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

[Zhou, Wanding]

Thank you Tim. That makes sense. It seems only occurring in Windows. Is there a known lower memory limit or stack usage in Windows?

Windows Server 2012 R2 Standard / x64

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

Error: cannot allocate vector of size 6.6 Mb
Execution halted
Error: 'Calloc' could not allocate memory (27514181 of 1 bytes)
Fatal error: error during cleanup

Thanks again,

Wanding

On Nov 27, 2021, at 4:15 PM, Tim Triche, Jr. <tim.triche using gmail.com<mailto:tim.triche using gmail.com>> wrote:

Recursion issue. Make sure some constructor isn’t constructing itself into oblivion. This is a nasty one

--t

On Nov 27, 2021, at 5:48 AM, Zhou, Wanding <Wanding.Zhou using pennmedicine.upenn.edu<mailto:Wanding.Zhou using pennmedicine.upenn.edu>> 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/
Phone (o):  (215) 590-0473

  [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


	[[alternative HTML version deleted]]