[NMF-user] Loading NMF fails when in a container

[Renaud Gaujoux]

Hi,

this code is executed when querying the number of available cores on the
machine.
It uses the result from `parallel::detectCores(all.tests = isOpenBSD)`,
where `isOpenBSD=TRUE` on Open BSD hosts.
Can you please submit an issue on Github for this?
Thanks.

Bests,
Renaud



Renaud Gaujoux, PhD
Systems Immunology - Technion, Haifa, Israel


On 30 November 2016 at 15:39, Roel Janssen <roel at gnu.org> wrote:

> Hello there.
>
> First of all, thanks for creating this package.  It's really useful.
> I've been trying to confine run-time environments in a container (so the
> program only has access to a subset of the operating system).
>
> When loading NMF from inside a container, it fails and I don't know what
> I'm missing.  Here's the output from inside the container:
>
> ---------------------------------- BEGIN ------------------------------
> ----
> user at container ~# R
>
> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > library(NMF)
> Loading required package: pkgmaker
> Loading required package: registry
>
> Attaching package: 'pkgmaker'
>
> The following object is masked from 'package:base':
>
>     isNamespaceLoaded
>
> Loading required package: rngtools
> Loading required package: cluster
> sh: wc: command not found
> Error : .onAttach failed in attachNamespace() for 'NMF', details:
>   call: if (n > 2) n <- n - 1L
>   error: missing value where TRUE/FALSE needed
> Error: package or namespace load failed for 'NMF'
> >
> ----------------------------------- END ------------------------------
> -----
>
> I couldn't find 'if (n > 2) n <- n - 1L' in the source code, so I am
> clueless on what goes wrong here.
>
> Any ideas?
>
> Kind regards,
> Roel Janssen
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