Re: unbounded variable from `FATAL: kernel too old` ?

[Ricardo Wurmus]

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