[Bioc-devel] avoiding circular dependencies between a Data package and a Software package

Michael Lawrence l@wrence@mich@el @ending from gene@com
Sat Oct 6 20:05:33 CEST 2018

I think you're doing the right thing, suggesting the data package from the
software package. This might require some manual intervention on the build
system side to ensure that the software package is installed before passing
full check, so that the data package can be installed/checked and finally
the software package checked. I guess a note about this could be added to
the page at the cited URL.


On Sat, Oct 6, 2018 at 10:42 AM Tim Triche, Jr. <tim.triche using gmail.com>

> Last night I submitted MTseeker and its companion package MTseekerData,
> both festooned with examples that run smoothly and pass BiocCheck.
> HOWEVER! Breaking up the data into a Data package inadvertently seems to
> have created a circular dependency between the Software and Data packages.
> I haven't had to deal with this in the past, and mostly sidestepped it by
> skipping a Depends: entry in Data.
> (cf. https://support.bioconductor.org/p/113711 , which I will update with
> answers from here to try and avoid having other people with the same
> problem bug youse plural)
> The issue seems to be that, since the MTseeker-defined MVRanges and
> MAlignments classes (which, as you might imagine, subclass the VRanges and
> GAlignments classes) hold the data stored in MTseekerData, the examples in
> MTseekerData call the `show` method (and others) on the objects and this
> create issues.  The most bizarre of these complained at installation about
> (sp?) .lazyLoadCacheManager() (I'm having trouble reproducing this exact
> error but it was memorable).  Does this ring a bell for anyone? Is there an
> elegant workaround?
> I can't imagine I'm the first person to have this issue.  I know there are
> also various automagic hooks in BioC to load a package upon discovering a
> data structure that belongs to it (and not before) -- should I be using
> attachNamespace() somehow to side-step this problem?  (Eventually I do want
> to submit BAM files to ExperimentHub for an end-to-end example and unit
> tests, but the more pressing issue here was BiocCheck).
> Any feedback is much appreciated. It's kind of a drag when all the examples
> and vignettes pass and build, but only with a side-stepping of
> dependencies. That can't possibly be the correct solution, yet I'm at a
> loss to find documentation (which I'm sure exists somewhere) that explains
> how to avoid this (and/or implement the hooks).
> Thank you,
> --t
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list