From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id ULWPLhAzqGDPRQEAgWs5BA (envelope-from ) for ; Sat, 22 May 2021 00:24:16 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id EI5VKhAzqGBmCgAA1q6Kng (envelope-from ) for ; Fri, 21 May 2021 22:24:16 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 34D851B584 for ; Sat, 22 May 2021 00:24:16 +0200 (CEST) Received: from localhost ([::1]:34906 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkDZ0-00012l-9S for larch@yhetil.org; Fri, 21 May 2021 18:24:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50854) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkDYo-00012V-40 for bug-guix@gnu.org; Fri, 21 May 2021 18:24:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54673) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkDYn-0003Uv-T7 for bug-guix@gnu.org; Fri, 21 May 2021 18:24:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkDYn-0007hI-OQ for bug-guix@gnu.org; Fri, 21 May 2021 18:24:01 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#48576: R: .libPaths dereferences symbolic links; requires restart after "guix install STUFF" Resent-From: Maxime Devos Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Fri, 21 May 2021 22:24:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 48576 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 48576@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.162163579929534 (code B ref -1); Fri, 21 May 2021 22:24:01 +0000 Received: (at submit) by debbugs.gnu.org; 21 May 2021 22:23:19 +0000 Received: from localhost ([127.0.0.1]:37986 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkDY7-0007gH-He for submit@debbugs.gnu.org; Fri, 21 May 2021 18:23:19 -0400 Received: from lists.gnu.org ([209.51.188.17]:50640) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkDY4-0007g9-Ki for submit@debbugs.gnu.org; Fri, 21 May 2021 18:23:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50796) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkDY4-00010V-Eg for bug-guix@gnu.org; Fri, 21 May 2021 18:23:16 -0400 Received: from laurent.telenet-ops.be ([2a02:1800:110:4::f00:19]:37844) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkDY2-0003Rw-1D for bug-guix@gnu.org; Fri, 21 May 2021 18:23:16 -0400 Received: from ptr-bvsjgyjmffd7q9timvx.18120a2.ip6.access.telenet.be ([IPv6:2a02:1811:8c09:9d00:aaf1:9810:a0b8:a55d]) by laurent.telenet-ops.be with bizsmtp id 7aP72500H0mfAB401aP7W9; Sat, 22 May 2021 00:23:07 +0200 Message-ID: From: Maxime Devos Date: Sat, 22 May 2021 00:22:56 +0200 Content-Type: multipart/signed; micalg="pgp-sha512"; protocol="application/pgp-signature"; boundary="=-NYgOiLnIyAAyKASeBxhE" User-Agent: Evolution 3.34.2 MIME-Version: 1.0 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r21; t=1621635787; bh=ltdno/RiX9Mn/SbqCnbbBEZJFXBrrQx24qqkgH8LlTQ=; h=Subject:From:To:Date; b=vVuvFjRcd7BBtoeU64JsSz5UBSESR+gtCe6Vn6tHkKF/o6TSmAIaqBzDIEXzUQfql bmCZBHfdHBcttnMdx1niu+APSAvLul57MJqhvcTujG5V9FhgAhXyrWlwbtNKr6wQJx sfsnW9vCrBsuX7Bl7LPcWccZn0Ow49RJL7NqSXw3ykb0z9DR2VPPP9xb3y+v88Xwov z2K72K7x6br1BUolZWed4cIl93kUfFVJF11yIzYmWRRawg/2JrLc6n0hsXr/sQqh+0 oOTJ4VT5qU8DSPuNbEOiOlxlR8sMlzfC8NzkxKwV3GD+UwgGgcCZTBWAxk5tsyBUpd HuPFpb6Pbbogw== Received-SPF: pass client-ip=2a02:1800:110:4::f00:19; envelope-from=maximedevos@telenet.be; helo=laurent.telenet-ops.be 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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, 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: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1621635856; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:list-id:list-help:list-unsubscribe:list-subscribe: list-post:dkim-signature; bh=ltdno/RiX9Mn/SbqCnbbBEZJFXBrrQx24qqkgH8LlTQ=; b=uEeIdtohJ9s9vMJJG/BRpXMVY75Kax5300uTinQhrl5iY27LOwf6LLi0R1bXILNT+hLFpi MdYNS/9H5VCs/BEQGF0f2bxvIx3jm9Zb5KxTJyoVFwDuOHS4MGeoAz0LH3ehWfA1QTfPAK eAc1uPRBY+mdDuIjdEKqM6jyarhMct2sL3I6qcd1/iX5w6br/HDShqyl/QiGRWN2o19DqQ 9dzOXaYTbEGrk8Rcq6NGeGQoMr5o8i7Wn+yzMns8MKDvf9LZXOIWs8LuHIdwxYa0RhdhW/ USOqJLITieWBF4IpylJvSdz2M8UaNwrdNNpl+O2NF1gPTS8jPC9BlYusK53tdA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1621635856; a=rsa-sha256; cv=none; b=LPw9Mq9FLpRN0CNuGk6aRusEFj3vtrnt3HZTh0+ylJUEXjkdsnsWCnYTb2bedcXD3Tbjoy 3I+6dPn8u6wlvA1MKKfuZzl+3yPut326MQluVZiTGwQGkagU+maaab4btqosWgv6MwAu3h Q8TctBbSRABswU0fDG9R2VpGZSO17cWpLH1RBPVbKe9lmyvPN/stmHZBv5X+FJ+xYy+5IX vUgSTx94vrB877vVp5UmqeFtpkfkqlVQ5h2Ji7/mY5DYNtdOFUn8V4Ho3HWttnoyunrPpG /1HybcTS+/sZVtl9o7pjEmZfjKKHWX3EhDUNyGz4h9reCuOpGNuRPdahSYwKdQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=telenet.be header.s=r21 header.b=vVuvFjRc; dmarc=fail reason="SPF not aligned (relaxed)" header.from=telenet.be (policy=none); spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Spam-Score: -1.94 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=telenet.be header.s=r21 header.b=vVuvFjRc; dmarc=fail reason="SPF not aligned (relaxed)" header.from=telenet.be (policy=none); spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Queue-Id: 34D851B584 X-Spam-Score: -1.94 X-Migadu-Scanner: scn0.migadu.com X-TUID: YLRDc4l9GvtT --=-NYgOiLnIyAAyKASeBxhE Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Today I started R (from Emacs). I needed mefa::rep.data.frame, so I ran "guix install r-mefa -p ../prof" (actually guix package -p ../prof -m ../manifest.scm, but that shouldn't matter for the purposes of the bug report) (r-mefa is not in the guix repo yet) Now it is installed, I typed in the R prompt: > mefa::rep.data.frame Error in loadNamespace(name) : there is no package called =E2=80=98mefa=E2= =80=99 The solution is to exit the R prompt and restart. Can we do better? It appears the search path is set with .libPaths: > .libPaths function (new)=20 { if (!missing(new)) { new <- Sys.glob(path.expand(new)) paths <- c(new, .Library.site, .Library) paths <- paths[dir.exists(paths)] .lib.loc <<- unique(normalizePath(paths, "/")) } else .lib.loc } > .libPaths() [1] "/gnu/store/5cgx6pkhr300v706sv46gx9ypnwanngw-profile/site-library" = =20 [2] "/gnu/store/6laxfxgjxnisi5fzhvqv82wjrgs7q0md-r-minimal-4.0.4/lib/R/libr= ary" It seems like the symbolic link of ../prof is dereferenced to /gnu/store/5cgx6pkhr300v706sv46gx9ypnwanngw-profile. Promising is the documentation (? base::normalizePath) of base::normalizePa= th: [...] Where the Unix-alike platform supports it attempts to turn paths into absolute paths in their canonical form (no =E2=80=98./=E2=80=99, = =E2=80=98../=E2=80=99 nor **symbolic links**). [...] (emphasis mine) Maybe we make a copy of normalizePath (base:::guix_normalizeLibraryPath?) d= oing the same as base::normalizePath but without dereferencing symbolic links, and adjust .libPaths to use our variant base:::guix_normalizeLibraryPath in= stead of normalizePath? Greetings, Maxime. --=-NYgOiLnIyAAyKASeBxhE Content-Type: application/pgp-signature; name="signature.asc" Content-Description: This is a digitally signed message part Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNATURE----- iI0EABYKADUWIQTB8z7iDFKP233XAR9J4+4iGRcl7gUCYKgywRccbWF4aW1lZGV2 b3NAdGVsZW5ldC5iZQAKCRBJ4+4iGRcl7qwiAP9EjJ3p6Oq/4/7gbK2w7+tfPIhg z5Nmgqr7Whbz7WV6dQEA4L5t/Q2oBg4EUee1ecsbXhFsG4/NfEtJvaOqqMv7sAA= =ePwV -----END PGP SIGNATURE----- --=-NYgOiLnIyAAyKASeBxhE--