Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

t/00-compile.t fails without GD.pm #323

Closed
eserte opened this issue Aug 28, 2019 · 6 comments

Comments

@eserte
Copy link

commented Aug 28, 2019

If GD.pm is not installed, then the test suite of BioPerl-1.7.6 fails:

#   Failed test 'bin/bp_chaos_plot compiled ok'
#   at t/00-compile.t line 589.
#          got: '512'
#     expected: '0'
Can't locate GD.pm in @INC (you may need to install the GD module) (@INC contains: ...  .) at bin/bp_chaos_plot line 8.BEGIN failed--compilation aborted at bin/bp_chaos_plot line 8. at t/00-compile.t line 598, <GEN1900> line 2.
# Looks like you failed 1 test of 513.
t/00-compile.t ...................... 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/513 subtests 
@carandraug

This comment has been minimized.

Copy link
Member

commented Aug 29, 2019

Confirmed. The GD dependency was made a suggestion instead of requirement because of issue #314 . But of course, if GD is missing the compile tests fail. Not sure how others want to address it. I lean on making GB a requirement again or kicking bp_chaos_plot out from core.

@bosborne

This comment has been minimized.

Copy link
Member

commented Aug 29, 2019

It's also Bio::Align::Graphics that's using GD. My vote would be to remove them from the core. There are a few different ways to install the GD library itself these days, but I'm not sure that all users can easily do this install.

@carandraug

This comment has been minimized.

Copy link
Member

commented Aug 29, 2019

It's also Bio::Align::Graphics that's using GD.

Yeah, but that's already been removed from core since 1.7.3

@cjfields

This comment has been minimized.

Copy link
Member

commented Aug 29, 2019

I vote we strip bp_chaos_plot from core. Do we have a happy retirement home for little-used scripts?

carandraug added a commit that referenced this issue Aug 29, 2019
bp_chaos_plot: remove script (issue #323)
* bin/bp_chaos_plot: remove scrit with problematic requirement on GD.
* dist.ini: remove handling of GD dependency.
* Changes: mention this change.
@carandraug

This comment has been minimized.

Copy link
Member

commented Aug 29, 2019

I vote we strip bp_chaos_plot from core.

Done.

Do we have a happy retirement home for little-used scripts?

No. It might be worth considering removing all scripts and have a separate distribution for them. I'd guess that at least some of the simpler ones could be implemented in p5-bpwrapper.

@carandraug carandraug closed this Aug 29, 2019

@cjfields

This comment has been minimized.

Copy link
Member

commented Aug 29, 2019

I think those that only use core modules and no additional dependencies are probably harmless, but ones like bp_chaos_plot (though they may be useful) add unnecessary overhead, particularly with tricky-to-install modules like GD.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
4 participants
You can’t perform that action at this time.