On 4/7/20 06:15, Kasper Daniel Hansen wrote:
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’
tss tss... naughty!
That might be relevant in light
For what it's worth, I have been getting seemingly the same error from
HDF5Array, only on windows, on the package builder:
https://master.bioconductor.org/checkResults/3.11/bioc-LATEST/MAST/tokay2-buildsrc.html
I have been hoping it will magically go away, as I do not have access to any
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 Hervé Pagès
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
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
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
whi
