From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: Re: [PATCH] gnu: r: Use uname from Guix Date: Thu, 27 Oct 2016 16:38:18 +0200 Message-ID: <871sz1eu1x.fsf@gnu.org> References: <87shrj9mbu.fsf@gnu.org> <87vawdgagk.fsf@elephly.net> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57633) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bzlnn-0003q1-UI for guix-devel@gnu.org; Thu, 27 Oct 2016 10:37:13 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bzlni-00058S-UO for guix-devel@gnu.org; Thu, 27 Oct 2016 10:37:07 -0400 In-reply-to: <87vawdgagk.fsf@elephly.net> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ricardo Wurmus Cc: guix-devel@gnu.org Ricardo Wurmus writes: > Roel Janssen 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 >> 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. Right. I will try to remember this better in the future too. >> (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! Thanks! I applied the changes above and pushed it in b5ce25cc0. Kind regards, Roel Janssen