From unknown Fri Aug 15 12:53:49 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#59836 <59836@debbugs.gnu.org> To: bug#59836 <59836@debbugs.gnu.org> Subject: Status: [PATCH 0/1] Fix julia-documenter and so many Julia packages Reply-To: bug#59836 <59836@debbugs.gnu.org> Date: Fri, 15 Aug 2025 19:53:49 +0000 retitle 59836 [PATCH 0/1] Fix julia-documenter and so many Julia packages reassign 59836 guix-patches submitter 59836 zimoun severity 59836 normal tag 59836 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 05 10:37:31 2022 Received: (at submit) by debbugs.gnu.org; 5 Dec 2022 15:37:31 +0000 Received: from localhost ([127.0.0.1]:36764 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DX8-0004Vm-UP for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:37:31 -0500 Received: from lists.gnu.org ([209.51.188.17]:58170) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DX7-0004Vg-ER for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:37:29 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p2DX7-0000Sr-95 for guix-patches@gnu.org; Mon, 05 Dec 2022 10:37:29 -0500 Received: from mail-wm1-x334.google.com ([2a00:1450:4864:20::334]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p2DWz-0003Co-Ac for guix-patches@gnu.org; Mon, 05 Dec 2022 10:37:23 -0500 Received: by mail-wm1-x334.google.com with SMTP id n9-20020a05600c3b8900b003d0944dba41so5637826wms.4 for ; Mon, 05 Dec 2022 07:37:18 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=cZALgD7LoeC5RUH2mSiJhLoGN3bRYas27KOEM4MPPOI=; b=UrjuQ0y06NKIY54f6XfD2n/dYX8Gt2BZRWw6ja4mWnz2/cLZTfI+BQsy7xgR0QL/se AUY1qKUt/Sgpq3l8ly4Z6pZrn1F/1PUGWRRQKzuqAwRyFgPDYYrPg6KiOxI2Jbbk4lXJ bkQm/LZOtj4kXm3FYkbBanaMuUq1+Q773G1ofaU0GA6fDYJkvIOqVZ6F39U36Aaxnliy ovDxZIgVnpauMSg0zZIXzz32l3GmajRU6lVxHNwjLmIb3M/acvvrsEH/PH+/wWEQb/Ep bXlSRwFP0aP0VwUrcOOYe3baBwJZZRb2jx0Hog4BXiBE4xWaQLby45QvE01uSQzulAAv PW0w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=cZALgD7LoeC5RUH2mSiJhLoGN3bRYas27KOEM4MPPOI=; b=p8+qEkdoE6xbas4bRz/Xl09oBZaH/QdzQiUNVB5Eb783vi/1tgBgfoMb/BjybpAAoM O+bDYWxFhXRhDBCY1HV3hV8w8oDIrc/86XFAyF8PwN5DqnvZfY/3/jl8kBFW6nHUn5wz xsXxIIBu7Zu80/r6k+FEkyxuFVrx8tx86xnlzp4uiKO3xdLfWVD/YQX7pAFeCNygAt75 ddX+JQMUq/fPDP29axjQJvekboPwQTSB0TFGe6e5XcKYwLPp/6DxwgYCKN6nFf/7R1eN rxLCjeRakj7/Dx/yw3YIfnjDEDM4J75XIsGPWMKuXBo53F4V5Qx/l/OIn6K7aKtD0Um5 xoDA== X-Gm-Message-State: ANoB5pmvRVBRYgSDhLB8SdrNhVoenvBJKE1kKt1tslY5jQox0htPISzT QM5zG3Hg03LlXop5MsWahsFl8IDOuS4= X-Google-Smtp-Source: AA0mqf4xDRSLG1X+fW9IZJ5chB1LYTOQnBwmMe/Y2GhwFN8BZcrraCqBpAHAt2MOsegqE3XpJDJgaA== X-Received: by 2002:a05:600c:3543:b0:3cf:74bb:feb1 with SMTP id i3-20020a05600c354300b003cf74bbfeb1mr58996329wmq.102.1670254637310; Mon, 05 Dec 2022 07:37:17 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id bg9-20020a05600c3c8900b003cf483ee8e0sm23643129wmb.24.2022.12.05.07.37.16 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 Dec 2022 07:37:16 -0800 (PST) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 0/1] Fix julia-documenter and so many Julia packages Date: Mon, 5 Dec 2022 16:37:10 +0100 Message-Id: <20221205153710.10684-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 X-Debbugs-CC: ludo@gnu.org, efraim@flashner.co.il Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::334; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x334.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: zimoun 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: -2.3 (--) Hi, Commit 83ede5a02e1fc531d912eb92eb0a22a4b897997c updating Git from 2.38.0 to 2.38.1 fixes several securtity issues. But it changes the default behaviour of "git submodule", hence breaking the test suite of julia-documenter. This patch backports the fix from upstream. This fix has not been released yet. An update to lastest Julia Documenter implies other updates. I am working on it but it is ~160 patches (from new packages to updates) and it is not ready yet. Therefore, this patch allows to have again all the Julia packages instead of the current: 77.4% substitutes available (243 out of 314). Cheers, simon zimoun (1): gnu: julia-documenter: Fix test suite regression. gnu/packages/julia-xyz.scm | 9 +++++++++ 1 file changed, 9 insertions(+) base-commit: 48329575c87bbee7166eedf10b1699599e67c49d -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 05 10:39:07 2022 Received: (at 59836) by debbugs.gnu.org; 5 Dec 2022 15:39:07 +0000 Received: from localhost ([127.0.0.1]:36787 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DYg-0004Xn-Mm for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:39:06 -0500 Received: from mail-wr1-f50.google.com ([209.85.221.50]:34492) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DYe-0004X6-So for 59836@debbugs.gnu.org; Mon, 05 Dec 2022 10:39:05 -0500 Received: by mail-wr1-f50.google.com with SMTP id o5so19208535wrm.1 for <59836@debbugs.gnu.org>; Mon, 05 Dec 2022 07:39:04 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=lo5nPB94Rwr1QWmQwE3Zgdw/Wp/LRws25b3AiX6BvDE=; b=HOjycNM+FAvyEyKCkkSAHg9JwlZOYMLUDNzMm0O6B1TMlu1u9u++9f+9T9DmRVW72j 9uwu/NDg7CqIaK1+Q5do3y9ijliIeVllp+AZlLK98ic+gtoNatA3r9QhlPlWL+6g4e7p NFK3vgoYPCzpp0NAkJN5ubEJfW2trXXPpVOWamIqAD+XiaL50YI8Pt7/nwIXjtoGQvuS ATHynHbkbEnplmYjfyHL1CSZlslg23iszF9jUiDYJRAHoIpdLZZHQIzCu/nNowf2MaJ9 SA7GUz2mTMbJkRr6aTVzBGXhQ1bSSG+daZbG8ArvED7/DE93JswLXp6pfIXrU/OM1gB1 +k/g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=lo5nPB94Rwr1QWmQwE3Zgdw/Wp/LRws25b3AiX6BvDE=; b=cdChT+VBr1L6WuVibBAgk5lRV8gDHHHE4YILZLIoQ7Evpn7gHbJLWY8oYWUuHOIND8 brk5fuuoJNPbSETaw7NW7fk6B6J2Cj709C55bHelDur7hwwoBvr4BfE6Qq37lyzlCWE0 AtrzqnEdJM/+9EeKvYsWaHiQhspW8DrHx9ye5s81m0/VRTBc2ILkivjojk+HNLfj+UMB L2qUMZMNn+27aDGgyic1lOQiXTtpwIA7N9qy1t8aXda2bUPdrVm5Lj2/QFY4yODHAivt 0QwO08eWpMLbQRt3oVWI0+uvp3qe1bWJf3Nsn8p+o2qI1e5NXdk6iBclkoLzuQmz+c63 Ludw== X-Gm-Message-State: ANoB5pndkMhbf4mW3BlQOYCLudZhMBJvKMmY3A8jmZGWerqs36/WJ91R tUE+QZHktpt+4MxptFJuEI5xXdA0GrU= X-Google-Smtp-Source: AA0mqf6osJvaJDproTPiebBpW3Jj3tVI2kQkHJ4jXo790AGN3LmK1yoia+LFsMLjlrAjloYGvYYmPQ== X-Received: by 2002:a5d:6dd1:0:b0:236:75a8:58d with SMTP id d17-20020a5d6dd1000000b0023675a8058dmr52037936wrz.295.1670254739019; Mon, 05 Dec 2022 07:38:59 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id l41-20020a05600c1d2900b003d1e4f3ac8esm188922wms.33.2022.12.05.07.38.58 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 05 Dec 2022 07:38:58 -0800 (PST) From: zimoun To: 59836@debbugs.gnu.org Subject: [PATCH 1/1] gnu: julia-documenter: Fix test suite regression. Date: Mon, 5 Dec 2022 16:38:51 +0100 Message-Id: <20221205153851.11268-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 59836 Cc: zimoun 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 (-) * gnu/packages/julia-xyz.scm (julia-documenter)[arguments]<#:phases>: Substitute a work around to fix the change of 'git submodule' default behaviour introduced by Git v2.38.1. --- gnu/packages/julia-xyz.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 28c759a5c0..ac6584825b 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1472,6 +1472,15 @@ (define-public julia-documenter (("pip install") (string-append (search-input-file inputs "bin/pip") " install"))))) + (add-after 'link-depot 'fix-test-git-submodule + ;; Git v2.38.1 fixes security issues and changes the default + ;; behaviour of `git submodule`. This substitution is a backport + ;; of the upstream patch, not yet released, fixing the test suite. + ;; https://github.com/JuliaDocs/Documenter.jl/commit/b5a5c65d02d136743e7c18ffebf8baba900484fc + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "test/utilities.jl" + (("submodule add") + "-c protocol.file.allow=always submodule add")))) (add-after 'link-depot 'remove-javascript-downloads (lambda _ (substitute* "src/Writers/HTMLWriter.jl" -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 05 10:58:29 2022 Received: (at 59836-done) by debbugs.gnu.org; 5 Dec 2022 15:58:29 +0000 Received: from localhost ([127.0.0.1]:36890 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DrQ-0004k7-UA for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:58:29 -0500 Received: from eggs.gnu.org ([209.51.188.92]:57586) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DrO-0004k1-UV for 59836-done@debbugs.gnu.org; Mon, 05 Dec 2022 10:58:27 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p2DrJ-00071b-ET; Mon, 05 Dec 2022 10:58:21 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:In-Reply-To:Date:References:Subject:To: From; bh=NE647ujZKm3HoODrPXC7b6HhAdNfbDFaqbU93VWifUw=; b=MKttduJQnWGvQRor6XJc 9xD/2YIGl+8rBOgGLKysYGsjkoOLsy3X4R6ciC/poieRQ0DWN5WfjHOfqhfJIQRYO6l7t6il2/+cL uxACOV2L+j0c7tEaz6GpONfzGiz7xLyMoVIOutIbpkcPcgUHeq0nwgxkT5tkQQEhsfag1/3EpdgU5 1SJjHWWMl/R+ftCX3S+/8Jzu5lM40VsxwzwvbIC/486mQCRXsfZGQixWmLMBXzIknL3wIjySgZD99 EgxfVBfkxJyY58mIqecyC0j4P0l1cIzSlCayeHyDS7i82qs4vQJv3bMpPckUpV8xxSc5S9NfDevnd SqkWjmIxApKLzQ==; Received: from [2001:660:6102:320:e120:2c8f:8909:cdfe] (helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p2DrJ-0000Aa-17; Mon, 05 Dec 2022 10:58:21 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: zimoun Subject: Re: bug#59836: [PATCH 0/1] Fix julia-documenter and so many Julia packages References: <20221205153710.10684-1-zimon.toutoune@gmail.com> <20221205153851.11268-1-zimon.toutoune@gmail.com> Date: Mon, 05 Dec 2022 16:58:19 +0100 In-Reply-To: <20221205153851.11268-1-zimon.toutoune@gmail.com> (zimoun's message of "Mon, 5 Dec 2022 16:38:51 +0100") Message-ID: <87ilipq1us.fsf_-_@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 59836-done Cc: 59836-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: -3.3 (---) Hi, zimoun skribis: > * gnu/packages/julia-xyz.scm (julia-documenter)[arguments]<#:phases>: > Substitute a work around to fix the change of 'git submodule' default > behaviour introduced by Git v2.38.1. Well done; applied, thanks! Ludo=E2=80=99. From unknown Fri Aug 15 12:53:49 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 03 Jan 2023 12:24:08 +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