From patchwork Mon Jul 26 07:25:19 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Lars-Dominik Braun X-Patchwork-Id: 31608 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8799E27BC78; Mon, 26 Jul 2021 08:26:14 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 4EE5427BC6B for ; Mon, 26 Jul 2021 08:26:14 +0100 (BST) Received: from localhost ([::1]:42704 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m7v09-0001zo-EM for patchwork@mira.cbaines.net; Mon, 26 Jul 2021 03:26:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35198) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m7uzy-0001yD-Iv for guix-patches@gnu.org; Mon, 26 Jul 2021 03:26:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38281) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m7uzy-0001I6-CA for guix-patches@gnu.org; Mon, 26 Jul 2021 03:26:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m7uzy-00073B-AX for guix-patches@gnu.org; Mon, 26 Jul 2021 03:26:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#49740] [PATCH] [core-updates?] gnu: r-with-tests: Hardcode path to =?utf-8?b?Y29yZXV0aWxz4oCZ?= rm Resent-From: Lars-Dominik Braun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 26 Jul 2021 07:26:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 49740 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 49740@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.162728434727060 (code B ref -1); Mon, 26 Jul 2021 07:26:02 +0000 Received: (at submit) by debbugs.gnu.org; 26 Jul 2021 07:25:47 +0000 Received: from localhost ([127.0.0.1]:49824 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m7uzj-00072O-C0 for submit@debbugs.gnu.org; Mon, 26 Jul 2021 03:25:47 -0400 Received: from lists.gnu.org ([209.51.188.17]:58420) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m7uze-00072D-86 for submit@debbugs.gnu.org; Mon, 26 Jul 2021 03:25:45 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35144) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m7uzd-0001sE-CE for guix-patches@gnu.org; Mon, 26 Jul 2021 03:25:42 -0400 Received: from mout-p-102.mailbox.org ([80.241.56.152]:57162) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_CHACHA20_POLY1305:256) (Exim 4.90_1) (envelope-from ) id 1m7uzZ-0000rJ-9u for guix-patches@gnu.org; Mon, 26 Jul 2021 03:25:39 -0400 Received: from smtp2.mailbox.org (smtp2.mailbox.org [IPv6:2001:67c:2050:105:465:1:2:0]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-384) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by mout-p-102.mailbox.org (Postfix) with ESMTPS id 4GYBKN4nr7zQjnS for ; Mon, 26 Jul 2021 09:25:28 +0200 (CEST) X-Virus-Scanned: amavisd-new at heinlein-support.de DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=6xq.net; s=MBO0001; t=1627284326; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type; bh=UxPj0lcoHyIJ0qjd53kV649rmPKqs+euU0D+w5upCCY=; b=ye6Q5Q7DaQjhFwl9qLGGX/4ozrwQ1fosSUj14RKz3KLKGDFfttc/1jOyWbjEgVw2eeLvzM 1bW12OwWHgJKA6CJN4HDnMBNBBItHV/cnQh228CyPPSfYaPRcSEWjyDE+r93zQFwkl3u5c X7JUsnyT5pX6T31zfDdPkzfRMTDNLzPAfWHNATj6SqGR2UJwoRihBVSfLepJWusRoIRXHw 8MpAyHGU1X+6xcBjCMHg83jjaK89ltx2/C/tOYT+xuPy00RvctZhjLiYLZwh871beQMqs4 Q97w7k+e6++dwyjN9bblc8TaAYFrKMW1uE5TtqfGUpQGaoOptdrCdGqVuOhdcA== Received: from smtp2.mailbox.org ([80.241.60.241]) by spamfilter05.heinlein-hosting.de (spamfilter05.heinlein-hosting.de [80.241.56.123]) (amavisd-new, port 10030) with ESMTP id vVDS-MD9nawf for ; Mon, 26 Jul 2021 09:25:20 +0200 (CEST) Date: Mon, 26 Jul 2021 09:25:19 +0200 From: Lars-Dominik Braun Message-ID: MIME-Version: 1.0 Content-Disposition: inline X-Rspamd-Queue-Id: CDC611863 X-Rspamd-UID: 931f6b Received-SPF: pass client-ip=80.241.56.152; envelope-from=lars@6xq.net; helo=mout-p-102.mailbox.org X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H4=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches When running R in a container like this guix environment --no-cwd -C --ad-hoc r-minimal -- Rscript -e 'Sys.timezone()' it would print an additional line sh: rm: command not found before exiting. * gnu/packages/statistics.scm (r-with-tests) [#:phases]: Add substitute* to patch call to `rm` and rename phase to reflect what it does now. --- gnu/packages/statistics.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ce9f1bf888..7ba7d9f20d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -213,12 +213,15 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (substitute* "src/library/base/makebasedb.R" (("compress = TRUE") "compress = FALSE")) #t)) - (add-before 'configure 'patch-uname + (add-before 'configure 'patch-coreutils-paths (lambda* (#:key inputs #:allow-other-keys) - (let ((uname-bin (string-append (assoc-ref inputs "coreutils") - "/bin/uname"))) + (let* ((coreutils (assoc-ref inputs "coreutils")) + (uname-bin (string-append coreutils "/bin/uname")) + (rm-bin (string-append coreutils "/bin/rm"))) (substitute* "src/scripts/R.sh.in" - (("uname") uname-bin))) + (("uname") uname-bin)) + (substitute* "src/unix/sys-std.c" + (("rm -Rf ") (string-append rm-bin " -Rf ")))) #t)) (add-after 'unpack 'build-reproducibly (lambda _