The longtests builds only run the tests in the longtests/ folder.
Best, H. On 2/21/24 09:56, alan murphy wrote: > Hey Herve, > > Thanks for this, I'm going to implement that now. One thing I > wondered, is it only the tests in the longtest/ folder that run on > these weekly builds or both those and the tests in test/? I'm > wondering should I duplicate the tests in both folders that I want to > run in both? > > Cheers, > Alan. > ------------------------------------------------------------------------ > *From:* Hervé Pagès <hpages.on.git...@gmail.com> > *Sent:* Tuesday 6 February 2024 18:58 > *To:* alan murphy <alanmurp...@hotmail.com>; Bioc-devel@r-project.org > <bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] Fw: MungeSumstats Bioconductor > > Hi Alan, > > The specs of the Linux servers have not changed. > > However we've recently observed some of these random kills by the > Linux kernel for a couple of other packages, and we started an > application to get funding to increase the amount of RAM on these > machines. > > These random kills are a desperate attempt by the Linux kernel to keep > the machine alive when it's under extremely high load and running out > of resources. Unfortunately this is not something that anybody will be > able to easily reproduce as it only happens under special > circumstances e.g. during the daily builds when dozens of packages are > being checked simultaneously. > > Regardless of whether we'll manage to increase the memory on the Linux > servers, it seems to me that the most memory-hungry unit tests in > MungeSumstats would be a better fit for the long tests. These tests > are run once a week instead of daily, and use less workers (4 instead > of 28). This means that each package has access to more resources. > > See https://contributions.bioconductor.org/long-tests.html > <https://contributions.bioconductor.org/long-tests.html> for how to > set up the long tests in your package. > > Let me know if you have questions or need help with this. > > Best, > > H. > > On 2/2/24 09:14, alan murphy wrote: >> Hi, >> >> I'm the maintainer of the MungeSumstats package which is currently failing >> on the devel nebbiolo1 Linux platform because of RAM requirements of the >> unit tests. These tests use large reference datasets (like >> BSgenome.Hsapiens.1000genomes.hs37d5::BSgenome.Hsapiens.1000genomes.hs37d5) >> which cause the issue, e.g. from the output of the devel linux >> test<https://bioconductor.org/checkResults/3.19/bioc-LATEST/MungeSumstats/nebbiolo1-checksrc.html> >> >> <https://bioconductor.org/checkResults/3.19/bioc-LATEST/MungeSumstats/nebbiolo1-checksrc.html>: >> >> ``` >> >> Validating RSIDs of 92 SNPs using BSgenome::snpsById... >> Killed >> >> ``` >> which is from this >> function:https://github.com/neurogenomics/MungeSumstats/blob/cccf77b2249f52be59fe1749f13a386ffaaae528/R/load_ref_genome_data.R#L49 >> >> <https://github.com/neurogenomics/MungeSumstats/blob/cccf77b2249f52be59fe1749f13a386ffaaae528/R/load_ref_genome_data.R#L49> >> >> I would like to keep these units tests as they are very important for me to >> know if things have gone wrong. I can't scale down the RAM usage, it is only >> using a few rows of data as it, the issue is that the reference sets are >> massive rather than the actual set being tested. I currently don't have a >> lot of these tests set to run on windows/mac platforms so I rely on the >> Linux machines to run this. I am not sure what has changed but a few >> releases back, the same tested were not causing this issue and would >> complete on linux - has the machine spec changed? Is there any chance RAM >> could be increased for these tests or is there a way to specify not to run >> the specific unit tests on the Bioconductor server so I can at least keep >> these for my github actions workflows? See below for the automated message I >> got about these errors. >> >> Any other suggestions on ways around this would be greatly appreciated! >> >> Thanks, >> Alan. >> ________________________________ >> From: CoreTeam Bioconductor<bioconductorcoret...@gmail.com> >> <mailto:bioconductorcoret...@gmail.com> >> Sent: Friday 2 February 2024 16:43 >> To:alanmurp...@hotmail.com <mailto:alanmurp...@hotmail.com> >> <alanmurp...@hotmail.com> <mailto:alanmurp...@hotmail.com> >> Subject: MungeSumstats Bioconductor >> >> Hello Package Maintainer, >> >> We would like to bring to your attention that your package is failing in >> devel on the linux platform. This is very problematic. Please investigate >> the issues and fix the package to avoid deprecation. >> >> https://bioconductor.org/checkResults/devel/bioc-LATEST/ >> <https://bioconductor.org/checkResults/devel/bioc-LATEST/> >> <https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow> >> <https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow> >> >> If you have further questions or concerns please reach out on >> thebioc-de...@r-project.org >> <mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org> >> <mailto:bioc-devel@r-project.org> >> >> We appreciate your quick attention to this matter >> >> Cheers, >> On behalf of the Bioconductor Core Team >> >> [[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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
