[Bioc-devel] HDF5Array failure on windows

Tue, Apr 7, 2020 6:15 AM

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> 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 on behalf of 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

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Best,
Kasper

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[Bioc-devel] HDF5Array failure on windows

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