List of formula *maybe* needing perl bumping

[tseemann]

@sjackman @suujia

grep PERL *rb | grep env | sort | sed 's/^/* \[ \] /'

• [x] abricate.rb: (bin/name).write_env_script("#{libexec}/bin/#{name}", :PERL5LIB => ENV["PERL5LIB"])
• [x] bioperl.rb: bin.env_script_all_files libexec, "PERL5LIB" => ENV["PERL5LIB"]
• [x] bioperl.rb: (bin/name).write_env_script executable, :PERL5LIB => ENV["PERL5LIB"]
• [x] circos.rb: (bin/"circos").write_env_script("#{libexec}/bin/circos", :PERL5LIB => ENV["PERL5LIB"])
• [x] edirect.rb: (bin/name).write_env_script(script, :PERL5LIB => ENV["PERL5LIB"])
• [x] lrsim.rb: (bin/"simulateLinkedReads").write_env_script(prefix/"simulateLinkedReads.pl", :PERL5LIB => ENV["PERL5LIB"])
• [x] maker.rb: (bin/name).write_env_script("#{libexec}/bin/#{name}", :PERL5LIB => ENV["PERL5LIB"])
• [x] meme.rb: (bin/"meme").write_env_script(libexec/"bin/meme", :PERL5LIB => ENV["PERL5LIB"])
• [x] mlst.rb: (bin/"mlst").write_env_script("#{libexec}/bin/mlst", :PERL5LIB => ENV["PERL5LIB"])
• [x] repeatmasker.rb: (bin/"RepeatMasker").write_env_script(libexec/"RepeatMasker", :PERL5LIB => ENV["PERL5LIB"])
• [x] simulate-pcr.rb: bin.env_script_all_files libexec, "PERL5LIB" => ENV["PERL5LIB"]
• [x] transdecoder.rb: (bin/executable).write_env_script(prefix/executable, :PERL5LIB => ENV["PERL5LIB"])

[sjackman]

$ head -n1 /home/linuxbrew/.linuxbrew/Cellar/lrsim/1.0/simulateLinkedReads.pl
#!/usr/bin/env perl

lrsim seems okay.

[hwalinga]

I think the issue I had with edirect is related to this, so I thought I post it here instead of opening a new issue.

I got:

Parser.c: loadable library and perl binaries are mismatched (got handshake key 0xce00080, needed 0xcd00080)

However, when I installed from source edirect worked fine. So for anybody stumbling upon this issue looking for a work-around:

brew reinstall --build-from-source edirect

[jonchang]

@hwalinga can you open a pull request that bumps the revision of edirect? Thanks!

[hwalinga]

@jonchang I know too little about Perl or Linuxbrew to know what is exactly going on, and why the --build-from-source flag fixed it. Sorry.

[sjackman]

@hwalinga Try running brew bump-revision edirect to open a PR to rebuild a new bottle for edirect.

[sjackman]

All of these issues have now been addressed.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[tseemann]

@sjackman can we close this now then?

[sjackman]

@dmohadjel Could you please test that each of the above formulae work using interactively brew install foo and brew linkage --check foo and brew test foo?

[dmohadjel]

@sjackman I tested all the formulae and most were successful aside from the following:

Running brew test circos would return

==> /home/dmohadjel/.linuxbrew/Cellar/circos/0.69-6_1/bin/circos -conf /home/dmohadjel/.linuxbrew/Cellar/circos/0.69-6_1/libexec/example/etc/circos.conf -debug_group summary,timer
Last 15 lines from /home/dmohadjel/.cache/Homebrew/Logs/circos/test.01.circos:
2019-07-17 12:17:51 -0700

/home/dmohadjel/.linuxbrew/Cellar/circos/0.69-6_1/bin/circos
-conf
/home/dmohadjel/.linuxbrew/Cellar/circos/0.69-6_1/libexec/example/etc/circos.conf
-debug_group
summary,timer

Clone.c: loadable library and perl binaries are mismatched (got handshake key 0xce00080, needed 0xcd00080)
Error: brewsci/bio/circos: failed

I would not get this error when installing circos with brew install --build-from-source circos.

Running brew test lrsim would return

==> /home/dmohadjel/.linuxbrew/Cellar/lrsim/1.0/bin/simulateLinkedReads -h 2>&1
Error: brewsci/bio/lrsim: failed
An exception occurred within a child process:
  Test::Unit::AssertionFailedError: <2> expected but was
<1>.

Again, I wouldn't get this error when installing with brew install --build-from-source lrsim.

Running brew test mlst would return

==> /home/dmohadjel/.linuxbrew/Cellar/mlst/2.16.1/bin/mlst --version
XS.c: loadable library and perl binaries are mismatched (got handshake key 0xce00080, needed 0xcd00080)
Error: brewsci/bio/mlst: failed
An exception occurred within a child process:
  Test::Unit::AssertionFailedError: <0> expected but was
<1>. 

And again the error did not occur when installed using brew install --build-from-source mlst.

Lastly, I haven't been able to use any of the commands with transdecoder. I get the following error every time:

Error: Unsupported type NilClass for nil

[sjackman]

Great. Thanks, Dara! Please open one PR for each of these failed formulae to bump the revision.

[sjackman]

Use brew install -sdv transdecoder and see if you can get a backtrace to troubleshoot it.

[dmohadjel]

@sjackman I still get this error when trying brew install -sdv transdecoder, and I don't arrive to the prompt after failing.

Error: Invalid formula: /home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-bio/Formula/transdecoder.rb
Unsupported type NilClass for nil

However, the installation will be successful if I run

brew install -sdv https://raw.githubusercontent.com/dmohadjel/homebrew-bio/transdecoder-5.5.0/Formula/transdecoder.rb

[sjackman]

brew tap brewsci/bio is failing for me now.

==> Tapping brewsci/bio
Cloning into '/home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-bio'...
Error: Invalid formula: /home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/brewsci/homebrew-bio/Formula/transdecoder.rb
Unsupported type NilClass for nil
Error: Cannot tap brewsci/bio: invalid syntax in tap!

I'm not entirely sure when this issue started. Perhaps there has been a recent pull request to Homebrew/brew to cause this breakage. I don't have time at the moment to look into it. I've opened PR https://github.com/brewsci/homebrew-bio/pull/699 to work around the issue.