Thanks Herve. That's super helpful. I will use your trick! Best,
Wanding > On Nov 29, 2021, at 5:51 PM, Hervé Pagès <hpages.on.git...@gmail.com> wrote: > > On 29/11/2021 09:25, Zhou, Wanding wrote: >> 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) > > This shows the Windows arch that R uses by default on Windows. But we use > --force-multiarch when running 'R CMD check' on our Windows builders to force > 'R CMD check' to run all the examples, unit tests, and vignettes in the two > supported Windows archs: 32-bit and 64-bit. > > The error was happening during the following step: > > ** running examples for arch 'i386' > > and not during the following step: > > ** running examples for arch 'x64' > > So yes, this is a Windows 32-bit only error. > >> http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-checksrc.html >> >> <http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-checksrc.html> >> Does that mean all the examples added together cannot use over 3G memory? > > Yes. > >> I still don't think I am using that much but I will remove some examples and >> see that solves the problem > > Here is one way to see how much memory 'R CMD check' consumes when running > the examples: > > 1. Run 'R CMD check' on the package. This collates all the examples in > sesame.Rcheck/sesame-Ex.R. > > 2. Comment out the last line (quit('no')) in sesame.Rcheck/sesame-Ex.R. > > 3. From R do: source("sesame.Rcheck/sesame-Ex.R", echo=TRUE). At the same > time, monitor memory usage in another terminal e.g. by running 'top' on > Linux/macOS. > > 4.Once all the examples have finished, do gc(). > > This is what I get on my laptop when doing the above with sesame 1.13.3: > > > gc() > > used (Mb) gc trigger (Mb) max used (Mb) > > Ncells 15062911 804.5 24349446 1300.5 24349446 1300.5 > > Vcells 278380669 2123.9 473158124 3610.0 473157073 3610.0 > > > That's a memory consumption of 4.9G which is confirmed by the 'top' command I > was running in another terminal. > > It would be awesome if 'R CMD check' could do the above for us i.e. report > the amount of memory used by the examples. Any volunteer to request this > feature on the R-devel mailing list? > > Hope this helps, > H. > >> Very best, >> Wanding >>> On Nov 29, 2021, at 12:15 PM, Hervé Pagès <hpages.on.git...@gmail.com >>> <mailto:hpages.on.git...@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 >>> <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 >>>> <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/ <https://zhou-lab.github.io/> >>>> Phone (o): (215) 590-0473 >>>> [[alternative HTML version deleted]] >>>> _______________________________________________ >>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >>> >>> -- >>> Hervé Pagès >>> >>> Bioconductor Core Team >>> hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com> > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
