Great! Thank you very much for this news!
Best regards, Jacopo Il ven 15 dic 2023, 15:36 Kern, Lori <lori.sheph...@roswellpark.org> ha scritto: > I can update the SPB to have that environment variable set. I will also > cross check it with the current variables set on the daily builder. > It may not be until next week that it is implemented. > > Cheers, > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Jacopo > Ronchi <jacopo.ron...@unimib.it> > *Sent:* Friday, December 15, 2023 8:47 AM > *To:* Hervé Pagès <hpages.on.git...@gmail.com> > *Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] Wrong skipping of tests when builidng on > Bioconductor and R CMD check timeout > > 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://secure-web.cisco.com/1VAUfQTzP732tzYFyWRl9R-VpUe0qcrj11ANCzhi1M7PXdmEUq8BM7_xAJMn24SuX7fWWohKPYZhB0230fNWhTyL4DmAVWLPvmLQrY5ekH9gk0wIeUU8p_IHNHwooLmCYzg1EM9sBSbHTBa-lYfH_5RxRsfe9G46Fzgh4qD9LOMpVZH1EVerXKPfVHgQIJIXjWIkiyjvKSPcnIEXFgTHXVrklHZnSW_X7ba5yCvjOLPEAsUhPpIdJdDbYUEhR37AlDIl7CI6ww6vt95xFIBwEpTv8AsSrGIUY7opOomIPbtZTZiiznEYRC6gZQPGmhUrd/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FBiobase%2F > >> ("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://secure-web.cisco.com/1Rk_soQiHKHVPFUyxQEVFg-vcGG0WAJR6XK9z24AVEnrYfyKPY9vQ4_mh_dSEWnq5yhsoMSsoBYGZdR9X6XGeGTieTjRz0eFyhxsZ6EwtJp5WanZk4hoMSYlCzTQlbWTrp0W0U3GNKSqDkKWI9JcB6yDgdJkYsz3_A3DTSPZ5utwV_dF7MrGbC9_ccpBq33AGenBIHH43zCquE-F0QDPTJI85Sufi4xzh9O0DjBTFaGekjHHCm2WVF406Ga6Ij_IBAQBNBO78-SU9THFiK386l4E_sv0N9hiMQM-6BU7wXBS8dtxYQfa7Z42RMzZ_6Rax/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FMIRit_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://secure-web.cisco.com/1t_chbGIX4WJMDly2eKHQVIQpJrLIk6btaSJFXmsAvTCDJdPb2q582j8KL_pHAsvyEk6vf9cZQIgXFklUgaF4-S8hH_x5UKMaXRmQ3K7L636Q_PoaC9K0RGMV9w6RsIQhcjS6DDm_OCye1kDN8WEWuTZCAG3ggOVedpvX6BTPDsD5zcCV7q5BNCYVeS2p3gsdDakvSo4ZAG8zVa2d84L6JxYMu2uiy6rY75cpPpd22LWYqci2uv_cPX7ksHoCYV6pe__CH96I592NQszAK36OA_uJXI0Xq9lmJEmqItqY1IkOuTMdUS56j-9w7B0LUgnL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > This email message may contain legally privileged and/or confidential > information. 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