From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id YI61FWahZWEWGQAAgWs5BA (envelope-from ) for ; Tue, 12 Oct 2021 16:53:26 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id qL1bEWahZWEiLgAA1q6Kng (envelope-from ) for ; Tue, 12 Oct 2021 14:53:26 +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 E96E9385FC for ; Tue, 12 Oct 2021 16:53:25 +0200 (CEST) Received: from localhost ([::1]:40524 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1maJ9h-0007jB-0i for larch@yhetil.org; Tue, 12 Oct 2021 10:53:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:39386) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1maJ9L-0006z1-EK for guix-patches@gnu.org; Tue, 12 Oct 2021 10:53:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:35529) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1maJ9L-0001y0-5T for guix-patches@gnu.org; Tue, 12 Oct 2021 10:53:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1maJ9L-0004nU-4l for guix-patches@gnu.org; Tue, 12 Oct 2021 10:53:03 -0400 Subject: bug#50813: [PATCH] gnu: python-pandas: Update to 1.3.3. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-To: guix-patches@gnu.org Resent-Date: Tue, 12 Oct 2021 14:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: cc-closed 50813 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Felix Gruber Cc: 50813-done@debbugs.gnu.org Mail-Followup-To: 50813@debbugs.gnu.org, ludo@gnu.org, felgru@posteo.net Received: via spool by 50813-done@debbugs.gnu.org id=D50813.163405034518252 (code D ref 50813); Tue, 12 Oct 2021 14:53:02 +0000 Received: (at 50813-done) by debbugs.gnu.org; 12 Oct 2021 14:52:25 +0000 Received: from localhost ([127.0.0.1]:47031 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1maJ8i-0004kF-OB for submit@debbugs.gnu.org; Tue, 12 Oct 2021 10:52:25 -0400 Received: from eggs.gnu.org ([209.51.188.92]:37300) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1maJ8g-0004jn-L8 for 50813-done@debbugs.gnu.org; Tue, 12 Oct 2021 10:52:23 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:43484) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1maJ8a-0001RO-3x; Tue, 12 Oct 2021 10:52:16 -0400 Received: from [193.50.110.91] (port=34622 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1maJ8Z-0003Et-Qr; Tue, 12 Oct 2021 10:52:16 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <87zgrldwzk.fsf@gnu.org> <20211010150434.1966-1-felgru@posteo.net> Date: Tue, 12 Oct 2021 16:52:13 +0200 In-Reply-To: <20211010150434.1966-1-felgru@posteo.net> (Felix Gruber's message of "Sun, 10 Oct 2021 15:04:28 +0000") Message-ID: <87lf2yuwgy.fsf_-_@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1634050406; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-to: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post; bh=WegoapWIJHKPKoiNDSpA/eOU0wOGhkQIaIHgHEp/xEc=; b=iwerFVab5bNvqJohoAnAd7YnhAU2gk80U/RabuD426HWwkEAqZSYWEXK/hfB4gtwNoOH4l 97E3a32nMuZudynYGwMLepPdOcy75tIzFq2xz4alGkr5kXDVOVj16DVOhpFTdVUnqaIjY0 +X6LHZOTRB9vu4C90+Tqkh+XmjHwXOc5ud7Xl1pZaqu5c+NSpW4+gpUTg2L5gzuUYwuVZQ Ph7tCag08IJD5drHumIhfpCcvZOKW1MBozhwB1w4PZa0i4Db/t7t6h6vku4pUdYP/ueYLc SvB77AJo7KZQlzdfohKatClvwA3OjFFyjpCGJcQGsUo5GetQByhjrtHJtwh82g== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1634050406; a=rsa-sha256; cv=none; b=oj2aX8FcUAUsjQd9ZtQf3d/0Pc860UAy1mJNqiQo/3fThjZ2JatGkvQsQob2mBuuPHBLR5 EU3erla7Hessc7PnTkdCsHzRxvSabvo4nzzpM6sQxk6crA845kUL0JhIfZF3Yj38ub9s+n PAzQIEIq2Q4J9OO005Mj9RnvyMeh5olqMpf9UzC58ds1PVPTu7GCZH8pPOgyNZVHBaUoT1 olR75w8zrvwApwXl0J1f9SopA78fa/k8iRaumITaRQzpKbcrITuzUpFw6QMyqRYq1N+HF0 cf7XCa3H4h5NAuAp6HfXKs4Rzb2ggdvgDFdVG1YTl3UZSpUk2A2ggwANjgi+8A== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: -2.91 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: E96E9385FC X-Spam-Score: -2.91 X-Migadu-Scanner: scn0.migadu.com X-TUID: UVat5RFchMDX Hi Felix, Felix Gruber skribis: > On 10/7/21 11:07 AM, Ludovic Court=C3=A8s wrote: >>=20 >> Felix Gruber skribis: >>=20 >>> * gnu/packages/python-science.scm (python-pandas): Update to 1.3.3. >>=20 >> The upgrade appears to cause build failures for python-dask and >> pigx-rnaseq (via snakemake) among other things. >>=20 >> Could you take a look? > > I could not reproduce the build failure in pigx-rnaseq. For python-dask > the build failure could be fixed by upgrading it to 2021.9.1, whose > changelog mentioned that they've deactivated a failing test when > building against Pandas >=3D 1.3.3. After updating dask, its dependent > packages python-distributed and python-eliot failed to build. I've > fixed both by updating them to their latest releases and disabling > failing tests. > I've also took the oppurtunity to update the synapse package which was > the only package depending on python-eliot. Neat. >> For the record, I tried to build everything reported by =E2=80=98guix re= fresh -l >> python-pandas=E2=80=99 though some of them (ocaml4.07-re, etc.) would al= ready >> fail to build before the upgrade. > > Of the remaining packages reported by `guix refresh -l python-pandas`, > I've identified the following packages with build failures: > > * clipper@2.0 > sometimes fails due to nondeterministic test > `test_get_FDR_cutoff_mean`. The docstring of this test already says > "Difficult to test because of random sampling" followed by a TODO. > I've thus deactivated this test, to make it build deterministically. > * pplacer@1.1.alpha19 > already failed on master due to unbuildable ocaml4.07-re@1.10.3. > * python-scikit-rebate@0.6 > Already failed on master in test `skrebate`: > ModuleNotFoundError: No module named 'sklearn.externals.joblib' > (A guix refresh -u python-scikit-rebate would update it to 0.62 which > was buildable, but this version seemed to come without any tests, so > I'm not sure if this is the right solution.) > * orange@3.28.0 > Already failed to build on mater, because its dependency > python-orange-canvas-core. > I've looked into updating both to their latest version, but that > would require updating python-pygments to >=3D 2.8.0 which would entail > rebuilding 561 dependent packages. > * imp@2.13.0 > I was running out of memory while building imp, which in the end > killed the build process. It seems that my 8GB of RAM are not > sufficient to build imp, so I cannot tell if the update of > python-pandas might break imp. > * tadbit@1.0.1 > depends on imp, so I couldn't build it either. > > I've prepared patches for those packages that I was able to fix. Awesome. > gnu: python-pandas: Update to 1.3.3. > gnu: python-dask: Update to 2021.9.1. > gnu: python-distributed: Update to 2021.09.1. > gnu: python-eliot: Update to 1.13.0. > gnu: synapse: Update to 1.44.0. > gnu: clipper: Disable non-deterministic test. python-dask and pigx-rnaseq build fine for me with this patch series, along with everything in between. Applied, thank you! Ludo=E2=80=99.