From: Ricardo Wurmus <rekado@elephly.net>
To: zimoun <zimon.toutoune@gmail.com>
Cc: help-guix@gnu.org
Subject: Re: unbounded variable from `FATAL: kernel too old` ?
Date: Wed, 30 May 2018 22:09:43 +0200 [thread overview]
Message-ID: <87r2lsq514.fsf@elephly.net> (raw)
In-Reply-To: <CAJ3okZ1ktvvLJsf4PwUeJYL9r2W08xmjw-ixCcWcN3CXNtuZpg@mail.gmail.com>
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 “pigx-rnaseq” or “pigx” packages with
the latest version of Guix; you don’t 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 “core-updates” 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’m afraid there’s no easy way to convince the C library that your
kernel is compatible, because it’s very likely that it isn’t if it
wasn’t heavily patched.
--
Ricardo
next prev parent reply other threads:[~2018-05-30 20:14 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-05-30 18:47 unbounded variable from `FATAL: kernel too old` ? zimoun
2018-05-30 20:09 ` Ricardo Wurmus [this message]
2018-05-31 9:59 ` zimoun
2018-05-31 11:57 ` Ricardo Wurmus
2018-05-31 16:39 ` zimoun
2018-05-31 17:30 ` Ricardo Wurmus
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