Glad you found the culprit.
Actually, the use of data.table::fwrite() seems to cause a memory leak. More
precisely, if I repeatedly run the full exportMethylome example in a terminal,
the memory usage (reported by 'top' in another terminal) grows at a rate of 0.8
Gb per run. I observed this on
Dear Hervé,
thank you (and Martin) for the advice. I was able to locate the culprit: it
was a data.table::fwrite( ) statement, the behaviour of which must have
changed since the last release. I put this example in a NOT RUN block.
Kind regards,
Aaron
Am Mi., 17. Apr. 2019 um 12:41 Uhr
maybe as an aid to debugging this, after running R CMD check on
_1.5.1.tar.gz one can run just the examples with
R -f pkg.Rcheck/pkg-Ex.R
or interactively with something like
R
> source("pkg.Rcheck/pkg-Ex.R", echo = TRUE, max = Inf)
Martin
On 4/17/19, 5:31 AM, "Bioc-devel on behalf of
Hi Aaron,
I used 'top' on merida1 (one of our 2 Mac builders, MacOS El Capitan) to
monitor memory usage of 'R CMD check methimpute_1.5.1.tar.gz' and also observed
a pick at more than 6Gb there, like on my Linux laptop (Ubuntu 16.04 LTS). Note
that memory usage stays relatively low (< 1Gb) for
Dear Hervé,
thank you for your reply and the explanations. I have checked the R CMD
check on my system (MacOS Mojave) and the whole check does not exceed 1Gb
of RAM. I am also surprised why it would need that much, because all the
examples are pretty slim, so even if all objects are kept, I am
Dear bioconductor-devel,
I am trying to fix an "Error: memory exhausted (limit reached?)" error that
arises during Rcheck on tokay2 (Windows Server 2012 R2 Standard / x64) .
The package builds and passes Rcheck just fine on all other hosts. Is this
something I can fix? The function in question is
