GNU bug report logs - #37988
[PATCH 0/6] Add flowWorkspace from BioConductor

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From: zimoun <zimon.toutoune <at> gmail.com>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 37988 <at> debbugs.gnu.org
Subject: [bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib.
Date: Wed, 30 Oct 2019 14:29:19 +0100

Hi Ricardo,

Thank you for reviewing.

On Wed, 30 Oct 2019 at 12:39, Ricardo Wurmus <rekado <at> elephly.net> wrote:

> > * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable.
>
> > +    (arguments
> > +     `(#:phases
> > +       (modify-phases %standard-phases
> > +         ;; Contains unverified binaries:
> > +         ;; src/win/lib/{i386,x64}/libprotobuf.a
> > +         (add-after 'unpack 'remove-win-folder
> > +           (lambda _
> > +             (delete-file-recursively "src/win")
> > +             #t))
>
> This should be done in a snippet instead.

What does it mean?


> > +         ;; Fix non-conventional packaging.
> > +         ;; The dependency to protobuf-2.6.0 is included as tgz and build
> > +         ;; by the R package itself.
> > +         (add-after 'unpack 'fix-wrong-hard-coded
> > +           (lambda _
> > +             (with-directory-excursion "src"
> > +               (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
> > +             (substitute* "src/protobuf-2.6.0/configure"
> > +               (("#! /bin/sh") (string-append "#!" (which "sh"))))
> > +             #t)))))

> Can we just use our protobuf package instead of using the bundled sources?

I do not know and I have not tried yet.
The package claims the dependency to 2.6.0 and we do not have this one.
As said in the cover letter to these patches, we could patch to
correctly package without the bundle source and this is IMHO the way
to go. However it is more work and it is better to have the package
available than no package at all.

Well, I will give another look to see if a quick improvement can be done. :-0



All the best,
simon

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