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 Hervé Pagès <hpa...@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-boun...@r-project.org on behalf of kasperdanielhan...@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]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> >
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> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=pNn2sHW_Vo7GJjsEgdNz2QJq4GrASIW3z6QSRefcLkY&s=28DlcVps0EVU-QaF8utnvHUFuj1DpJIZrrXrlPqIb28&e=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
Best,
Kasper
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