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
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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
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Fax: (206) 667-1319
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