[Bioc-devel] unix package in suggest leads to check error

[Alexey Sergushichev]

Hi Herve,

We don't have tests for this part in the package tests (we have separate
integration tests for that), but the full package functionality depends on
bringing up an opencpu server, which uses the unix package to evaluate
HTTP-requests within R environment. The servePhantasus function, which
starts opencpu server, doesn't work properly on a Linux machine without
unix package.

On the other hand, now I'm thinking that "suggests" is not the best way for
that package either, as it's really a proper dependency on linux systems. I
guess we'll just a code to check for the presence of the package in the
corresponding functions.

--
Alexey

On Fri, Apr 19, 2024 at 2:18 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Hi Alex,
> On 4/19/24 09:53, Alexey Sergushichev wrote:
>
> Hi,
>
> Our package "phantasus" requires the "unix" package to properly work on
> *nix systems,
>
> I just tried to run 'R CMD check' on phantasus on my Linux laptop where I
> don't have the unix package installed, and everything went fine. In
> particular all the examples and unit tests passed with no problem. So I'm
> not sure what you mean when you say that the unix package is required for phantasus
> "to properly work".
>
> So unless I'm missing something, I see no reason to list unix in the
> Suggests field of your package.
>
> Best,
>
> H.
>
>  but works well without it on Windows and Mac OS (actually we
> depend on the opencpu package, which requires it). I've tried to put this
> package into suggest field, but now the package failed Bioc checks on
> Windows and Mac (https://bioconductor.org/checkResults/devel/bioc-LATEST/phantasus/palomino3-checksrc.html)
> with the following message:
>
> ```
> * checking package dependencies ... ERROR
> Package suggested but not available: 'unix'
>
> The suggested packages are required for a complete check.
> Checking can be attempted without them by setting the environment
> variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
> ```
>
> Is there any way to keep this package in suggestions and not to fail the
> checks? Or are there any other recommendations for this case?
>
> Best,
> Alexey
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________Bioc-devel using r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core Teamhpages.on.github using gmail.com
>
>

	[[alternative HTML version deleted]]