From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms4r.migadu.com with LMTPS id qC9+IjJCumOLIwAATbCpxg (envelope-from ); Sun, 08 Jan 2023 05:10:26 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id +GnlITJCumMUOwEA9RJhRA (envelope-from ); Sun, 08 Jan 2023 05:10:26 +0100 Received: from chaos.caltech.edu (chaos.caltech.edu [131.215.34.119]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-256) server-signature RSA-PSS (2048 bits) server-digest SHA256) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 28EDFF18D; Sun, 8 Jan 2023 05:10:23 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=ghic.org; s=dkim_rsa_2048_202210; h=MIME-Version:Content-Transfer-Encoding:Content-Type :References:In-Reply-To:Date:Cc:To:From:Subject:Message-ID:Sender:Reply-To: Content-ID:Content-Description:Resent-Date:Resent-From:Resent-Sender: Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=N06UlMG5zIA8Bii+KsvB8m9BmoFszRw0JvNO6+Qytdk=; b=UaFF5DDghxYw+WV71ZYC9rlUR8 G9pgcGAdlBuv7d3b92YASxGm+L4aRDyolFTy4Yt47rJIIo5BXvqMudkDH8RHMzZML8DKp58xUilOz afkcwir2QtoMRv3HpAcbYv5bsrvqbSCRac7dKZ4a2HmrZrFjMORTMbN94aV1fSFL5o88LQBcswEH8 hnjbWbaySoULgaiZ2JZ3AoeUdwsTrgug3HdGstIUyiK9jMr2GR/HaP6bGQRZBzf+8MoCffKc21o0F VXoqiBu/FI90+5IIKUrWECj3BEDMnuijm0jh0GmTWly/Mw/kfQMxDkAAG0K0WhLleX90r5ZbkX8fl QOmcI+ZQ==; Received: from [2600:1700:5d80:ad60:2a05:d6da:f4d7:19b1] by chaos.caltech.edu with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.94.2) (envelope-from ) id 1pEN0m-0003Ra-Hj; Sat, 07 Jan 2023 20:10:20 -0800 Message-ID: <336d19155aed2cffbbc289720b995f73bd5a33ce.camel@ghic.org> Subject: Re: snakemake mode test failures with emacs 28.2 on Debian From: Diane Trout To: Kyle Meyer Cc: snakemake-mode@inbox.kyleam.com Date: Sat, 07 Jan 2023 20:10:19 -0800 In-Reply-To: <875ydhkhtc.fsf@kyleam.com> References: <875ydhkhtc.fsf@kyleam.com> Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable User-Agent: Evolution 3.46.2-1 MIME-Version: 1.0 X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Spam-Score: -4.00 X-Migadu-Queue-Id: 28EDFF18D Authentication-Results: aspmx1.migadu.com; none X-Migadu-Scanner: scn1.migadu.com X-Migadu-Spam-Score: -4.00 X-TUID: YrW1YB8w+jBX On Sat, 2023-01-07 at 19:09 -0500, Kyle Meyer wrote: > Diane Trout writes: >=20 > > Hi, > >=20 > > I noticed there's 3 ert test failures running Emacs 28.2 on Debian > > unstable. >=20 > Thanks for reporting. >=20 > With Emacs 28.2 and snakemake 7.7.0 from Guix, the tests pass on my > end. > It looks like Debian unstable currently has snakemake 7.12.1-1.=C2=A0 My > guess is that these failures are triggered by a snakemake change. >=20 > I'll try to look into that within the next couple of days. I discovered the snakemake ert tests run on my Debian testing system but fail in the unstable package build environment. I read through the snakemake.el code and figured out how it was calling the snakemake executable. I found the problem, and it's not related to snakemake-mode, it looks like snakemake executable has an incompatibility with python3.11. Upstream's solution is here and involves using a more recently updated depedency. https://github.com/snakemake/snakemake/issues/1952 $ python3.11 /usr/bin/snakemake --dryrun aa.out Building DAG of jobs... Traceback (most recent call last): File "/usr/lib/python3/dist-packages/snakemake/__init__.py", line 730, in snakemake success =3D workflow.execute( ^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/snakemake/workflow.py", line 942, in execute self.scheduler =3D JobScheduler( ^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/snakemake/scheduler.py", line 105, in __init__ from ratelimiter import RateLimiter File "/usr/lib/python3/dist-packages/ratelimiter.py", line 36, in class RateLimiter(object): File "/usr/lib/python3/dist-packages/ratelimiter.py", line 127, in RateLimiter __aexit__ =3D asyncio.coroutine(__exit__) ^^^^^^^^^^^^^^^^^ AttributeError: module 'asyncio' has no attribute 'coroutine' $ python3.10 -Wd /usr/bin/snakemake --dryrun aa.out Building DAG of jobs... /usr/lib/python3/dist-packages/ratelimiter.py:127: DeprecationWarning: "@coroutine" decorator is deprecated since Python 3.8, use "async def" instead __aexit__ =3D asyncio.coroutine(__exit__) Job stats: job count min threads max threads ----- ------- ------------- ------------- aa 1 1 1 total 1 1 1 [Sat Jan 7 19:56:59 2023] rule aa: output: aa.out jobid: 0 reason: Missing output files: aa.out resources: tmpdir=3D/tmp Job stats: job count min threads max threads ----- ------- ------------- ------------- aa 1 1 1 total 1 1 1 Reasons: (check individual jobs above for details) missing output files: aa This was a dry-run (flag -n). The order of jobs does not reflect the order of execution. /usr/lib/python3.10/tempfile.py:999: ResourceWarning: Implicitly cleaning up _warnings.warn(warn_message, ResourceWarning)