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-boun...@r-project.org> on behalf of Tim Daniel Rose
<tim.r...@wzw.tum.de>
Sent: Thursday, October 21, 2021 9:03 AM
To: bioc-devel@r-project.org <bioc-devel@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.r...@wzw.tum.de
web: www.lipitum.de<http://www.lipitum.de>
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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