Re: [PATCH] gnu: r: Update to 3.3.1.

[Ricardo Wurmus]

myglc2 <address@hidden> writes:

> Ricardo Wurmus <address@hidden> writes:
>
>> myglc2 <address@hidden> writes:
>>
>>> I imagine that, in the spirit of guix, we also want a user to be able to
>>> "help themself" instead of depending on a 'manager.' This would probably
>>> require an additional R "package manager component" that is usable by a
>>> manager or user. Such a thing would certainly showcase the unique
>>> capabilities of guix.
>>
>> We have importers that generate Guix package expressions from CRAN or
>> Bioconductor.  Taken one step further we might have a transparent
>> wrapper to quickly install any version of a package even if it is not
>> yet part of Guix.
>>
>> This might work like this:
>>
>> * user issues “guix package --install --via cran address@hidden
>>
>> * Guix runs the CRAN importe to recursively generate package expressions
>>   for “gdtools” at the given version.  The package does not have to
>>   exist in Guix yet.  The generated package expressions are cached
>>   somewhere (e.g. ~/.cache/guix/…genomation…).
>>
>> * Guix loads the newly imported package expressions from
>>   ~/.cache/guix/…genomation… and tries to build them.
>>
>> * Optionally, users can take the imported expressions, clean them up and
>>   send them as patches to us :)
>>
>> This obviously depends on the quality of the importers, but I think it
>> wouldn’t take much effort to make this a reality.
>
> Could this approach also support earlier R versions? Reasons one would
> want this:
>
> - one comes back to a project after sebatical. Because new R versions
>   have been installed the analysis gives different results and/or is
>   broken.
>   
> - one needs to re-run an analysis to reproduce a result or to do
>   sensitivity studies.
>
> In such cases it is far preferable, but usually problematic, to
> reconstruct the environment in which the anaysis was run. If guix could
> be used to do this, it would be a compelling argument for adoption in a
> research lab situation.

At the institute where I work and where Guix is deployed we never
upgrade users packages centrally.  Scientists use per-project manifests
to keep a list of packages they want to have installed for their current
work.

After returning from vacation their software is still the same as only
they upgrade things.

We also encourage them to record the git hash of both package
repositories we use (one for Guix upstream and another for our custom
Guix BIMSB repo) at the time they instantiate a manifest.  We provide a
wrapper that essentially just runs “git describe” on the two repos.

Given the manifest and the two git hashes a user can reproduce the exact
same binary state of a profile.  This is more granular than thinking in
terms of version numbers as this captures the complete graph of
dependencies.

>> The main problem with offering magic like this is that it must be
>> reliable or else it would just be frustrating users.
>
> Agreed. But any experienced R user knows that package installation can
> be a drama. So it does not have to be perfect to match or exceed user
> expectaions. If the user's alternatives are ...
>
> 1) wait for sysadmin to do it
>
> 2) give this a shot
>
> ... most users will happily try pushing this button ;-)

This has also been my experience here at the MDC.  Some are already
using the CRAN importer themselves to install packages via Guix that I
haven’t packaged for them yet.  (Admittedly, as bioinformaticians they
are likely more comfortable with the command line than scientists in
other fields.)

~~ Ricardo