From mboxrd@z Thu Jan  1 00:00:00 1970
From: Ricardo Wurmus <rekado@elephly.net>
Subject: Re: [PATCH] gnu: r: Use uname from Guix
Date: Thu, 27 Oct 2016 15:58:35 +0200
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To: Roel Janssen <roel@gnu.org>
Cc: guix-devel@gnu.org


Roel Janssen <roel@gnu.org> writes:

> Dear Guix,
>
> When running R, it executes a wrapper script that relies on
> @code{uname} to be available in PATH:
>
>> R_HOME_DIR=/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R
>> if test "${R_HOME_DIR}" = "/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R"; then
>>    case "linux-gnu" in
>>    linux*)
>>      run_arch=`uname -m`
>>      case "$run_arch" in
>>         x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
>>           libnn=lib64
>
> Running R in a pure, ad-hoc environment will therefore signal a warning
> that it cannot execute "uname".
>
> With the following patch, it no longer makes this assumption.  Instead
> it uses an absolute path to a uname binary from the Guix store.
>
>>From e364cb25204edea4d8bfb9cfc52764f811c58e72 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Wed, 26 Oct 2016 17:09:19 +0200
> Subject: [PATCH] gnu: r: Use uname from Guix
>
> * gnu/packages/statistics.scm (r): Use uname from Guix.
> ---
>  gnu/packages/statistics.scm | 7 +++++++
>  1 file changed, 7 insertions(+)
>
> diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
> index 1b8d074..5e4cd8c 100644
> --- a/gnu/packages/statistics.scm
> +++ b/gnu/packages/statistics.scm
> @@ -118,6 +118,12 @@ be output in text, PostScript, PDF or HTML.")
>                              "/lib/R/lib"))
>         #:phases
>         (modify-phases %standard-phases
> +         (add-before 'configure 'patch-uname
> +           (lambda* (#:key inputs #:allow-other-keys)
> +             (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
> +                                             "/bin/uname")))
> +               (substitute* "src/scripts/R.sh.in"
> +                 (("uname") uname-bin)))))

Please add #t to the end, because “substitute*” doesn’t have a return value.

>           (add-before
>            'configure 'set-default-pager
>            ;; Set default pager to "cat", because otherwise it is "false",
> @@ -169,6 +175,7 @@ be output in text, PostScript, PDF or HTML.")
>       `(;; We need not only cairo here, but pango to ensure that tests for the
>         ;; "cairo" bitmapType plotting backend succeed.
>         ("pango" ,pango)
> +       ("coreutils" ,coreutils)
>         ("curl" ,curl)
>         ("tzdata" ,tzdata)
>         ("gfortran" ,gfortran)

This looks good to me.  Thanks!

~~ Ricardo