Re: [Bioc-devel] Spurious "dims [product 864] do not match the length of object [432]" on macOS
Hi, If you are a newbie to the terminal, all you need to do is to extract the R code from your vignette using `R CMD Stangle xcms-lcms-ms.Rmd`(assume you are under the vignettes directory). Then use `R -d valgrind -f xcms-lcms-ms.R` to check for the memory issue. In the ideal case, it can directly tell you where the problem is. If you have bad luck then you should read through some tutorials and figure out how to dig deeper into this problem. Here is a nice introduction for using Valgrind in R: https://kevinushey.github.io/blog/2015/04/05/debugging-with-valgrind/ Best, Jiefei On Sat, Sep 25, 2021 at 9:02 PM Neumann, Steffen wrote: > > Hi, > > On Fri, 2021-09-24 at 07:28 -0400, Martin Morgan wrote: > > Errors that are intermittent and platform-specific are often due to > > memory corruption, and can be investigated on Linux platforms with > > valgrind or similar tools. Have you taken this approach? > > I am afraid that is beyond my skillset :-( > > Yours, > Steffen > > > -- > > Upcoming events: > * Save-the-date: 22.-24.11.2021 3rd metaRbolomics Hackathon, Wittenberg > (Germany) > > https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon > > --- > IPB HalleBioinformatics and Scientific Data > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > 06120 Halle +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Spurious "dims [product 864] do not match the length of object [432]" on macOS
Hi, On Fri, 2021-09-24 at 07:28 -0400, Martin Morgan wrote: > Errors that are intermittent and platform-specific are often due to > memory corruption, and can be investigated on Linux platforms with > valgrind or similar tools. Have you taken this approach? I am afraid that is beyond my skillset :-( Yours, Steffen -- Upcoming events: * Save-the-date: 22.-24.11.2021 3rd metaRbolomics Hackathon, Wittenberg (Germany) https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon --- IPB HalleBioinformatics and Scientific Data Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Spurious "dims [product 864] do not match the length of object [432]" on macOS
Errors that are intermittent and platform-specific are often due to memory corruption, and can be investigated on Linux platforms with valgrind or similar tools. Have you taken this approach? On 9/24/21, 3:22 AM, "Bioc-devel" wrote: Hi, for several years xcms is suffering from absolutely spurious issues on macOS. There is no pattern regarding release/devel, R versions, different macOS machines like merida1 in 2019, to machv2 today and a few occurances inbetween. The tssue usually resolves itself after a few days without any code change. Interestingly, 864=432*2, so something is duplicated somewhere. Also, today was the first time I saw BiocParallel mentioned near the error, see below. => Has anyone observed such a domension mismatch, maybe in other packages, and has any idea what could be the (spurious) cause ? Yours, Steffen Quitting from lines 149-152 (xcms-lcms-ms.Rmd) Error: processing vignette 'xcms-lcms-ms.Rmd' failed with diagnostics: BiocParallel errors element index: 1 first error: BiocParallel errors element index: 1 first error: dims [product 864] do not match the length of object [432] https://github.com/sneumann/xcms/issues/422 -- Upcoming events: * Save-the-date: 22.-24.11.2021 3rd metaRbolomics Hackathon, Wittenberg (Germany) https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon --- IPB HalleBioinformatics and Scientific Data Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Spurious "dims [product 864] do not match the length of object [432]" on macOS
Hi, for several years xcms is suffering from absolutely spurious issues on macOS. There is no pattern regarding release/devel, R versions, different macOS machines like merida1 in 2019, to machv2 today and a few occurances inbetween. The tssue usually resolves itself after a few days without any code change. Interestingly, 864=432*2, so something is duplicated somewhere. Also, today was the first time I saw BiocParallel mentioned near the error, see below. => Has anyone observed such a domension mismatch, maybe in other packages, and has any idea what could be the (spurious) cause ? Yours, Steffen Quitting from lines 149-152 (xcms-lcms-ms.Rmd) Error: processing vignette 'xcms-lcms-ms.Rmd' failed with diagnostics: BiocParallel errors element index: 1 first error: BiocParallel errors element index: 1 first error: dims [product 864] do not match the length of object [432] https://github.com/sneumann/xcms/issues/422 -- Upcoming events: * Save-the-date: 22.-24.11.2021 3rd metaRbolomics Hackathon, Wittenberg (Germany) https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon --- IPB HalleBioinformatics and Scientific Data Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
