From debbugs-submit-bounces@debbugs.gnu.org Sun Aug 20 07:17:16 2017 Received: (at submit) by debbugs.gnu.org; 20 Aug 2017 11:17:16 +0000 Received: from localhost ([127.0.0.1]:46119 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1djOEF-000059-QQ for submit@debbugs.gnu.org; Sun, 20 Aug 2017 07:17:15 -0400 Received: from eggs.gnu.org ([208.118.235.92]:60954) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1djOED-0008WV-C7 for submit@debbugs.gnu.org; Sun, 20 Aug 2017 07:17:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1djOE7-0007m9-82 for submit@debbugs.gnu.org; Sun, 20 Aug 2017 07:17:08 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_20 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:55938) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1djOE7-0007lz-4j for submit@debbugs.gnu.org; Sun, 20 Aug 2017 07:17:07 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:51924) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1djOE3-00051E-CT for bug-guix@gnu.org; Sun, 20 Aug 2017 07:17:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1djOE0-0007jN-8K for bug-guix@gnu.org; Sun, 20 Aug 2017 07:17:03 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21135) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1djOE0-0007it-1g for bug-guix@gnu.org; Sun, 20 Aug 2017 07:17:00 -0400 Received: from localhost (port-92-200-139-185.dynamic.qsc.de [92.200.139.185]) by mx.zohomail.com with SMTPS id 1503227814064367.77374138627886; Sun, 20 Aug 2017 04:16:54 -0700 (PDT) User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: "'bug-guix\@gnu.org'" Subject: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= 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: Sun, 20 Aug 2017 13:16:50 +0200 Message-ID: <87valiwkt9.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) 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: -4.0 (----) R provides a function “Sys.which”, which embeds the full path to “which” at configure time. The path it embeds is that of “which” *before* grafts. The final package does not retain any reference to the “which” package, however. What’s worse: this cannot be fixed by adding “which” to the environment, as “Sys.which” holds a reference to the ungrafted “which” package. This is a problem in containers, where the ungrafted “which” will not be available even when the “which” package is added to the container. It may also be a security problem, because R references an ungrafted package. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 04:51:36 2017 Received: (at 28157) by debbugs.gnu.org; 22 Aug 2017 08:51:36 +0000 Received: from localhost ([127.0.0.1]:48566 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk4uN-0003oP-VK for submit@debbugs.gnu.org; Tue, 22 Aug 2017 04:51:36 -0400 Received: from eggs.gnu.org ([208.118.235.92]:57388) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk4uL-0003oC-QK for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 04:51:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dk4uB-0007zX-6C for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 04:51:28 -0400 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]:54629) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dk4uB-0007zT-2B; Tue, 22 Aug 2017 04:51:23 -0400 Received: from [193.50.110.251] (port=36972 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1dk4u9-0008El-9K; Tue, 22 Aug 2017 04:51:21 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= References: <87valiwkt9.fsf@elephly.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 5 Fructidor 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: Tue, 22 Aug 2017 10:51:18 +0200 In-Reply-To: <87valiwkt9.fsf@elephly.net> (Ricardo Wurmus's message of "Sun, 20 Aug 2017 13:16:50 +0200") Message-ID: <877exwc7eh.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.2 (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: 28157 Cc: 28157@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 (-----) Ricardo Wurmus skribis: > R provides a function =E2=80=9CSys.which=E2=80=9D, which embeds the full = path to =E2=80=9Cwhich=E2=80=9D > at configure time. The path it embeds is that of =E2=80=9Cwhich=E2=80=9D= *before* > grafts. Where=E2=80=99s that reference? I couldn=E2=80=99t find it: --8<---------------cut here---------------start------------->8--- $ guix build r-minimal [...] @ build-succeeded /gnu/store/xz3jhg34z1znlzkz45pva2x0ik96w3qh-r-minimal-3.4= .0.drv - /gnu/store/jzfg7j6wbp28z5zfdh16wyhkqy3azm2z-r-minimal-3.4.0 $ guix gc --references /gnu/store/jzfg7j6wbp28z5zfdh16wyhkqy3azm2z-r-minima= l-3.4.0|grep which $ guix build r-minimal --no-grafts /gnu/store/9xmz92jgmgalf4i07fdiddn658zlccpw-r-minimal-3.4.0 $ guix gc --references /gnu/store/9xmz92jgmgalf4i07fdiddn658zlccpw-r-minima= l-3.4.0 |grep which $ guix build which /gnu/store/xaiq6waavhfrfhxjb35whzc6y4617nzz-which-2.21 $ grep -r -e -which-2.21 /gnu/store/9xmz92jgmgalf4i07fdiddn658zlccpw-r-mini= mal-3.4.0 $ grep -r which-2.21 /gnu/store/9xmz92jgmgalf4i07fdiddn658zlccpw-r-minimal-= 3.4.0 $ grep -r bin/which /gnu/store/9xmz92jgmgalf4i07fdiddn658zlccpw-r-minimal-3= .4.0 --8<---------------cut here---------------end--------------->8--- Normally the grafting code replaces all the store references, unless the reference is somehow obfuscated (which would be surprising here.) Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 05:19:54 2017 Received: (at 28157) by debbugs.gnu.org; 22 Aug 2017 09:19:54 +0000 Received: from localhost ([127.0.0.1]:48607 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk5Lm-0004VR-Db for submit@debbugs.gnu.org; Tue, 22 Aug 2017 05:19:54 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21057) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk5Lk-0004VJ-VD for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 05:19:53 -0400 Received: from localhost (port-92-200-124-26.dynamic.qsc.de [92.200.124.26]) by mx.zohomail.com with SMTPS id 1503393589473996.7710283035002; Tue, 22 Aug 2017 02:19:49 -0700 (PDT) References: <87valiwkt9.fsf@elephly.net> <877exwc7eh.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= In-reply-to: <877exwc7eh.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: Tue, 22 Aug 2017 11:19:45 +0200 Message-ID: <8760dgvu1a.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28157 Cc: 28157@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 (+) Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> R provides a function “Sys.which”, which embeds the full path to “which” >> at configure time. The path it embeds is that of “which” *before* >> grafts. > > Where’s that reference? I couldn’t find it: You can see the reference (before commit a8cd352304807ef60d06c35da07c5456f036688c) within an R session. If you type “Sys.which” the code for “Sys.which” will be printed. $ /gnu/store/hzc1fnrjv8ys399glbzmhds21fm9zzva-r-minimal-3.4.0/bin/R -e 'Sys.which' | grep /gnu/store which <- "/gnu/store/ppyczjc1figwv6yb6brg938y49856avb-which-2.21/bin/which" (The reference is the same as “guix build --no-grafts which”.) > Normally the grafting code replaces all the store references, unless the > reference is somehow obfuscated (which would be surprising here.) Right. In the case of R, the environment for a package is serialized to a possibly compressed data file (.Rdb) with an index (.Rdx). “Sys.which” is part of the “base” package and I cannot find a plain text reference to “bin/which” in the binaries for “base”. I don’t know if we can (or should) disable compression for Rdb files. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 05:30:01 2017 Received: (at 28157) by debbugs.gnu.org; 22 Aug 2017 09:30:02 +0000 Received: from localhost ([127.0.0.1]:48611 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk5VZ-0004jb-DC for submit@debbugs.gnu.org; Tue, 22 Aug 2017 05:30:01 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21038) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk5VX-0004j9-EO for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 05:29:59 -0400 Received: from localhost (port-92-200-124-26.dynamic.qsc.de [92.200.124.26]) by mx.zohomail.com with SMTPS id 1503394196551550.2708135005724; Tue, 22 Aug 2017 02:29:56 -0700 (PDT) References: <87valiwkt9.fsf@elephly.net> <877exwc7eh.fsf@gnu.org> <8760dgvu1a.fsf@elephly.net> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= In-reply-to: <8760dgvu1a.fsf@elephly.net> 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: Tue, 22 Aug 2017 11:29:53 +0200 Message-ID: <874lt0vtke.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28157 Cc: 28157@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: > Ludovic Courtès writes: […] >> Normally the grafting code replaces all the store references, unless the >> reference is somehow obfuscated (which would be surprising here.) > > Right. In the case of R, the environment for a package is serialized to > a possibly compressed data file (.Rdb) with an index (.Rdx). > “Sys.which” is part of the “base” package and I cannot find a plain text > reference to “bin/which” in the binaries for “base”. > > I don’t know if we can (or should) disable compression for Rdb files. If we need to do that I think it should happen in “src/library/base/makebasedb.R”. This file is used to create the base library and it calls saveRDS with “compressed = TRUE” by default. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 05:39:03 2017 Received: (at 28157) by debbugs.gnu.org; 22 Aug 2017 09:39:03 +0000 Received: from localhost ([127.0.0.1]:48617 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk5eJ-0004wu-JP for submit@debbugs.gnu.org; Tue, 22 Aug 2017 05:39:03 -0400 Received: from eggs.gnu.org ([208.118.235.92]:41152) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk5eI-0004wS-Sj for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 05:39:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dk5e8-0005BI-Fc for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 05:38:57 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_40,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:55162) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dk5e8-0005B9-C7; Tue, 22 Aug 2017 05:38:52 -0400 Received: from [193.50.110.251] (port=37066 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1dk5e7-0005aN-TR; Tue, 22 Aug 2017 05:38:52 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= References: <87valiwkt9.fsf@elephly.net> <877exwc7eh.fsf@gnu.org> <8760dgvu1a.fsf@elephly.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 5 Fructidor 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: Tue, 22 Aug 2017 11:38:50 +0200 In-Reply-To: <8760dgvu1a.fsf@elephly.net> (Ricardo Wurmus's message of "Tue, 22 Aug 2017 11:19:45 +0200") Message-ID: <87o9r87xhx.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.2 (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: 28157 Cc: 28157@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 (-----) Ricardo Wurmus skribis: > Right. In the case of R, the environment for a package is serialized to > a possibly compressed data file (.Rdb) with an index (.Rdx). > =E2=80=9CSys.which=E2=80=9D is part of the =E2=80=9Cbase=E2=80=9D package= and I cannot find a plain text > reference to =E2=80=9Cbin/which=E2=80=9D in the binaries for =E2=80=9Cbas= e=E2=80=9D. Doh! That=E2=80=99s a problem. The GC won=E2=80=99t detect those referenc= es either, which can lead to early-deletion problems. > I don=E2=80=99t know if we can (or should) disable compression for Rdb fi= les. We=E2=80=99ll probably have to disable it. (According to =E2=80=98file=E2= =80=99 it=E2=80=99s no a standard compression format like gzip; maybe raw zlib without gzip headers?) Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 07:02:29 2017 Received: (at 28157) by debbugs.gnu.org; 22 Aug 2017 11:02:29 +0000 Received: from localhost ([127.0.0.1]:48682 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk6x3-00073d-DE for submit@debbugs.gnu.org; Tue, 22 Aug 2017 07:02:29 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21137) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk6x1-00073U-3U for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 07:02:27 -0400 Received: from localhost (141.80.245.109 [141.80.245.109]) by mx.zohomail.com with SMTPS id 1503399745555432.4269548954421; Tue, 22 Aug 2017 04:02:25 -0700 (PDT) References: <87valiwkt9.fsf@elephly.net> <877exwc7eh.fsf@gnu.org> <8760dgvu1a.fsf@elephly.net> <87o9r87xhx.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= In-reply-to: <87o9r87xhx.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: Tue, 22 Aug 2017 13:02:23 +0200 Message-ID: <871so3x3uo.fsf@elephly.net> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28157 Cc: 28157@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 (+) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> Right. In the case of R, the environment for a package is serialized to >> a possibly compressed data file (.Rdb) with an index (.Rdx). >> “Sys.which” is part of the “base” package and I cannot find a plain text >> reference to “bin/which” in the binaries for “base”. > > Doh! That’s a problem. The GC won’t detect those references either, > which can lead to early-deletion problems. > >> I don’t know if we can (or should) disable compression for Rdb files. > > We’ll probably have to disable it. (According to ‘file’ it’s no a > standard compression format like gzip; maybe raw zlib without gzip > headers?) Here’s a patch: --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename=0001-gnu-r-minimal-Do-not-compress-serialized-files.patch >From bbacb223cbd6f1ba0ca77eda9d168e325537e3f3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Aug 2017 12:59:48 +0200 Subject: [PATCH] gnu: r-minimal: Do not compress serialized files. * gnu/packages/statistics.scm (r-minimal)[arguments]: Replace build phase "patch-which" with "do-not-compress-serialized-files". [propagated-inputs]: Move "which" from here... [inputs]: ...to here. --- gnu/packages/statistics.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dc7491acd..676752e03 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -127,10 +127,10 @@ be output in text, PostScript, PDF or HTML.") #:phases (modify-phases %standard-phases ;; FIXME: see bug #28157. - (add-before 'configure 'patch-which + (add-before 'configure 'do-not-compress-serialized-files (lambda* (#:key inputs #:allow-other-keys) - (substitute* "src/library/base/R/unix/system.unix.R" - (("@WHICH@") "which")) + (substitute* "src/library/base/makebasedb.R" + (("compress = TRUE") "compress = FALSE")) #t)) (add-before 'configure 'patch-uname (lambda* (#:key inputs #:allow-other-keys) @@ -250,10 +250,8 @@ be output in text, PostScript, PDF or HTML.") ("libxt" ,libxt) ("pcre" ,pcre) ("readline" ,readline) + ("which" ,which) ("zlib" ,zlib))) - ;; FIXME: By default Sys.which embeds a reference to "which", but this - ;; reference is not detected by Guix (see bug #28157). - (propagated-inputs `(("which" ,which))) (native-search-paths (list (search-path-specification (variable "R_LIBS_SITE") -- 2.14.1 --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit I have built r-minimal with it and confirmed that “which” is retained as a reference. I don’t know if this causes any other problems down the road, but I think it should not be a problem. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 09:41:04 2017 Received: (at 28157) by debbugs.gnu.org; 22 Aug 2017 13:41:04 +0000 Received: from localhost ([127.0.0.1]:48821 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk9QW-00043L-G7 for submit@debbugs.gnu.org; Tue, 22 Aug 2017 09:41:04 -0400 Received: from eggs.gnu.org ([208.118.235.92]:38570) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk9QV-00042l-1v for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 09:41:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dk9QN-0002px-CW for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 09:40:58 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_20,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:57946) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dk9QN-0002pt-8s; Tue, 22 Aug 2017 09:40:55 -0400 Received: from [193.50.110.251] (port=38452 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1dk9QM-0003OC-RJ; Tue, 22 Aug 2017 09:40:55 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= References: <87valiwkt9.fsf@elephly.net> <877exwc7eh.fsf@gnu.org> <8760dgvu1a.fsf@elephly.net> <87o9r87xhx.fsf@gnu.org> <871so3x3uo.fsf@elephly.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 5 Fructidor 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: Tue, 22 Aug 2017 15:40:52 +0200 In-Reply-To: <871so3x3uo.fsf@elephly.net> (Ricardo Wurmus's message of "Tue, 22 Aug 2017 13:02:23 +0200") Message-ID: <878tib4t5n.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.2 (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: 28157 Cc: 28157@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 (-----) Ricardo Wurmus skribis: > Here=E2=80=99s a patch: That was fast. :-) > From bbacb223cbd6f1ba0ca77eda9d168e325537e3f3 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Tue, 22 Aug 2017 12:59:48 +0200 > Subject: [PATCH] gnu: r-minimal: Do not compress serialized files. > > * gnu/packages/statistics.scm (r-minimal)[arguments]: Replace build phase > "patch-which" with "do-not-compress-serialized-files". > [propagated-inputs]: Move "which" from here... > [inputs]: ...to here. [...] > (modify-phases %standard-phases > ;; FIXME: see bug #28157. > - (add-before 'configure 'patch-which > + (add-before 'configure 'do-not-compress-serialized-files > (lambda* (#:key inputs #:allow-other-keys) > - (substitute* "src/library/base/R/unix/system.unix.R" > - (("@WHICH@") "which")) Shouldn=E2=80=99t we keep the =E2=80=98patch-which=E2=80=99 phase? > + (substitute* "src/library/base/makebasedb.R" > + (("compress =3D TRUE") "compress =3D FALSE")) Perhaps move the comment about this bug right above this, so we know why we don=E2=80=99t compress. Otherwise LGTM! Any idea how much extra storage this incurs on disk? Thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 10:03:17 2017 Received: (at 28157) by debbugs.gnu.org; 22 Aug 2017 14:03:17 +0000 Received: from localhost ([127.0.0.1]:49652 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk9m0-0006e2-QT for submit@debbugs.gnu.org; Tue, 22 Aug 2017 10:03:17 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21052) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dk9lx-0006dq-Lr for 28157@debbugs.gnu.org; Tue, 22 Aug 2017 10:03:15 -0400 Received: from localhost (141.80.245.109 [141.80.245.109]) by mx.zohomail.com with SMTPS id 1503410589904657.1233507245657; Tue, 22 Aug 2017 07:03:09 -0700 (PDT) References: <87valiwkt9.fsf@elephly.net> <877exwc7eh.fsf@gnu.org> <8760dgvu1a.fsf@elephly.net> <87o9r87xhx.fsf@gnu.org> <871so3x3uo.fsf@elephly.net> <878tib4t5n.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= In-reply-to: <878tib4t5n.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: Tue, 22 Aug 2017 16:03:06 +0200 Message-ID: <87ziarvgx1.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28157 Cc: 28157@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 (+) Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> Here’s a patch: > > That was fast. :-) > >> From bbacb223cbd6f1ba0ca77eda9d168e325537e3f3 Mon Sep 17 00:00:00 2001 >> From: Ricardo Wurmus >> Date: Tue, 22 Aug 2017 12:59:48 +0200 >> Subject: [PATCH] gnu: r-minimal: Do not compress serialized files. >> >> * gnu/packages/statistics.scm (r-minimal)[arguments]: Replace build phase >> "patch-which" with "do-not-compress-serialized-files". >> [propagated-inputs]: Move "which" from here... >> [inputs]: ...to here. > > [...] > >> (modify-phases %standard-phases >> ;; FIXME: see bug #28157. >> - (add-before 'configure 'patch-which >> + (add-before 'configure 'do-not-compress-serialized-files >> (lambda* (#:key inputs #:allow-other-keys) >> - (substitute* "src/library/base/R/unix/system.unix.R" >> - (("@WHICH@") "which")) > > Shouldn’t we keep the ‘patch-which’ phase? I don’t think so. I only added this to work around the bug. By default it does the right thing and embeds the full path to “which” (at configure time) in the library. Since the binaries are now uncompressed, the references are visible to Guix, so we should keep the reference instead of just a dangling pointer to “which”, in my opinion. >> + (substitute* "src/library/base/makebasedb.R" >> + (("compress = TRUE") "compress = FALSE")) > > Perhaps move the comment about this bug right above this, so we know why > we don’t compress. Otherwise LGTM! Okay! > Any idea how much extra storage this incurs on disk? The previous “r-minimal”: total: 607.6 MiB The new one: total: 611.2 MiB -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 22 10:33:52 2017 Received: (at 28157-done) by debbugs.gnu.org; 22 Aug 2017 14:33:52 +0000 Received: from localhost ([127.0.0.1]:49691 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dkAFb-0007M7-Sp for submit@debbugs.gnu.org; Tue, 22 Aug 2017 10:33:52 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21086) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dkAFZ-0007Ly-VB for 28157-done@debbugs.gnu.org; Tue, 22 Aug 2017 10:33:50 -0400 Received: from localhost (141.80.245.109 [141.80.245.109]) by mx.zohomail.com with SMTPS id 1503412424090647.2319661514077; Tue, 22 Aug 2017 07:33:44 -0700 (PDT) References: <87valiwkt9.fsf@elephly.net> <877exwc7eh.fsf@gnu.org> <8760dgvu1a.fsf@elephly.net> <87o9r87xhx.fsf@gnu.org> <871so3x3uo.fsf@elephly.net> <878tib4t5n.fsf@gnu.org> <87ziarvgx1.fsf@elephly.net> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#28157: =?utf-8?B?4oCcci1taW5pbWFs4oCd?= retains no reference to =?utf-8?B?4oCcd2hpY2jigJ0=?= In-reply-to: <87ziarvgx1.fsf@elephly.net> 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: Tue, 22 Aug 2017 16:33:41 +0200 Message-ID: <87tw0zvfi2.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28157-done Cc: 28157-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: 1.0 (+) Pushed to master with bd3a184613e20155a8b3e417f00f4d59ff0935e6. Thanks for the assistance! -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Sun Jun 22 11:48:59 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 20 Sep 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