrodriguezr opened this issue Nov 28, 2022 · 0 comments

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@lmrodriguezr
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  • 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.
  • 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?

I'm trying to install the latest version of tRNAscan-SE:
brew install trnascan

Which fails with the following message:

==> Downloading http://trna.ucsc.edu/software/trnascan-se-2.0.11.tar.gz
Already downloaded: /Users/miguel/Library/Caches/Homebrew/downloads/adc41dd58bd9477ee5c19c4831481bcdf14134c43b3935711ac58a3e01d97241--trnascan-se-2.0.11.tar.gz
==> Installing trnascan from brewsci/bio
==> ./configure --prefix=/usr/local/Cellar/trnascan/2.0.11
==> make install
Last 15 lines from /Users/miguel/Library/Logs/Homebrew/trnascan/02.make:
sed -e 's,\@bindir\@,/usr/local/Cellar/trnascan/2.0.11/bin,g' -e 's,\@libdir\@,/usr/local/Cellar/trnascan/2.0.11/lib,g' -e 's,[@]PERL[@],/usr/bin/perl,g' -e 's,\@INFERNAL\@,,g'  < ./tRNAscan-SE.src > tRNAscan-SE
chmod +x tRNAscan-SE
sed -e 's,\@bindir\@,/usr/local/Cellar/trnascan/2.0.11/bin,g' -e 's,\@libdir\@,/usr/local/Cellar/trnascan/2.0.11/lib,g' -e 's,[@]PERL[@],/usr/bin/perl,g' -e 's,\@INFERNAL\@,,g'  < ./tRNAscan-SE.conf.src > tRNAscan-SE.conf
chmod +x tRNAscan-SE.conf
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /private/tmp/trnascan-20221128-1367-ojvt96/tRNAscan-SE-2.0/missing autoheader)
/private/tmp/trnascan-20221128-1367-ojvt96/tRNAscan-SE-2.0/missing: line 81: autoheader: command not found
WARNING: 'autoheader' is missing on your system.
         You should only need it if you modified 'acconfig.h' or
         'configure.ac' or m4 files included by 'configure.ac'.
         The 'autoheader' program is part of the GNU Autoconf package:
         <http://www.gnu.org/software/autoconf/>
         It also requires GNU m4 and Perl in order to run:
         <http://www.gnu.org/software/m4/>
         <http://www.perl.org/>
make: *** [config.h.in] Error 127

Do not report this issue to Homebrew/brew or Homebrew/core!

This is the full log gist: https://gist.github.com/0ced1127535a04abd7e909996a07546c

The missing autoheader message seems to be a red herring:

> autoheader --version
autoheader (GNU Autoconf) 2.71
Copyright (C) 2021 Free Software Foundation, Inc.
License GPLv3+/Autoconf: GNU GPL version 3 or later
<https://gnu.org/licenses/gpl.html>, <https://gnu.org/licenses/exceptions.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Roland McGrath and Akim Demaille.

However, just in case I reinstalled autoconf (brew reinstall autoconf) and reran brew install trnascan with the exact same result.

Any help with this would be greatly appreciated.

Thanks!!!

Miguel.

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