From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 04:55:28 2017 Received: (at submit) by debbugs.gnu.org; 1 Feb 2017 09:55:28 +0000 Received: from localhost ([127.0.0.1]:52841 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cYrdQ-00034X-Bb for submit@debbugs.gnu.org; Wed, 01 Feb 2017 04:55:28 -0500 Received: from eggs.gnu.org ([208.118.235.92]:59011) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cYrdO-00034I-IQ for submit@debbugs.gnu.org; Wed, 01 Feb 2017 04:55:27 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cYrdI-00013S-9S for submit@debbugs.gnu.org; Wed, 01 Feb 2017 04:55:21 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: * X-Spam-Status: No, score=1.5 required=5.0 tests=BAYES_40,RP_MATCHES_RCVD, URIBL_RHS_DOB autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:50991) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cYrdI-00013O-6j for submit@debbugs.gnu.org; Wed, 01 Feb 2017 04:55:20 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:49972) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cYrdG-0002Au-Sz for bug-guix@gnu.org; Wed, 01 Feb 2017 04:55:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cYrdD-00012E-RJ for bug-guix@gnu.org; Wed, 01 Feb 2017 04:55:18 -0500 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:34687) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cYrdD-00012A-OP for bug-guix@gnu.org; Wed, 01 Feb 2017 04:55:15 -0500 Received: from reverse-83.fdn.fr ([80.67.176.83]:49792 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cYrdC-0001Dp-W3 for bug-guix@gnu.org; Wed, 01 Feb 2017 04:55:15 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: bug-guix@gnu.org Subject: R packages are not bit-reproducible X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 13 =?utf-8?Q?Pluvi=C3=B4se?= an 225 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-unknown-linux-gnu Date: Wed, 01 Feb 2017 10:55:09 +0100 Message-ID: <8737fydyma.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.7 (----) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.7 (----) R packages build non-deterministically: https://www.gnu.org/software/guix/packages/reproducibility.html --8<---------------cut here---------------start------------->8--- $ wget -q -O - https://mirror.hydra.gnu.org/nar/imiwif0wn7dxcc7f4zdq09y1l11= 32pqj-r-zoo-1.7-14 | bunzip2 | guix archive -x one $ wget -q -O - https://bayfront.guixsd.org/nar/gzip/imiwif0wn7dxcc7f4zdq09y= 1l1132pqj-r-zoo-1.7-14 | gunzip | guix archive -x two $ diff -ru one two diff -ru one/site-library/zoo/DESCRIPTION two/site-library/zoo/DESCRIPTION --- one/site-library/zoo/DESCRIPTION 2017-02-01 10:49:49.700423133 +0100 +++ two/site-library/zoo/DESCRIPTION 2017-02-01 10:49:57.224462007 +0100 @@ -28,4 +28,4 @@ Maintainer: Achim Zeileis Repository: CRAN Date/Publication: 2016-12-19 09:38:14 -Built: R 3.3.2; x86_64-unknown-linux-gnu; 2017-01-15 03:12:57 UTC; unix +Built: R 3.3.2; x86_64-unknown-linux-gnu; 2017-01-23 21:48:44 UTC; unix Binary files one/site-library/zoo/Meta/package.rds and two/site-library/zoo= /Meta/package.rds differ --8<---------------cut here---------------end--------------->8--- First there=E2=80=99s a timestamp in =E2=80=98DESCRIPTION=E2=80=99 (this is= discussed at ). The .rds differences seem less trivial but there=E2=80=99s apparently a fix= at . Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 06:08:56 2017 Received: (at 25598) by debbugs.gnu.org; 1 Feb 2017 11:08:56 +0000 Received: from localhost ([127.0.0.1]:52879 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cYsmW-0004lM-0h for submit@debbugs.gnu.org; Wed, 01 Feb 2017 06:08:56 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:56228) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cYsmU-0004lD-Ce for 25598@debbugs.gnu.org; Wed, 01 Feb 2017 06:08:55 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 05D1838073C; Wed, 1 Feb 2017 12:08:52 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:user-agent:references :received:received:received; s=mdc; t=1485947326; x=1487761727; bh=fXr1VetaPWwBDknvhduSqqbaUtNkIHWr/4C1mdATukc=; b=aGvbcDqywqmi 6skd/tffwKtCgG+VszOIUOm42swiI3Vb+KDWEx/nHQLUYcOwlehFQgZErV8fHdWd /XofHkwBZRRitB/h1Mx2Od0Dd4BxVEh4zm3PbK3VrQPxFJKdZ/D/LNBv9vrCZHoe agjOz7f6IhEKsD3sO5iGkdPHfS+CDQc= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id rY9NWKUJnuoJ; Wed, 1 Feb 2017 12:08:46 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 1 Feb 2017 12:08:46 +0100 (CET) Received: from localhost (141.80.180.135) by HTCATWO.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.319.2; Wed, 1 Feb 2017 12:08:45 +0100 References: <8737fydyma.fsf@gnu.org> User-agent: mu4e 0.9.16; emacs 25.1.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#25598: R packages are not bit-reproducible In-Reply-To: <8737fydyma.fsf@gnu.org> Date: Wed, 1 Feb 2017 12:08:45 +0100 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.000.1202-22764.006 X-TM-AS-Result: No--7.569500-0.000000-31 X-TM-AS-MatchedID: 150567-154390-147015-700454-703788-700133-701837-705178-1 48035-148036-10008-23116-30060-41000-42003 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 25598 Cc: 25598@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) --=-=-= Content-Type: text/plain It looks like R 3.3.2 already includes the fixes but they need to be explicitly requested when installing packages. Attached is a patch that seems to fix this. --=-=-= Content-Type: text/x-patch; charset="utf-8" Content-Disposition: inline; filename="0001-build-r-build-system-Use-deterministic-built-date.patch" Content-Transfer-Encoding: 8bit >From fa42971cb7099e3b370565de5d3f454faecf0369 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Feb 2017 11:42:34 +0100 Subject: [PATCH] build: r-build-system: Use deterministic built date. Fixes . * guix/build/r-build-system.scm (install): Pass "--built-timestamp" option to make build deterministic. --- guix/build/r-build-system.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/guix/build/r-build-system.scm b/guix/build/r-build-system.scm index 3fc13eb83..24aa73d4f 100644 --- a/guix/build/r-build-system.scm +++ b/guix/build/r-build-system.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Ricardo Wurmus +;;; Copyright © 2015, 2017 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -84,6 +84,7 @@ (params (append configure-flags (list "--install-tests" (string-append "--library=" site-library) + "--built-timestamp=1970-01-01" "."))) (site-path (string-append site-library ":" (generate-site-path inputs)))) -- 2.11.0 --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 08:00:40 2017 Received: (at 25598) by debbugs.gnu.org; 1 Feb 2017 13:00:40 +0000 Received: from localhost ([127.0.0.1]:52913 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cYuWd-0000p6-Pn for submit@debbugs.gnu.org; Wed, 01 Feb 2017 08:00:39 -0500 Received: from eggs.gnu.org ([208.118.235.92]:42426) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cYuWb-0000ov-TO for 25598@debbugs.gnu.org; Wed, 01 Feb 2017 08:00:38 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cYuWS-0000FB-Bq for 25598@debbugs.gnu.org; Wed, 01 Feb 2017 08:00:32 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.5 required=5.0 tests=BAYES_05,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36665) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cYuWS-0000F7-8k; Wed, 01 Feb 2017 08:00:28 -0500 Received: from reverse-83.fdn.fr ([80.67.176.83]:50238 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cYuWR-0003GI-IU; Wed, 01 Feb 2017 08:00:27 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: bug#25598: R packages are not bit-reproducible References: <8737fydyma.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 13 =?utf-8?Q?Pluvi=C3=B4se?= an 225 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-unknown-linux-gnu Date: Wed, 01 Feb 2017 14:00:25 +0100 In-Reply-To: (Ricardo Wurmus's message of "Wed, 1 Feb 2017 12:08:45 +0100") Message-ID: <87bmumcbh2.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 25598 Cc: 25598@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Hi! Ricardo Wurmus skribis: > From fa42971cb7099e3b370565de5d3f454faecf0369 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Wed, 1 Feb 2017 11:42:34 +0100 > Subject: [PATCH] build: r-build-system: Use deterministic built date. > > Fixes . > > * guix/build/r-build-system.scm (install): Pass "--built-timestamp" > option to make build deterministic. Great. I think it=E2=80=99s fine for master, that=E2=80=99s 276 packages b= ut they don=E2=80=99t take long to build. Does that also help with the .rds discrepancies? Thank you for the super-fast reply! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 10 07:38:20 2017 Received: (at 25598) by debbugs.gnu.org; 10 Feb 2017 12:38:20 +0000 Received: from localhost ([127.0.0.1]:33881 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ccASy-0000Rl-4y for submit@debbugs.gnu.org; Fri, 10 Feb 2017 07:38:20 -0500 Received: from eggs.gnu.org ([208.118.235.92]:48468) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ccASx-0000RZ-Bf for 25598@debbugs.gnu.org; Fri, 10 Feb 2017 07:38:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ccASp-0004uM-6n for 25598@debbugs.gnu.org; Fri, 10 Feb 2017 07:38:14 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:41234) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ccASp-0004uG-3M; Fri, 10 Feb 2017 07:38:11 -0500 Received: from [193.50.110.68] (port=57612 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1ccASo-0003fw-D0; Fri, 10 Feb 2017 07:38:10 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: [PATCH] More reproducibility fixes for R. References: X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 22 =?utf-8?Q?Pluvi=C3=B4se?= an 225 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-unknown-linux-gnu Date: Fri, 10 Feb 2017 13:38:07 +0100 In-Reply-To: (Ricardo Wurmus's message of "Thu, 9 Feb 2017 15:47:21 +0100") Message-ID: <87bmuafcgg.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 25598 Cc: Guix-devel , 25598@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Hi! Ricardo Wurmus skribis: > attached are more reproducibility fixes for R. Unfortunately, it seems > that files of type =E2=80=9Crdb=E2=80=9D, =E2=80=9Crdx=E2=80=9D, and =E2= =80=9Crds=E2=80=9D are still not reproducible. > This leaves us with the following files in R that are currently not > reproducible: Could it be that --built-timestamp is not honored for R modules within R? Do the Debian patches mentioned in #25598 help? > From e8cd2114b824ab6fed671c2214956ee22deeaedf Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Thu, 9 Feb 2017 14:34:57 +0100 > Subject: [PATCH 1/2] gnu: r: Fix syntax for INSTALL_OPTS. > > This is a follow-up to commit 4621acfd8272fa93d0530faa5f015b26a194b587. > > * gnu/packages/statistics.scm (r)[arguments]: Ensure that > "--built-timestamp" appears on the same line as the other INSTALL_OPTS. So the previous attempt had no effect, right? LGTM. > From 95b939f662a29b3cc6973a2fba286f32faf010c1 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Thu, 9 Feb 2017 15:40:02 +0100 > Subject: [PATCH 2/2] gnu: r: Fix more reproducibility problems. > > * gnu/packages/statistics.scm (r)[arguments]: Patch locations in the > build system that need special treatment for reproducibility. LGTM, thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 08 06:54:45 2017 Received: (at 25598) by debbugs.gnu.org; 8 Mar 2017 11:54:45 +0000 Received: from localhost ([127.0.0.1]:45435 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1claB2-0003bQ-7Q for submit@debbugs.gnu.org; Wed, 08 Mar 2017 06:54:45 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:50966) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1claAz-0003bG-UW for 25598@debbugs.gnu.org; Wed, 08 Mar 2017 06:54:42 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id ABA6D3807EA; Wed, 8 Mar 2017 12:54:40 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :message-id:date:date:in-reply-to:subject:subject:from:from :user-agent:received:received:received; s=mdc; t=1488974075; x= 1490788476; bh=HZRgrRH2isHVb7cNT7brVS16Wk0CnVfpHbvaLz10Ceo=; b=e w9x39ThqlEnHsNEPq+7IiMhNNXy0kiWPIH3nPnFel/SipVWK/oPHKSTWOKIMnlxx Sj1PEAWCSGwN/Od22EBY2dm9G77h0iitMdfxP0cF+S5Ve7IZ7eCXamXbcpu1uPK4 4/llScbww1Lju32G3UrC0vfOR/PUimYKQMk8hsSMK0= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 2w4tm8mnOfNF; Wed, 8 Mar 2017 12:54:35 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Wed, 8 Mar 2017 12:54:35 +0100 (CET) Received: from localhost (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.319.2; Wed, 8 Mar 2017 12:53:43 +0100 User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: [PATCH] More reproducibility fixes for R. In-Reply-To: <87bmuafcgg.fsf@gnu.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 8 Mar 2017 12:53:43 +0100 Message-ID: <87efy82ddk.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.100.1062-22928.006 X-TM-AS-Result: No--12.323800-0.000000-31 X-TM-AS-MatchedID: 150567-703786-703731-139010-700133-701928-701837-862883-7 03657-701762-188198-711432-704311-706023-700752-701236-863277-852515-106660 -705178-711888-703586-710718-702358-105250-700107-703330-139703-700486-1480 04-148133-20043-42000-42003 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 25598 Cc: Guix-devel , 25598@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> attached are more reproducibility fixes for R. Unfortunately, it seems >> that files of type “rdb”, “rdx”, and “rds” are still not reproducible. >> This leaves us with the following files in R that are currently not >> reproducible: > > Could it be that --built-timestamp is not honored for R modules within > R? With these two patches the flag *should* be honoured. I don’t understand yet where the rds differences come from, but I’ll investigate this now. > Do the Debian patches mentioned in #25598 help? R 3.3.2 already includes the patches that were posted on Debian bug #774031. The patch at #782764 is the equivalent of our change to the r-build-system to pass down the flag to R packages. >> From e8cd2114b824ab6fed671c2214956ee22deeaedf Mon Sep 17 00:00:00 2001 >> From: Ricardo Wurmus >> Date: Thu, 9 Feb 2017 14:34:57 +0100 >> Subject: [PATCH 1/2] gnu: r: Fix syntax for INSTALL_OPTS. >> >> This is a follow-up to commit 4621acfd8272fa93d0530faa5f015b26a194b587. >> >> * gnu/packages/statistics.scm (r)[arguments]: Ensure that >> "--built-timestamp" appears on the same line as the other INSTALL_OPTS. > > So the previous attempt had no effect, right? Yeah, it was not effective and I failed to use “guix build --check” properly (without grafts), so I thought everything was fine already. >> From 95b939f662a29b3cc6973a2fba286f32faf010c1 Mon Sep 17 00:00:00 2001 >> From: Ricardo Wurmus >> Date: Thu, 9 Feb 2017 15:40:02 +0100 >> Subject: [PATCH 2/2] gnu: r: Fix more reproducibility problems. >> >> * gnu/packages/statistics.scm (r)[arguments]: Patch locations in the >> build system that need special treatment for reproducibility. > > LGTM, thanks! I pushed both to master. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 08 12:56:42 2017 Received: (at 25598) by debbugs.gnu.org; 8 Mar 2017 17:56:42 +0000 Received: from localhost ([127.0.0.1]:46604 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1clfpK-0001Uk-7M for submit@debbugs.gnu.org; Wed, 08 Mar 2017 12:56:42 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21048) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1clfpH-0001Ub-TY for 25598@debbugs.gnu.org; Wed, 08 Mar 2017 12:56:41 -0500 Received: from localhost (xd933f0d3.dyn.telefonica.de [217.51.240.211]) by mx.zohomail.com with SMTPS id 1488995797722738.6427579019767; Wed, 8 Mar 2017 09:56:37 -0800 (PST) User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus To: Guix-devel Subject: Re: [PATCH] More reproducibility fixes for R. In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 08 Mar 2017 18:56:34 +0100 Message-ID: <87bmtb3b59.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 25598 Cc: 25598@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) Ricardo Wurmus writes: > attached are more reproducibility fixes for R. Unfortunately, it seems > that files of type “rdb”, “rdx”, and “rds” are still not reproducible. > This leaves us with the following files in R that are currently not > reproducible: […] > /lib/R/library/boot/help/paths.rds > /lib/R/library/class/help/paths.rds > /lib/R/library/cluster/help/paths.rds > /lib/R/library/codetools/help/paths.rds > /lib/R/library/foreign/help/paths.rds > /lib/R/library/KernSmooth/help/paths.rds > /lib/R/library/lattice/help/paths.rds > /lib/R/library/MASS/help/paths.rds > /lib/R/library/Matrix/help/paths.rds > /lib/R/library/mgcv/help/paths.rds > /lib/R/library/nlme/help/paths.rds > /lib/R/library/nnet/help/paths.rds > /lib/R/library/rpart/help/paths.rds > /lib/R/library/spatial/help/paths.rds > /lib/R/library/survival/help/paths.rds […] > > I’ll try to figure out if there’s something we can do to make them > reproducible (there’s a Debian bug report with relevant information). I > had originally assumed that 3.3.2 already included fixes for this. The paths.rds files contain temporary paths like this: /tmp/guix-build-r-3.3.2.drv-0/RtmpCmeE9W/R.INSTALL43fb733deccc/survival/ These paths contain the random strings produced by “mkdtemp”. This happens in “src/main/sysutils.c”. I don’t know if we need these files. All of them are part of the recommended packages. I don’t know if these are also built by Debian. I patched the package in a previous commit to override the built timestamp, and it does seem to have an effect on the DESCRIPTION file, but it does not affect the .rd* files. More investigation required. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 14 04:24:55 2017 Received: (at control) by debbugs.gnu.org; 14 Mar 2017 08:24:55 +0000 Received: from localhost ([127.0.0.1]:54715 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cnhlH-0000C6-5f for submit@debbugs.gnu.org; Tue, 14 Mar 2017 04:24:55 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21023) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cnhlE-0000Bx-RQ for control@debbugs.gnu.org; Tue, 14 Mar 2017 04:24:53 -0400 Received: from localhost (xd933fe09.dyn.telefonica.de [217.51.254.9]) by mx.zohomail.com with SMTPS id 1489479888252271.44746811853213; Tue, 14 Mar 2017 01:24:48 -0700 (PDT) Date: Tue, 14 Mar 2017 09:24:45 +0100 To: control@debbugs.gnu.org From: Ricardo Wurmus Subject: control message for bug #25598 X-Spam-Score: 1.1 (+) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: owner 25598 ! [...] Content analysis details: (1.1 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 1.0 SPF_SOFTFAIL SPF: sender does not match SPF record (softfail) -0.0 RCVD_IN_MSPIKE_H2 RBL: Average reputation (+2) [135.84.80.216 listed in wl.mailspike.net] 0.1 MISSING_MID Missing Message-Id: header X-Debbugs-Envelope-To: control X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" Message-Id: X-Spam-Score: 1.0 (+) owner 25598 ! From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 16 03:54:24 2017 Received: (at 25598) by debbugs.gnu.org; 16 Mar 2017 07:54:24 +0000 Received: from localhost ([127.0.0.1]:57915 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1coQEp-0003Rq-SR for submit@debbugs.gnu.org; Thu, 16 Mar 2017 03:54:24 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21005) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1coQEo-0003Rg-CX for 25598@debbugs.gnu.org; Thu, 16 Mar 2017 03:54:22 -0400 Received: from localhost (x590fee92.dyn.telefonica.de [89.15.238.146]) by mx.zohomail.com with SMTPS id 1489650855522326.4249956121531; Thu, 16 Mar 2017 00:54:15 -0700 (PDT) From: Ricardo Wurmus To: 25598@debbugs.gnu.org Subject: [PATCH] gnu: r: Fix remaining reproducibility problems. Date: Thu, 16 Mar 2017 08:54:02 +0100 Message-Id: <20170316075402.29869-1-rekado@elephly.net> X-Mailer: git-send-email 2.12.0 X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 25598 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Fixes . * gnu/packages/statistics.scm (r)[arguments]: Add remaining reproducibility fixes to "build-reproducibly" phase. --- gnu/packages/statistics.scm | 35 ++++++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 656895273..2a20abd86 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -134,11 +134,44 @@ be output in text, PostScript, PDF or HTML.") #t)) (add-after 'unpack 'build-reproducibly (lambda _ - ;; Ensure that gzipped files are reproducible + ;; The documentation contains time stamps to demonstrate + ;; documentation generation in different phases. + (substitute* "src/library/tools/man/Rd2HTML.Rd" + (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S") + "(removed for reproducibility)")) + + ;; Remove timestamp from tracing environment. This fixes + ;; reproducibility of "methods.rd{b,x}". + (substitute* "src/library/methods/R/trace.R" + (("dateCreated = Sys.time\\(\\)") + "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")")) + + ;; Ensure that gzipped files are reproducible. (substitute* '("src/library/grDevices/Makefile.in" "doc/manual/Makefile.in") (("R_GZIPCMD\\)" line) (string-append line " -n"))) + + ;; The "srcfile" procedure in "src/library/base/R/srcfile.R" + ;; queries the mtime of a given file and records it in an object. + ;; This is acceptable at runtime to detect stale source files, + ;; but it destroys reproducibility at build time. + ;; + ;; Instead of disabling this feature, which may have unexpected + ;; consequences, we reset the mtime of generated files before + ;; passing them to the "srcfile" procedure. + (substitute* "src/library/Makefile.in" + (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line) + (string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n")) + (("@\\$\\(MAKE\\) Rdobjects" line) + (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n " + line))) + (substitute* "src/library/tools/Makefile.in" + (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line) + (string-append + line + "\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n"))) + ;; This library is installed using "install_package_description", ;; so we need to pass the "builtStamp" argument. (substitute* "src/library/tools/Makefile.in" -- 2.12.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 16 05:00:48 2017 Received: (at 25598) by debbugs.gnu.org; 16 Mar 2017 09:00:48 +0000 Received: from localhost ([127.0.0.1]:57939 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1coRH5-00055Y-Q6 for submit@debbugs.gnu.org; Thu, 16 Mar 2017 05:00:48 -0400 Received: from eggs.gnu.org ([208.118.235.92]:50248) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1coRH3-00055K-KB for 25598@debbugs.gnu.org; Thu, 16 Mar 2017 05:00:46 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1coRGt-0007rQ-V1 for 25598@debbugs.gnu.org; Thu, 16 Mar 2017 05:00:40 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.5 required=5.0 tests=BAYES_05,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:39883) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1coRGt-0007rM-RX; Thu, 16 Mar 2017 05:00:35 -0400 Received: from [193.50.110.167] (port=53210 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1coRGt-00013j-7Z; Thu, 16 Mar 2017 05:00:35 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: bug#25598: [PATCH] gnu: r: Fix remaining reproducibility problems. References: <8737fydyma.fsf@gnu.org> <20170316075402.29869-1-rekado@elephly.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 26 =?utf-8?Q?Vent=C3=B4se?= an 225 de la =?utf-8?Q?R?= =?utf-8?Q?=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-unknown-linux-gnu Date: Thu, 16 Mar 2017 10:00:32 +0100 In-Reply-To: <20170316075402.29869-1-rekado@elephly.net> (Ricardo Wurmus's message of "Thu, 16 Mar 2017 08:54:02 +0100") Message-ID: <8760j938b3.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 25598 Cc: 25598@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Hello! Ricardo Wurmus skribis: > Fixes . > > * gnu/packages/statistics.scm (r)[arguments]: Add remaining reproducibili= ty > fixes to "build-reproducibly" phase. Woow, impressive work. You=E2=80=99re a reproducibility hero! You=E2=80=99re welcome to push to master. Thank you! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 17 05:17:52 2017 Received: (at 25598-done) by debbugs.gnu.org; 17 Mar 2017 09:17:52 +0000 Received: from localhost ([127.0.0.1]:59608 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1coo1A-00075i-8D for submit@debbugs.gnu.org; Fri, 17 Mar 2017 05:17:52 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21114) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1coo18-00075b-DI for 25598-done@debbugs.gnu.org; Fri, 17 Mar 2017 05:17:50 -0400 Received: from localhost (141.80.148.179 [141.80.148.179]) by mx.zohomail.com with SMTPS id 1489742268237555.0099227660835; Fri, 17 Mar 2017 02:17:48 -0700 (PDT) References: <8737fydyma.fsf@gnu.org> <20170316075402.29869-1-rekado@elephly.net> <8760j938b3.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#25598: [PATCH] gnu: r: Fix remaining reproducibility problems. In-reply-to: <8760j938b3.fsf@gnu.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 17 Mar 2017 10:17:46 +0100 Message-ID: <871stwz2h1.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 25598-done Cc: 25598-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Ludovic Courtès writes: > You’re welcome to push to master. Done with commit 60c9190e21edfaa3a18be857b9a906b8521e948b. Thanks for the quick review! -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Mon Aug 18 21:49:38 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 14 Apr 2017 11:24:05 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator