parsnp 1.5.2

[SeekingMeaning]

Created with brew bump-formula-pr.

[sjackman]

==> ./configure --prefix=/tmp/parsnp-20200718-14335-26m7sz/parsnp-1.5.2/muscle
Failed to execute: ./configure

Looks like muscle is no longer included with parsnp. You can probably remove that stanza from install.

[sjackman]

Is this needed? What's the error without?

[sjackman]

Oh, I take it that it still includes muscle, but muscle no longer includes ./configure?
Are you interested in trying to use libmuscle instead of the vendored dep?

[SeekingMeaning]

Oh, I take it that it still includes muscle, but muscle no longer includes ./configure?

Yeah

Are you interested in trying to use libmuscle instead of the vendored dep?

I'm not sure; the comment right above this diff is cut off:

    # we still build this, but runtime will link against libmuscle
    # see: https://github.com/brewsci/homebrew-bio/pull/362

[sjackman]

Up to you. It's probably done this way just because that was easiest and didn't require modifying the build scripts.

[sjackman]

On macOS

==> brew audit brewsci/bio/parsnp --online --git --skip-style
90
==> FAILED
91
Error: 1 problem in 1 formula detected
92
Missing libraries:
93
  unexpected (/private/tmp/parsnp-20200724-16576-4ihhio/parsnp-1.5.2/muscle/lib/libMUSCLE-3.7.1.dylib)
94
Unexpected missing library linkage detected
95
brewsci/bio/parsnp:
96
  * parsnp has broken dynamic library links:
97

https://github.com/brewsci/homebrew-bio/pull/1107/checks?check_run_id=908471970#step:4:93

I just discovered that parsnp is the only formula that depends on libmuscle, and libmuscle is actually built from parsnp. I'd suggest removing the formula libmuscle and parsnp can install this library. I'm also fine with keeping both formulae, as it is now. One formula is easier to build though. If you keep both, libmuscle and parsnp need to updated together in a single PR.

[SeekingMeaning]

https://github.com/brewsci/homebrew-bio/pull/1107/checks?check_run_id=910151072#step:5:87
https://github.com/brewsci/homebrew-bio/pull/1107/checks?check_run_id=910151082#step:4:88

==> brew audit brewsci/bio/libmuscle --online --git --skip-style
==> FAILED
Error: 1 problem in 1 formula detected
brewsci/bio/libmuscle:
  * stable sha256 changed without the version also changing; please create an issue upstream to rule out malicious circumstances and to find out why the file changed.