Subject: Re: [bug#44613] [PATCH] Fix build for bedtools

From: zimoun <[email-masked]>
Date: Fri, 13 Nov 2020 14:34:06 +0100

Hi Roel,

On Fri, 13 Nov 2020 at 13:55, Roel Janssen <[email-masked]> wrote:

> I also tried removing the bundled htslib for bedtools, but didn't go
> this route for two reasons:
> - The bundled htslib for bedtools seems "slightly modified" (I didn't
> investigate further)
> - Replacing the references to libhts.a with $(pkg-config htslib --
> cflags --libs) produced various linker errors. So I stopped right
> there.
>
> I'm sure more tools will likely have failed because of the htslib
> upgrade (sorry about this!), so having htslib-1.9 around for some time
> may be a good fallback for now.

Thank for your explanations.

> Just to double-check: Is it OK to push the proposed patches?

I have not tried them but they LGTM.

All the best,
simon

PS:
I am always confused if the removal should be done in ’origin’ or in the
’add-after 'unpack’ phase; especially when the bundle is free software.
Other said, what should an user expect when fetching with “guix build -S”?
Anyway! :-)