Hi Martin, A very short summary is that on kjohnson3 a build/check on package launched by cron takes significantly longer than if one runs the same command manually in a terminal.
There's some further discussion on this at https://community-bioc.slack.com/archives/CEQ04GKEC/p1706816310942079 and and Jen has some nice documentation of their investigation at https://github.com/Bioconductor/BBS/issues/387 However since the original inquiry in this thread is about a package in submission, and so the relevant tests are run by the single package builder on merida1, I'm not sure it's pertinent to this particular issue. Cheers, Mike On Wed, 7 Feb 2024 at 16:34, Martin Grigorov <martin.grigo...@gmail.com> wrote: > Hi Kasper, > > According to > > https://github.com/Bioconductor/BBS/blob/9ebb2cf20e70e4bebf24a2a824a67193de821b08/3.19/bioc-mac-arm64/kjohnson3/config.sh#L17-L20 > the machine has 24 vCPUs. > The automatic/weekly build utilizes 12-16 out of those at any given time! > With the respective RAM and disk usage. > > By "by hand" do you mean to run the build/check of a given package on a > "calm" machine ? > It would be expected that it will be faster if it has all/most resources > just for it. > > Martin > > On Wed, Feb 7, 2024 at 5:12 PM Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > > > To be a bit more clear and vague at the same time: currently, some of our > > macOS builders exhibit weird slowdowns when the build system is run > > automatically compared to running builds "by hand". This is pretty weird, > > and hopefully we can figure out the cause and fix it. Specifically, > builds > > on kjohnson3 is (at the moment) weirdly slow. > > > > Best, > > Kasper > > > > On Wed, Feb 7, 2024 at 7:24 AM Jacopo Ronchi <jacopo.ron...@unimib.it> > > wrote: > > > > > Ok, understood. Thanks > > > > > > Il mer 7 feb 2024, 12:46 Vincent Carey <st...@channing.harvard.edu> ha > > > scritto: > > > > > > > We need a bit of internal discussion before committing to this > > notion. I > > > > will get back to the list on this. > > > > > > > > On Wed, Feb 7, 2024 at 6:34 AM Jacopo Ronchi < > jacopo.ron...@unimib.it> > > > > wrote: > > > > > > > >> Dear Vincent, thanks for your answer. So, at least for now, can I > > ignore > > > >> the warning on macOS for the submission of MIRit? > > > >> > > > >> Il mer 7 feb 2024, 12:26 Vincent Carey <st...@channing.harvard.edu> > > ha > > > >> scritto: > > > >> > > > >>> Thanks Jacopo. You shouldn't have to struggle. We are aware of > > > >>> disparities of platform > > > >>> performance and are working to improve the build process. It will > > take > > > >>> time. I believe that > > > >>> achievement of acceptable timings on the linux platform should be > the > > > >>> key goal at > > > >>> this time. > > > >>> > > > >>> On Wed, Feb 7, 2024 at 5:18 AM Jacopo Ronchi < > > jacopo.ron...@unimib.it> > > > >>> wrote: > > > >>> > > > >>>> Dear developers, > > > >>>> > > > >>>> I am struggling to reduce R CMD check times for my package, MIRit, > > on > > > >>>> macOS. The check on linux takes 4 minutes, while on macOS it needs > > > 9/10 > > > >>>> minutes. I have severely reduced the size of examples and tests, > > which > > > >>>> now > > > >>>> use smaller datasets and cached resources. > > > >>>> > > > >>>> On linux, unit tests require 30 seconds more or less, and examples > > 40 > > > >>>> seconds. On the other hand, macOS tests take 100 seconds, and 75 > for > > > the > > > >>>> examples. The issue is that sometimes the check runs in less than > 10 > > > >>>> minutes, sometimes it needs a little bit more. > > > >>>> > > > >>>> However I am out of ideas on how to further reduce examples and > > > tests... > > > >>>> The vignette is really extensive, but since SPB uses the > > > "--no-vignette" > > > >>>> option this should not influence heavily on this behavior, at > least > > to > > > >>>> my > > > >>>> understanding. > > > >>>> > > > >>>> Sorry for bothering you, > > > >>>> Best regards, > > > >>>> Jacopo > > > >>>> > > > >>>> [[alternative HTML version deleted]] > > > >>>> > > > >>>> _______________________________________________ > > > >>>> Bioc-devel@r-project.org mailing list > > > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > >>>> > > > >>> > > > >>> The information in this e-mail is intended only for the person to > > whom > > > >>> it is > > > >>> addressed. If you believe this e-mail was sent to you in error and > > the > > > >>> e-mail > > > >>> contains patient information, please contact the Partners > Compliance > > > HelpLine > > > >>> at > > > >>> http://www.partners.org/complianceline . If the e-mail was sent to > > you > > > >>> in error > > > >>> but does not contain patient information, please contact the sender > > and > > > >>> properly > > > >>> dispose of the e-mail. > > > >> > > > >> > > > > The information in this e-mail is intended only for > th...{{dropped:16}} > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > -- > > Best, > > Kasper > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel