[Bioc-devel] mosbi package: Suggested dependency not available

[Hervé Pagès]

Hi Tim,

runibic has a compilation error on Mac because its native code uses 
OpenMP. However package code should not use OpenMP on Mac (see 
https://stat.ethz.ch/pipermail/r-sig-mac/2019-June/012995.html).

I just marked runibic as unsupported on Mac.

It seems that mosbi only uses runibic in one function, 
mosbi::run_unibic(), but that function is never called (the only place 
where I see a call to it is in the example section of its man page but 
the call is commented out). So the only reason that 'R CMD check' fails 
on Mac is because, by default, 'R CMD check' wants all the deps, even 
the suggested ones (i.e. soft deps), to be installed. To prevent this, I 
added a .BBSoptions file to mosbi, with the following line in it:

   CHECKprepend.mac: _R_CHECK_FORCE_SUGGESTS_=0

See for example the build report for piano 
https://bioconductor.org/checkResults/3.14/bioc-LATEST/piano/merida1-checksrc.html
for the effect that this will have on the exact command used during CHECK.

Cheers,
H.


On 21/10/2021 06:06, Kern, Lori wrote:
> Yes you will be fine. It looks like runibic is failing possibly of a missing dependency on our end and we will investigate.  Once the package builds your package should also build correctly.
> 
> 
> Cheers
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Tim Daniel Rose <tim.rose using wzw.tum.de>
> Sent: Thursday, October 21, 2021 9:03 AM
> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: [Bioc-devel] mosbi package: Suggested dependency not available
> 
> Hi everyone,
> 
> My new package mosbi
> (https://bioconductor.org/packages/devel/bioc/html/mosbi.html) gets a
> MacOS build 'ERROR', because a suggested dependency 'runibic' is not
> available for that platform.
> 
> The reviewers stated on github
> (https://secure-web.cisco.com/14eSzrEiAByl2rDPyDqX7C6ssESP9c7weoJHn1WbC4-92uBIuqNNPKwxibQdqC29ln5mUT8DswyAnmxgVprBPBgce_IfGc99QCllfD0NtVv_WcxcB4gLzIqjV8OIdaFeayLxT2e4SPC63XWfMCFjIjHhDfxs6_l4dA1LyUtVWMFBZPFikPZsUwBQ5AbSneNpm3ZgSugHP8xkrf2F-o1e725NfvIyFFKdRIk4lAQXie3mgLAsgX84leu4uiWSSdRzTClVu2kAWkHwDUD34pJlRs2tKgBDo7MC8CuhKL62uKugxJEQyVCHDBpYWtbZv0THZ/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2252) that it
> should be okay, but they could not reproduce the error locally.
> 
> On the release schedule site
> (https://bioconductor.org/developers/release-schedule/) it says, that
> packages need to pass builds and checks without errors until tomorrow.
> 
> I want to check here again, if it is okay like this or if I need to take
> further action.
> 
> Best,
> Tim
> 
> --
> Tim Daniel Rose, MSc
> 
> PhD candidate at
> Junior Research Group LipiTUM
> Chair of Experimental Bioinformatics
> TUM School of Life Sciences
> Technical University of Munich (TUM)
> 
> Maximus-von-Imhof-Forum 3
> 85354 Freising-Weihenstephan
> Germany
> 
> mail: tim.rose using wzw.tum.de
> web: www.lipitum.de<http://www.lipitum.de>
> 
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com