Subject: [bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib.

From: Ricardo Wurmus <[email-masked]>
Date: Wed, 30 Oct 2019 12:39:12 +0100

Hi,

thank you for the patches!

> * 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.

> +         ;; 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?

> +    (description "This package provides the headers and static library of
> +Protocol buffers 2.6.0 for other R packages to compile and link
> against.")

I would prefer not to mention the specific version here.

-- 
Ricardo