[Bioc-devel] HDF5Array failure on windows

Thanks for the two pointers.

Herve: we are using a number of unexpected functions from HDF5Array:
 ? ?HDF5Array:::.create_dir?,??HDF5Array:::.replace_dir?, 
?HDF5Array:::.shorten_assay2h5_links?

That might be relevant in light of that specific test error.

On Mon, Apr 6, 2020 at 1:13 PM Herv? Pag?s <hpages at fredhutch.org 
<mailto:hpages at fredhutch.org>> wrote:

    Hi Kasper, Martin,

    About bsseq's timeout: An important recent change to
    DelayedArray/HDF5Array is that, starting with DelayedArray 0.13.8,
    nothing in these packages uses parallel evaluation **by default**.
    Concretely this means that getAutoBPPARAM() now returns NULL on a fresh
    session instead of one of the parallelization backends defined in
    BiocParallel (e.g. MulticoreParam on Linux/Mac, SnowParam on Windows).
    This could slow down some code in bsseq or other packages that were
    benefiting from the automatic parallel evaluation. Now it's the
    responsibility of the user to set the parallelization backend (with
    setAutoBPPARAM) if they wish things like matrix multiplication,
    rowsum()
    or rowSums() use parallel evaluation again.

    Also BiocParallel has been moved from Depends to Suggests.

    About bsseq error on Windows: That seems indeed to be related to the
    HDF5Array error on the same platform. The unit tests in bsseq and
    HDF5Array both fail with the same error ("HDF5 dataset
    './.HDF5ArrayAUTO00014_dimnames/2' does not exist"). I'll take a look.
    What's puzzling is that we see this error on both Windows archs for
    bsseq (i.e. on 64-bit and 32-bit) while we only see it on 64-bit
    Windows
    for HDF5Array. This suggests something nasty and hard to troubleshoot..
    sigh!

    Cheers,
    H.


    On 4/6/20 06:59, Martin Morgan wrote:

     > 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://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_r-2Drelease_R-2Dexts.html-23Cross-5F002dreferences&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=pNn2sHW_Vo7GJjsEgdNz2QJq4GrASIW3z6QSRefcLkY&s=2r59fOKiJQ_AJBSaOXUDB1j3dD1txuMA-cJzCnnIE9k&e= 
    . 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 at r-project.org
    <mailto:bioc-devel-bounces at r-project.org> on behalf of
    kasperdanielhansen at gmail.com <mailto:kasperdanielhansen at 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
     >
     >? ? ? ?[[alternative HTML version deleted]]
     >
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    -- 
    Herv? Pag?s

    Program in Computational Biology
    Division of Public Health Sciences
    Fred Hutchinson Cancer Research Center
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-- 
Best,
Kasper