Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
Great! Thank you very much for this news! Best regards, Jacopo Il ven 15 dic 2023, 15:36 Kern, Lori 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 on behalf of Jacopo > Ronchi > *Sent:* Friday, December 15, 2023 8:47 AM > *To:* Hervé Pagès > *Cc:* 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 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 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
Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout
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 on behalf of Jacopo Ronchi Sent: Friday, December 15, 2023 8:47 AM To: Herv� Pag�s Cc: 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 ha scritto: > Dear Herv�, > > 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 Herv� Pag�s 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
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 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 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