Re: [PATCH]: gnu: Add bedops.

[ludo@gnu.org (Ludovic Courtès)]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> The build process for this application is a bit messy because the
> sources include tarballs of modified upstream libraries (jansson, bzip2,
> zlib), so we cannot just swap them out for system libraries.
>
> I'm in touch with the developers to see if we can get a build option to
> link against system libraries instead of the bundled copies.  To achieve
> this, though, the patches have to be extracted first (already submitted
> a patch upstream), and any feature that has been added by patching
> upstream library sources would have to be implemented a different way.
> Until then we can't do anything but go along with building these patched
> library copies even though it isn't pretty.

Uh, OK.  I hope that’ll be resolved quickly because it’s really
unpleasant, notably for security reasons.

> From 270b5a501c251e80a040342d4d39d4e236b90c97 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 11 Feb 2015 16:55:33 +0100
> Subject: [PATCH] gnu: Add bedops.
>
> * gnu/packages/bioinformatics.scm (bedops): New variable.

[...]

> +         'unpack 'unpack-tarballs
> +         (lambda _
> +           ;; XXX Bedops includes tarballs of minimally patched upstream
> +           ;; libraries jansson, zlib, and bzip2.  We cannot just use stock
> +           ;; libraries because at least one of the libraries (zlib) is
> +           ;; patched to add a C++ function definition (deflateInit2cpp).
> +           ;; Until the Bedops developers offer a way to link against system
> +           ;; libraries we have to build the in-tree copies of these three
> +           ;; libraries.

Could you s/XXX/FIXME/ and add a link to the upstream discussion, if
possible?

> +          (alist-delete 'check %standard-phases)))))

Could you use #:tests? #f instead?  I find it clearer.

OK with these changes!

Thanks,
Ludo’.