From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: unbounded variable from `FATAL: kernel too old` ? Date: Thu, 31 May 2018 13:57:07 +0200 Message-ID: <87bmcwox64.fsf@elephly.net> References: <87r2lsq514.fsf@elephly.net> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35096) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fOMCr-000263-3J for help-guix@gnu.org; Thu, 31 May 2018 07:57:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fOMCn-0002rJ-6a for help-guix@gnu.org; Thu, 31 May 2018 07:57:25 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21044) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fOMCm-0002qg-Te for help-guix@gnu.org; Thu, 31 May 2018 07:57:21 -0400 In-reply-to: List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: help-guix-bounces+gcggh-help-guix=m.gmane.org@gnu.org Sender: "Help-Guix" To: zimoun Cc: help-guix@gnu.org Hi again, >>> I am installing the rnaseq Pigx pipeline from >>> https://github.com/BIMSBbioinfo/pigx/tree/master/pipelines/rnaseq >> >> Oh, nice! > > Thank you to share !! > And nice paper ! :-) Thanks :) > Do you plan to implement a version with the GWL ? I=E2=80=99m thinking about it. There is no current plan to switch to somet= hing else from Snakemake, but once the pipelines have stabilised I=E2=80=99d lik= e to explore ways to simplify them. One of the changes might be to remove extraneous dependencies (e.g. fastqc =E2=80=93> fastq to cut out Java), or = to explore if we can simplify the workflow rules, maybe even to cut out Snakemake completely. Currently, Snakemake makes a couple of annoying workarounds necessary (like linking Rscript to ./pigx_temp/bin and putting that on the PATH, or to copy scripts to a writable location, or to use =E2=80=9Cshell=E2=80= =9D instead of the more convenient =E2=80=9Cscript=E2=80=9D rules=E2=80=A6), which I=E2=80= =99d love to get rid of. The GWL may need to acquire a few more changes before I can propose it as a viable alternative for the team. >> These variables are defined in Guix since quite some time, so you are >> probably using a rather old version of Guix. (The first two are defined >> in (gnu packages bioinformatics), the latter two in (gnu packages >> haskell).) > > `guix --version` reports 0.14.0. We haven=E2=80=99t made a new release in a while. I hope we can make a new one soon. In general you should be running =E2=80=9Cguix pull=E2=80=9D on = a regular basis. > But if the kernel is too old, then somehow the install is not really > complete. Right ? Unfortunately, this is a wart in software management with the kernel Linux. The big kernel binary is not part of the software dependency graph. We assume that it is available (and compatible) at runtime. Usually this is fine. Unfortunately, there are some old kernels that are no longer supported by the kernel developers and thus no longer supported by the glibc developers, who provide the interface that almost all applications use to talk to the kernel. You cannot upgrade the kernel with just Guix; you=E2=80=99d have to boot a system with that kernel. The kernel interface is pretty large, so it is very unfortunate that we cannot treat the kernel like any other dependency. I would think that this would be a smaller problem in a system like the Hurd. >> 3.0 is just a tad too old for the C library. What system is this? Is >> this SLES from mid 2013? Are you able to upgrade to at least Linux 3.10 >> or install the RHEL 6 kernel, which is known to work? > > Yes, it is an old Suse. > My ideas was to be able to fetch up-to-date softwares without > modifying the current configuration (lazy sysadmin's work ;-) Unfortunately, you=E2=80=99ll need a supported kernel version. 3.10 is the minimum for the current glibc. Installing a recent variant of the GNU system (e.g. with a recent Debian or GuixSD) would be a good idea. -- Ricardo