From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: unbounded variable from `FATAL: kernel too old` ? Date: Wed, 30 May 2018 22:09:43 +0200 Message-ID: <87r2lsq514.fsf@elephly.net> References: 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]:39329) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fO7UI-0007TV-A9 for help-guix@gnu.org; Wed, 30 May 2018 16:14:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fO7Px-00065E-HE for help-guix@gnu.org; Wed, 30 May 2018 16:10:02 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21045) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fO7Px-000640-5T for help-guix@gnu.org; Wed, 30 May 2018 16:09:57 -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, > I am installing the rnaseq Pigx pipeline from > https://github.com/BIMSBbioinfo/pigx/tree/master/pipelines/rnaseq Oh, nice! > I miss something with the Guix installation. > > `guix environment -l guix.scm` fails because of these unbounded variables: > - fastqc > - salmon > - ghc-pandoc-1 > - ghc-pandoc-citeproc-with-pandoc-1 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).) Note that you can also install the =E2=80=9Cpigx-rnaseq=E2=80=9D or =E2=80= =9Cpigx=E2=80=9D packages with the latest version of Guix; you don=E2=80=99t need to build the pipeline yourself. > Then, I have tried `guix pull`, which leads to: > > building path(s) `/gnu/store/7mw3mxnb5py6g2q6qaqf5mbaqxwr0jz3-perl-5.26.1' > FATAL: kernel too old > > I am not sure what does it mean ? > > (`uname -r` is 3.0.80-0.7-default) It means that your kernel is too old to work with the current version of the GNU C library (glibc). We applied some patches to the C library to ensure that it will work with the particular kernel that comes with RHEL 6 (i.e. a heavily modified kernel that self-reports its version as 2.6.32). The patched glibc package is not yet available in the master branch; it is currently only available in the =E2=80=9Ccore-updates=E2=80= =9D branch, which is due to be merged in the next few days. 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? I=E2=80=99m afraid there=E2=80=99s no easy way to convince the C library th= at your kernel is compatible, because it=E2=80=99s very likely that it isn=E2=80=99= t if it wasn=E2=80=99t heavily patched. -- Ricardo