Regarding the Renviron file i have seen on the GitHub repository of SPB that indeed it is not using the IS_BIOC_BUILD_MACHINE env variable. How should i do in order to pass the checks without errors for my package in submission?
Kind regards, Jacopo Il mer 13 dic 2023, 00:48 Jacopo Ronchi <jacopo.ron...@unimib.it> ha scritto: > Dear Hervé, > > Thank you very much for your answer. Regarding the issue that my package > encounters during the building on SPB i had the same doubt. Indeed when i > include that variable locally in my Renviron file everything works as > expected (tests that should be skipped on Bioconductor are indeed ignored). > So maybe the slight differences in variables between the two build systems > might be the answer. > > On the other hand, i did not consider the caching of resources used in > examples. Since i already use BiocFileCache in my package, i will extend > this also for other features used in examples! Thank you very much for this > very useful suggestion. > > Kind regards, > Jacopo > > Il mer 13 dic 2023, 00:00 Hervé Pagès <hpages.on.git...@gmail.com> ha > scritto: > >> Hi Jacopo, >> >> testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment >> variable to know whether it's on a BioC build machine or not. >> >> This environment variable is defined during the daily build via the >> Renviron.bioc file. Note that a link to this file is provided on the >> individual build reports e.g. here >> https://bioconductor.org/checkResults/3.19/bioc-LATEST/Biobase/ >> ("Renviron settings" link). >> >> Maybe this environment variable is not defined on the Single Package >> Builder (SPB)? The SPB is the build system used during the package >> submission process. It runs on the same machines as the daily builds but my >> understanding is that it uses a slightly different set of variables. Maybe >> Lori can shed some light? >> >> As for the timeout on merida1 (Intel Mac), have you considered using >> BiocFileCache to cache the data that you download in your examples? You >> might still get a timeout the next time 'R CMD check' will run on our build >> machines, but it should go significantly faster after that. >> >> Best, >> >> H. >> On 12/12/23 07:22, Jacopo Ronchi wrote: >> >> Dear Developers, >> >> I am currently in the process of submitting my package on Bioconductor and >> I am facing some issues during the R CMD check on the Bioconductor Build >> System. Since I was not able to find any answers to my doubts, I decided to >> ask for your help before doing anything wrong. >> >> The build report for my package is available >> here:http://bioconductor.org/spb_reports/MIRit_buildreport_20231211095232.html >> >> In particular, my package includes some functions where it accesses remote >> resources. Therefore, I included some "skip_on_bioc()" chunks at the >> beginning of these tests since I don't want my package to fail during the >> build process because of occasional down times. However, when I look at the >> build report, I notice that the relevant tests are not skipped. >> Furthermore, other tests that should be run are instead skipped on CRAN. I >> am referring to these lines: >> >> Skipped tests (2) >> On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5' >> >> Lastly, I have an error during R CMD check on macOS, and I really don't >> know how to reduce the running time on this operating system. Currently, I >> have reshaped the testing suite to reduce the time spent on unit tests. >> However, on macOS, i guess that most of the time consumed is due to >> examples. Nevertheless, the most time consuming functions retrieve >> gene-sets from external resources and I can't reduce the download size of >> KEGG pathways, for example. What should I do? >> >> Sorry again for bothering you, >> Best regards, >> Jacopo >> >> [[alternative HTML version deleted]] >> >> _______________________________________________bioc-de...@r-project.org >> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> -- >> Hervé Pagès >> >> Bioconductor Core teamhpages.on.git...@gmail.com >> >> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
