[Bioc-devel] HDF5Array failure on windows

[Martin Morgan]

Timeouts are often related to parallel evaluation, either competing for resources or underlying limitations in the robustness of the (parallel) code. Something close to best practice is to limit or eliminate parallel evaluation in examples, vignettes, and tests.

Documentation issues are usually related to the use of [] in \link[]{}, as described at https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences . The important point is that the [] information is the NAME OF THE HTML FILE of the documentation module, not the 'name' of the documentation module. The solution (from my perspective) is usually to simply omit the [] and let the R help system resolve the link dynamically (sometimes prompting the user to choose, if there multiple man pages).

Martin Morgan


On 4/6/20, 9:55 AM, "Bioc-devel on behalf of Kasper Daniel Hansen" <bioc-devel-bounces using r-project.org on behalf of kasperdanielhansen using gmail.com> wrote:

    We currently (and for a while) have had various errors in bsseq that seems
    to have come and go. We now have a failure on Windows which is related to
    HDF5. I see that HDF5Array also fails on Windows, which makes me believe
    the error could be upstream. There is also a warning about hep page links
    which HDF5Array has as well. Any comments on this is appreciated.
    
    Perhaps relatedly: we are getting a timeout on linux. On my own OS X setup,
    it completes in a timely fashion. Do we sometimes have unexplained timeouts
    related to HDF5?
    
    -- 
    Best,
    Kasper
    
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