[Bioc-devel] [External] Memory error from sesame build

[Zhou, Wanding]

Thanks for the input Herve. I saw your post but can you help me confirm that mine is on the 32-bit windows since it says mingw32 (64-bit)?

Windows Server 2012 R2 Standard / x64

* using platform: x86_64-w64-mingw32 (64-bit)


http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-checksrc.html

Does that mean all the examples added together cannot use over 3G memory? I still don't think I am using that much but I will remove some examples and see that solves the problem

Very best,

Wanding


On Nov 29, 2021, at 12:15 PM, Hervé Pagès <hpages.on.github using gmail.com<mailto:hpages.on.github using gmail.com>> wrote:

Hi Wanding,

A process cannot allocate more than 3Gb of memory on 32-bit Windows. See my other post on this list for more information about this:

 https://stat.ethz.ch/pipermail/bioc-devel/2021-November/018663.html

Cheers,
H.


On 22/11/2021 05:17, Zhou, Wanding wrote:
Hi,
Recently we are experience some memory issue on both development and release (mostly Windows) that causes the sesame package build to fail. We are trying to address it but it seems to run fine locally on our side.
This is the error on the development branch
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'sesame.Rmd' failed with diagnostics:
C stack usage  7977908 is too close to the limit
And this is the error on the release branch
data = data.frame(estimate=c(runif(10, 0, 10)))
plotLollipop(data)
Error in grid.newpage() :
  'Calloc' could not allocate memory (27541715 of 1 bytes)
Calls: <Anonymous> -> print.ggplot -> grid.newpage
Let me know if you are aware of something or have a clue. Any insight will be super helpful!
Thanks!
Zoom link: https://us02web.zoom.us/j/4248839577
----
Wanding Zhou, Ph.D.
Assistant Professor
Office: CTRB 9050
3501 Civic Center Blvd
Philadelphia, PA 19104
Lab:  https://zhou-lab.github.io/
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Hervé Pagès

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