Re: [Bioc-devel] nebbiolo1 - build report
The new report is available:https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Herv� Pag�s Sent: Wednesday, April 24, 2024 12:27 PM To: Kristian Ullrich ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] nebbiolo1 - build report * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * As for the error you will see when today's report gets published it's caused by the recent move of the pairwiseAlignment stuff from Biostrings to the new pwalign package. I fixed it in MSA2dist 1.7.6 so it will go away in tomorrow's report. Please resync your GitHub repo with git.bioconductor.org when you get a chance. H. On 4/24/24 09:18, Herv� Pag�s wrote: > > Hi Kristian, > > I believe that this is because the new report didn't get published yet > so the links in the email you received still points to yesterday's > report. We're investigating. > > Best, > > H. > > On 4/24/24 09:10, Kristian Ullrich wrote: >> Hi, >> >> I just got an email from bbs: >> >> Hi MSA2dist maintainer, >> >> According to the Multiple platform build/check report for BioC 3.19, >> the MSA2dist package has the following problem(s): >> >> o ERROR for 'R CMD INSTALL' on nebbiolo1. See the details here: >> >> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FMSA2dist%2Fnebbiolo1-install.html__%3B!!PxiZbSOawA!JXtUuFyazbia9xcI2poFmD8RwdzAoeA2p7qo-3E8uEECTMUF2RvOae17q7c7nyyINmLgkWqYpfynvaOjuqOgs8-a3E7pTy5hhQPfEg%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C50043778ddea452e058a08dc647c75f6%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638495732936269396%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=xrT6KZN0S9x5lltJLUTmmitRNT881m0wgfoBhW0OhMU%3D=0<https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/nebbiolo1-install.html__;!!PxiZbSOawA!JXtUuFyazbia9xcI2poFmD8RwdzAoeA2p7qo-3E8uEECTMUF2RvOae17q7c7nyyINmLgkWqYpfynvaOjuqOgs8-a3E7pTy5hhQPfEg$> >> >> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FMSA2dist%2Fnebbiolo1-install.html__%3B!!PxiZbSOawA!JXtUuFyazbia9xcI2poFmD8RwdzAoeA2p7qo-3E8uEECTMUF2RvOae17q7c7nyyINmLgkWqYpfynvaOjuqOgs8-a3E7pTy5hhQPfEg%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C50043778ddea452e058a08dc647c75f6%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638495732936285487%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=FZZ1d%2BNWcAGQgqYx5d4wkJWE4OjfwocSJTGWGiO%2BBzU%3D=0 >> > >> >> o ERROR for 'R CMD build' on nebbiolo1. See the details here: >> >> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FMSA2dist%2Fnebbiolo1-buildsrc.html__%3B!!PxiZbSOawA!JXtUuFyazbia9xcI2poFmD8RwdzAoeA2p7qo-3E8uEECTMUF2RvOae17q7c7nyyINmLgkWqYpfynvaOjuqOgs8-a3E7pTy6dYC38CA%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C50043778ddea452e058a08dc647c75f6%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638495732936292827%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=EWzdda0QeS0ADA55wWN7agnv7qfVmg96gQw%2FVQgQMLY%3D=0<https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/nebbiolo1-buildsrc.html__;!!PxiZbSOawA!JXtUuFyazbia9xcI2poFmD8RwdzAoeA2p7qo-3E8uEECTMUF2RvOae17q7c7nyyINmLgkWqYpfynvaOjuqOgs8-a3E7pTy6dYC38CA$> >> >> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FMSA2dist%2Fnebbiolo1-buildsrc.html__%3B!!PxiZbSOawA!JXtUuFyazbia9xcI2poFmD8RwdzAoeA2p7qo-3E8uEECTMUF2RvOae17q7c7nyyINmLgkWqYpfynvaOjuqOgs8-a3E7pTy6dYC38CA%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C50043778ddea452e058a08dc647c75f6%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638495732936297677%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=Y%2Fv5gS0o%2Fo%2FnKcEvxye%2F76wPpfdgpwYqrYDZfsLxwl4%3D=0 >> > >> >> However, if I check the the page, there are no ERROR listed: >> >> Report page was generated: >> >> This page was generated on 2024-04-23 11:37:19 -0400 (Tue, 23 Apr 2024). >> >> Should I just wait or where I can find the mentioned ERROR? >> >> Best regards >> >
Re: [Bioc-devel] SVMDO devel branch CITATION PROBLEM
Hi, You should increment your version in the DESCRIPTION file for the build system to recognize and propagate the change:https://contributions.bioconductor.org/description.html?q=version#description-ver. You can follow up with me if you don't see the change. It takes the devel builders about a day (starting at 3:00pm ET) to go through a complete cycle and then a few additional hours for content to propagate to the landing pages. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of erhanozer19 via Bioc-devel Sent: Monday, April 1, 2024 8:26 AM To: Bioconductor Devel Mailing list Subject: [Bioc-devel] SVMDO devel branch CITATION PROBLEM * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hello, In the Bioconductor, the release version page of SVMDO includes the CITATION information, provided by the CITATION file in the package, but it does not appear in the development version Bioconductor page of SVMDO. I checked the Bioconductor Code Browse. Both release and development branches have the CITATION file. How can I fix this problem? Sincerely, ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!OGeS-2mwQn7R_tPdm_M4CYDsZp6XJelizyQgWwTEK0SSH9RASVm5NT3631MrvHQ4aMLqHclEs99_pA2c7TEcDKceoEHm-Pr_uA%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7Cdd4bbab169014ff9fa1408dc524f2603%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638475747098806678%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=W0l4TR8sSvDpOduWDxuluLC0kc9bW6ulhlsEg8RsNdA%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!OGeS-2mwQn7R_tPdm_M4CYDsZp6XJelizyQgWwTEK0SSH9RASVm5NT3631MrvHQ4aMLqHclEs99_pA2c7TEcDKceoEHm-Pr_uA$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] fixing deltaCaptureC
Hi Michael, I see that it is passing for 3.18. The email might have been for devel, which is still failing. You should cherry-pick the commit and bump the version for the devel branch: https://contributions.bioconductor.org/git-version-control.html?q=cherry%20pick#bug-fix-in-release-and-devel<https://contributions.bioconductor.org/git-version-control.html?q=cherry%20pick#bug-fix-in-release-and-devel>. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Michael Shapiro Sent: Wednesday, March 27, 2024 8:06 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] fixing deltaCaptureC * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * My package deltaCaptureC is suddenly having build problems, specifically a problem building the vignette. It fails when attempting to display a ggplot object in the vignette, and this seems to be due to changes in ggplot. I've updated the .rda files for the plots and the vignette now builds properly locally. I bumped the version and pushed to RELEASE_3_18. I did this last week, but yesterday I got an email that it is still failing to build. Please advise. Many thanks, Michael The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!JHWqiJnNK-f8PoNHtJ-M96fMyX_swfUn9wmO5qwqAT_uD8hqueXvqS5MuQKMg4BHDKPR9-zmQUfD9SupcC58xTHtF7uPO5uhQg0Uqvf1%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C14abad3238fc483cafc208dc4e577cb1%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638471384882140984%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=z21%2BwXb4PzbWrF4uTeL2WIWcdauXw7Qmd3n7cGSd9d4%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!JHWqiJnNK-f8PoNHtJ-M96fMyX_swfUn9wmO5qwqAT_uD8hqueXvqS5MuQKMg4BHDKPR9-zmQUfD9SupcC58xTHtF7uPO5uhQg0Uqvf1$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor Devel Build Machines Set to Daily Build Schedule, Release Set to MWF
In preparation for the next release, the 3.19 devel builders will run daily except for Saturday. The release builders will run Monday, Wednesday, and Friday. R has also been updated on the release and devel builders. We'll also add the following flag to the Renviron.bioc for the devel Linux builder to catch ordered comparisons on language objects: _R_COMPARE_LANG_OBJECTS=eqonly For more information, see https://stat.ethz.ch/pipermail/r-devel/2024-March/083254.html. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor Devel Build Machines Set to MWF Schedule
The Bioconductor build machines running the 3.19 devel software builds are scheduled to run Mondays, Wednesdays, and Fridays to accommodate additional packages and allow slower machines to complete build cycles. Reports will be available on Monday, Wednesday, Friday for the Linux, Mac Intel, and Windows platforms at https://bioconductor.org/checkResults/3.19/bioc-LATEST/. Thanks for your understanding. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor Build System Maintenance 2/14
Maintenance will be performed on Nebbiolo1 and Nebbiolo2 on Wednesday 2/14, so Bioconductor build reports may not start again until Friday 2/16. Thanks for your patience. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Incorrect warning about failing package built
Hi Johannes, Looking at R CMD Check on devel, it looks like you're missing a `library(ReactomeGSA)` in reanalysing-public-data.Rmd, which is why it doesn't find the function `get_public_species()`. We only build the vignettes on the Linux builders, which this error is only caught there. Regarding the error kunpeng2, we could ask its maintainer to install ReactomeGSA.data, which appears to be missing. If this happens again, you can reach out to Martin on the Bioc Community Slack channel #arm-linux. He's very active and responsive. Lastly, regarding the notification that happened on the 2024/01/08, it's possible that it failed due to an issue with another package at that time which has since been resolved. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Johannes Griss Sent: Thursday, February 1, 2024 3:18 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Incorrect warning about failing package built * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hello, I just received a second warning the our package ReactomeGSA is failing in both release and devel on all platforms. Quickly checking the respective reports shows that this is not the case: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200958363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=tbYEx3lk0V%2BBLNUdbLHtclDpeGm9sq5W7Tv9lK%2BnNx8%3D=0<https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D=0<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U$> On release we have no errors or warnings at all, on devel, everything is fine in two instances while the others seem to have issues that we will look into. Is there anything I can do to fix that? Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98%24=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200977608%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=0x4xNPvAHnkGyUcEz4PVIOM8eCVTEWNpNUOkskspUEQ%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Availability of DropletUtils on BBS for an experiment package
Hi Leo, spatialLIBD is missing DropletUtils in Suggests in the DESCRIPTION. If you add it there and bump the version, it will pass check. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Leonardo Collado Torres Sent: Wednesday, November 29, 2023 9:11 AM To: Bioc-devel Subject: [Bioc-devel] Availability of DropletUtils on BBS for an experiment package * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi BioC-devel, Do you know why DropletUtils is not available on bioc 3.18 for the BBS? I keep seeing errors about it at https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.18%2Fdata-experiment-LATEST%2FspatialLIBD%2Fnebbiolo2-checksrc.html__%3B!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fEqcixawg%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C006d56be16e4471e318e08dbf0e545b7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638368639765624428%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=G3JE%2FgBKp137DCvhmhcREQb%2F4sG%2BBd0cZkjlJm1P034%3D=0<https://urldefense.com/v3/__https://master.bioconductor.org/checkResults/3.18/data-experiment-LATEST/spatialLIBD/nebbiolo2-checksrc.html__;!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fEqcixawg$> (which is an Experiment package, not a Software one) Quitting from lines 178-193 [import_to_r] (TenX_data_download.Rmd) Error: processing vignette 'TenX_data_download.Rmd' failed with diagnostics: there is no package called 'DropletUtils' --- failed re-building �TenX_data_download.Rmd� At https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDropletUtils.html__%3B!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fE7mWBMjo%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C006d56be16e4471e318e08dbf0e545b7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638368639765635135%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=w2%2BOmrICIKKycrQtbt56gSs0mt9Bc536baQbFhY8nts%3D=0<https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/html/DropletUtils.html__;!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fE7mWBMjo$> , I do see that all binaries and the source package are available. Thanks, Leo Leonardo Collado Torres, Ph. D. Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT Assistant Professor, Department of Biostatistics Johns Hopkins Bloomberg School of Public Health 855 N. Wolfe St., Room 385 Baltimore, MD 21205 lcolladotor.github.io lcollado...@gmail.com ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fEoKb0iBw%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C006d56be16e4471e318e08dbf0e545b7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638368639765640048%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=2HWrzvP60fFjOcb18vywyDZDaghU9rx1K%2FshsCVYrA8%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!MFQ9mQCSL0x9pjrtdNr8LWIDL0WyBTRjA94qKNvwpWf6HssqHzvkEzT004js2ZQHI93BSdxwPqalkF4csGWCa7fEoKb0iBw$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] autonomics : nebbiolo (only) fails to locate weave
There were some issues with that version of R-devel, so we updated R on Linux devel builder yesterday. The error message that appears today is different for autonomics and similar to what is reported on the arm64 linux devel builder. I'm updating R on the Mac and Windows devel builders today so the errors may be more consistent in the report in the next day or so. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Aditya Bhagwat via Bioc-devel Sent: Tuesday, November 14, 2023 4:23 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] autonomics : nebbiolo (only) fails to locate weave * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Dear BioC devel, autonomics devel install/build/checks: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fautonomics%2F__%3B!!PxiZbSOawA!IgmJQYkJiE1CYBM8ZqmpFDAktZXlKG3vQBZ46ZwM4E_ampRc78FQsVYDR1d9ibXt2-afvLKrWo3CZPAd-qfHmd4N1zY07ObozA%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C09ae275414054935240008dbe4f3643e%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638355506283269639%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=XUNdcigTbWuD%2FNTokrj98CUSb98ygmQBopJSE7APe1E%3D=0<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/autonomics/__;!!PxiZbSOawA!IgmJQYkJiE1CYBM8ZqmpFDAktZXlKG3vQBZ46ZwM4E_ampRc78FQsVYDR1d9ibXt2-afvLKrWo3CZPAd-qfHmd4N1zY07ObozA$> fine on palomino3 (win) and merida1 (mac). 'fails to locate weave' on nebbiolo (ubuntu). Could this be a nebbiolo rather than an autonomics issue? Thankyou : ) Aditya -- Aditya Bhagwat Translational Proteomics � Philipps-University Marburg Biological Pharmacological Center � Room A406 Tel.: +49 6421 28 27403 -- Aditya Bhagwat Translational Proteomics � Philipps-University Marburg Biological Pharmacological Center � Room A406 Tel.: +49 6421 28 27403 ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!IgmJQYkJiE1CYBM8ZqmpFDAktZXlKG3vQBZ46ZwM4E_ampRc78FQsVYDR1d9ibXt2-afvLKrWo3CZPAd-qfHmd4N1zYvu_blFg%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C09ae275414054935240008dbe4f3643e%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638355506283269639%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=%2BJTH2e1t2UqDhC4DDIxuVM5nHr8U9bAieVCdDZs173o%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!IgmJQYkJiE1CYBM8ZqmpFDAktZXlKG3vQBZ46ZwM4E_ampRc78FQsVYDR1d9ibXt2-afvLKrWo3CZPAd-qfHmd4N1zYvu_blFg$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?
Hi Johannes, I installed R 4.3.2 on the release builders on Thursday after the last Experiment package report. ReactomeGSA.data will be reinstalled tomorrow so this error will resolve soon; however, it's masking another error: ## ## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA ### ## ## * checking for file 'ReactomeGSA/DESCRIPTION' ... OK * preparing 'ReactomeGSA': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'analysing-scRNAseq.Rmd' using rmarkdown Quitting from lines 58-62 [unnamed-chunk-2] (analysing-scRNAseq.Rmd) Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics: Please run UpdateSeuratObject on your object --- failed re-building 'analysing-scRNAseq.Rmd' --- re-building 'using-reactomegsa.Rmd' using rmarkdown --- finished re-building 'using-reactomegsa.Rmd' SUMMARY: processing the following file failed: 'analysing-scRNAseq.Rmd' Error: Vignette re-building failed. Execution halted Lori was able to reproduce this on her local machine and suggested that you might need to update your data object in ReactomeGSA.data. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Johannes Griss Sent: Friday, November 3, 2023 4:52 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] ReactomeGSA missing in Bioconductor 3.18? * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi everyone, For a while the build system reported an error that our ReactomeGSA package cannot be build due to the missing dependency of the "ReactomeGSA.data" package which is required to build the vignettes and is listed in the "Suggests" section. ReactomeGSA.data seems to building fine though but depends on ReactomeGSA. Unfortunately, I cannot figure out how I could solve this issue. Thanks for your help! Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!KW1sKP9AN51aLOcF2htPL3H8DdEYyRlR4feh3rzZMthABEc8VLPbqk8QYjwb05YfNsq-zFxH0sEJydQkAbQ4HA-Z7GbN0LJjNQWmjo6Ekv4%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cd0b8a0d7666d4bbfc4b808dbdcaecbe7%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638346415598213348%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=v2kHQF1w6Ks5q0vmoZAnNo3ZKXjLeqLnMn5Ou7NKF64%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!KW1sKP9AN51aLOcF2htPL3H8DdEYyRlR4feh3rzZMthABEc8VLPbqk8QYjwb05YfNsq-zFxH0sEJydQkAbQ4HA-Z7GbN0LJjNQWmjo6Ekv4$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] No cairo device on merida1
This is a known issue that Cairo isn't enabled for the R 4.4 macos binaries that are installed on the macOS devel builders. Unfortunately this impacts a lot of packages. No action is needed. We appreciate your patience while waiting for the issue to be resolved upstream or until a suitable workaround is found. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Oleksii Nikolaienko Sent: Saturday, October 28, 2023 1:08 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] No cairo device on merida1 * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Dear Bioc team, my package is failing <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FepialleleR%2Fmerida1-buildsrc.html__%3B!!PxiZbSOawA!NZKQ_KQo8YYPfqPKmCWa79KTkqyge6ChWZj8Ync1tf45q4xfNzVNUtZr5mFgCSDfck20dmexXoSAkilrIWEJT3qh86IdWGytzLKSTQ%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C1a6db7e8bb474531948108dbd7d8be27%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638341098138703864%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=nQUotNdR3B%2BDxFb17ztYavkCi7teJW7YcpMVl7RLvAQ%3D=0 > on merida1 with the message "svg: Cairo-based devices are not available for this platform". I didn't find relevant issues at https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2FBioconductor%2FBBS__%3B!!PxiZbSOawA!NZKQ_KQo8YYPfqPKmCWa79KTkqyge6ChWZj8Ync1tf45q4xfNzVNUtZr5mFgCSDfck20dmexXoSAkilrIWEJT3qh86IdWGyDIie-rA%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C1a6db7e8bb474531948108dbd7d8be27%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638341098138703864%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=6TvbZYIm5IxmRK0QmzvnrBKQ7Q5bQah85YnsLGyBnb0%3D=0<https://urldefense.com/v3/__https://github.com/Bioconductor/BBS__;!!PxiZbSOawA!NZKQ_KQo8YYPfqPKmCWa79KTkqyge6ChWZj8Ync1tf45q4xfNzVNUtZr5mFgCSDfck20dmexXoSAkilrIWEJT3qh86IdWGyDIie-rA$> , therefore asking here - is there something missing at merida1 or I shouldn't include SVG in my vignettes? Best, Oleksii [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!NZKQ_KQo8YYPfqPKmCWa79KTkqyge6ChWZj8Ync1tf45q4xfNzVNUtZr5mFgCSDfck20dmexXoSAkilrIWEJT3qh86IdWGySMhZu7w%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C1a6db7e8bb474531948108dbd7d8be27%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638341098138703864%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=g9PbGAFReAKilvaXu9Q5cwhAqXegKC0rdfsUzNBAMfM%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!NZKQ_KQo8YYPfqPKmCWa79KTkqyge6ChWZj8Ync1tf45q4xfNzVNUtZr5mFgCSDfck20dmexXoSAkilrIWEJT3qh86IdWGySMhZu7w$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Push update to an existing remote branch
Hi Carlotta, The branch is named devel on git.bioconductor.org. If you want to push from your local main branch to your repo on git.bioconductor.org, you should do git push upstream main:devel See https://contributions.bioconductor.org/git-version-control.html for more details. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Carlotta Meyring Sent: Wednesday, October 18, 2023 9:26 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Push update to an existing remote branch * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi all, I have a package in review on g...@git.bioconductor.org<mailto:g...@git.bioconductor.org> and I have added a remote named upstream pointing to my package there. I want to push an updated version and $ git push origin main Works well, however $ git push upstream main Doesn't work with the error message being: error: cannot spawn https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2Fmyowngithubname.keys__%3B!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1WG6ql5jg%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C2fde39c6fc9c42077c1c08dbcfddf81f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638332324514380110%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ONFWPeZ%2Fbv%2BprbBfT7sdnkCb%2BUvhp74JHSfq0vnctZQ%3D=0<https://urldefense.com/v3/__https://github.com/myowngithubname.keys__;!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1WG6ql5jg$> : No such file or directory error: cannot spawn https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2Fmyowngithubname.keys__%3B!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1WG6ql5jg%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C2fde39c6fc9c42077c1c08dbcfddf81f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638332324514380110%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ONFWPeZ%2Fbv%2BprbBfT7sdnkCb%2BUvhp74JHSfq0vnctZQ%3D=0<https://urldefense.com/v3/__https://github.com/myowngithubname.keys__;!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1WG6ql5jg$> : No such file or directory fatal: unable to fork I already checked that the key is connected with my github account. Any help would be appreciated! Thanks in advance! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1V94yVPog%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C2fde39c6fc9c42077c1c08dbcfddf81f%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638332324514380110%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=rkroErA6QDGYHPNzRzOOqE1BiIo3A2CB%2BAItC%2FQbfn8%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!PPDIeiU5FM89AFOsTVru0b1uMeUr0M7bPpsBZsqQF-YAaYeq7kpNECHEqKCdcsKaBEha_SAAr2PlKX-75AI93_V0LmV7aBvvbOt-f85Dh1V94yVPog$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] cfTools build error
Ran, I don't see the error that you mention. The current error on the build report is that cfTools is missing cfToolsData, which I understand is a recently accepted experiment package. It should probably become available on Tuesday so I may see the error on the build report on Wednesday. When I look at cfTools, I see that you're managing tensorflow with basilisk, which is the right way to go about it. I've removed the cache for cfTools in basilisk on palomino4 , but this may not be helpful until we have cfToolsData next week. If we continue to see the problem, I can try removing the cache again and troubleshoot more. Martin, Regarding your question about updating tensorflow that is made available on the build machines for CRAN package tensorflow<https://cran.r-project.org/web/packages/tensorflow/index.html>, it should be fine to update tensorflow on kunpeng2. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Martin Grigorov Sent: Tuesday, October 10, 2023 3:14 PM To: RAN HU Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] cfTools build error * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi, https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fpypi.org%2Fproject%2Ftensorflow%2F2.10.0%2F*files__%3BIw!!PxiZbSOawA!PCH5e74i_iyFpJzRK4TpZKocPg4CQic6KN2P-81NJnswcL3UZlJgQ_LNH2b1xHbOyfz-oBh9_4nlay119oA0O1_yiPai9gBrNQcC%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cb5487ea55dcd49d6879208dbc9c5303c%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638325620989566974%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ueZgqhgyQOW8oziReHZyw%2By4VSB05n6Ko5RVi5cmeQs%3D=0<https://urldefense.com/v3/__https://pypi.org/project/tensorflow/2.10.0/*files__;Iw!!PxiZbSOawA!PCH5e74i_iyFpJzRK4TpZKocPg4CQic6KN2P-81NJnswcL3UZlJgQ_LNH2b1xHbOyfz-oBh9_4nlay119oA0O1_yiPai9gBrNQcC$> is the first release that provides a wheel for Linux ARM64 (aarch64). Would it be OK to update from 2.8.0 to 2.10.0 ? Or even better to 2.14.0 (latest and greatest)! Regards, Martin On Tue, Oct 10, 2023 at 9:30 PM RAN HU wrote: > Dear Bioc Team, > > I have a build error on palomino4 and kunpeng2 due to an environment > problem: Multiple platform build/check report for BioC 3.18 - All results > for package cfTools (bioconductor.org) > <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FcfTools%2F__%3B!!PxiZbSOawA!PCH5e74i_iyFpJzRK4TpZKocPg4CQic6KN2P-81NJnswcL3UZlJgQ_LNH2b1xHbOyfz-oBh9_4nlay119oA0O1_yiPai9myA1xWz%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cb5487ea55dcd49d6879208dbc9c5303c%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638325620989566974%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=l7ojno1fBG3mpn7ubSm6y5gcDwfEOhL6QRROUDeG3Fo%3D=0 > > > PackagesNotFoundError: The following packages are not available from > current channels: > - tensorflow=2.8.0 > > Could you help me solve this? Thank you in advance! > > Best, > > Ran > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!PCH5e74i_iyFpJzRK4TpZKocPg4CQic6KN2P-81NJnswcL3UZlJgQ_LNH2b1xHbOyfz-oBh9_4nlay119oA0O1_yiPai9i1oP1gO%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cb5487ea55dcd49d6879208dbc9c5303c%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638325620989566974%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=pW2Tmh5ffm0nU%2B3GsIaGdlyOPse%2FZzpcOUHrwFRK52I%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!PCH5e74i_iyFpJzRK4TpZKocPg4CQic6KN2P-81NJnswcL3UZlJgQ_LNH2b1xHbOyfz-oBh9_4nlay119oA0O1_yiPai9i1oP1gO$> > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!PCH5e74i_iyFpJzRK4TpZKocPg4CQic6KN2P-81NJnswcL3UZlJgQ_LNH2b1xHbOyfz-oBh9_4nlay119oA0O1_yiPai9i1oP1gO%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cb5487ea55dcd49d6879208dbc9c5303c%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638325620989566974%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=pW2Tmh5ffm0nU%2B3GsIaGdlyOPse%
Re: [Bioc-devel] arm64 on Mac build fails due to problem with MPO.db
There did seem to be an issue with the Annotation resource AH111553 that was
preventing MPO.db from being installed. I've refreshed it and reinstalled
MPO.db. I was able to manually install MoonlightR, Moonlight2R, as well as some
of the other packages you mentioned after these changes. We should see this
reflected in the report for next Thursday since the Mac ARM64 devel builds have
already started. Thanks everyone for your help and this discussion.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Herv� Pag�s
Sent: Thursday, October 12, 2023 3:33 PM
To: Zuguang Gu ; bioc-devel@r-project.org
; Matteo Tiberti ; Robert Castelo
Subject: Re: [Bioc-devel] arm64 on Mac build fails due to problem with MPO.db
* This email originates from a sender outside of CUNY. Verify the sender before
replying or clicking on links and attachments. *
On 10/12/23 12:25, Zuguang Gu wrote:
> The devel version of DOSE depends on MPO.db.
>
> I also found MoonlightR depends on DOSE only on its two functions:
> gseDO() and simplot().
>
> An analysis by the pkgndep package shows if you can reduce the
> dependency on both clusterProfiler and DOSE, a total of 46 upstream
> dependencies will be reduced (30 by clusterProfiler uniquely and 16 by
> both). You can use `pkgndep::dependency_database()` to query the
> dependencies, but the database was only updated to some version last year.
>
> MPO.db initializes an instance of AnnotationHub in its .onLoad(). I
> don't know whether that is the source of the error.
>
> .onLoad <- function(libname, pkgname) {
> ns <- asNamespace(pkgname)
> makeCachedActiveBinding("MPO.db", make_MPO.db, env=ns)
> namespaceExport(ns, "MPO.db")
> ah <- suppressMessages(AnnotationHub())
> dbfile <- ah[["AH111553", verbose=FALSE]]
> dbconn <- AnnotationDbi::dbFileConnect(dbfile)
> assign("dbconn", dbconn, envir=datacache)
> ann_objs <- createAnnObjs.MPO_DB("MPO", "MPO", dbconn, datacache)
> mergeToNamespaceAndExport(ann_objs, "MPO.db")
>
> }
I don't know either but we strongly recommend against .onLoad hooks
trying to access the internet. Once a package is installed, one should
be able to load it offline.
H.
>
>
> On Thu, 12 Oct 2023 at 20:37, Robert Castelo
> wrote:
>
> Hi,
>
> one of the kind of tools that Herv� is referring to is the package
> BiocPkgTools:
>
>
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2Fpackages%2FBiocPkgTools__%3B!!PxiZbSOawA!I-l3hH8fBjv8Ra_NJu0m8IOjrAwWhFztC1P9ujN5jgHmAGRNmoDlVzYH3d7wQH2uhleJZVIjMu8dpbNpRcHCwF8G3MmVH8SmzHYbNw%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Ce428b4f4e0ce4760d7fa08dbcb5a8328%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638327361855684577%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=8UmSVkZUUh3F7DKOZjR0R5q00hYPDzmhJo1A4gf7R6w%3D=0<https://urldefense.com/v3/__https://bioconductor.org/packages/BiocPkgTools__;!!PxiZbSOawA!I-l3hH8fBjv8Ra_NJu0m8IOjrAwWhFztC1P9ujN5jgHmAGRNmoDlVzYH3d7wQH2uhleJZVIjMu8dpbNpRcHCwF8G3MmVH8SmzHYbNw$>
>
> section "7 Dependency burden" in the vignette illustrates how to
> identify dependencies that you might want to get rid of.
>
> cheers,
>
> robert.
>
> On 12/10/23 18:24, Herv� Pag�s wrote:
> > On 10/12/23 00:45, Matteo Tiberti wrote:
> >
> >> Hi Herv�,
> >>
> >> Thank you for your comment and for looking into our package � it
> >> would definitely make sense to try and not depend on
> clusterProfiler
> >> if it is that heavy of a dependency (and we don�t use it so
> much as
> >> you mention), more in general working in the direction of removing
> >> little-used or heavy dependencies would speed things up all around
> >> and reduce the chance of having failures because of
> changes/failures
> >> of dep. packages. We will try and reassess the package imports in
> >> this direction.
> >>
> >> It would be great if we could obtain e.g. a dependency graph �
> or at
> >> least know how many (unique) dependencies each of our deps has,
> e.g.
> >> I saw that miniCRAN can do something similar
> >>
> > I think there are a number of tools already that you can use to do
> > this kind of analysis e.g. basic low-level tools like
> > tools::package_dependencies() but also more high-level ones with
> > advanced fu
Re: [Bioc-devel] "scry" build report error
We removed resource EH1524 from the cache so it could be redownloaded. scry's report does not show errors today: https://bioconductor.org/checkResults/devel/bioc-LATEST/scry/. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Kelly Street Sent: Tuesday, September 26, 2023 6:38 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] "scry" build report error * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hello all, We are getting a strange error in the recent build report <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fscry%2F__%3B!!PxiZbSOawA!ODjhdQq9byQk5g8hrf2t2PvaVrxRgb22w8weWOe9X-Pv37m5tDdBPtVvfBU7K4HYOTOcyrD83M1PxhpqXYlAvyHVs83pkC1u%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cbeea2b9769d5417e966608dbbee183b0%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313648038042589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=aW6kugdegge9sKHl38xIrwOKdUoXIqmzBcj%2BY%2Fn7DE0%3D=0 > for our package "scry" and I am wondering if anyone has encountered this issue before. In the vignette, we use a dataset from the DuoClustering2018 package, which does not seem to have any issues, itself. However, on palomino4, we get this error: Error: processing vignette 'scry.Rmd' failed with diagnostics: failed to load resource name: EH1524 title: sce_full_Zhengmix4eq reason: unknown input format Will Townes and I have been unable to reproduce this error locally (both on Macs), so I'm wondering if anyone knows how we might diagnose this problem? Thanks, Kelly [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!ODjhdQq9byQk5g8hrf2t2PvaVrxRgb22w8weWOe9X-Pv37m5tDdBPtVvfBU7K4HYOTOcyrD83M1PxhpqXYlAvyHVs6i_WdoX%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Cbeea2b9769d5417e966608dbbee183b0%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313648038042589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=nNSeM2tEA07WAFSKf5RGUueIPDegncuLP%2BKgf5X%2Bz2E%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!ODjhdQq9byQk5g8hrf2t2PvaVrxRgb22w8weWOe9X-Pv37m5tDdBPtVvfBU7K4HYOTOcyrD83M1PxhpqXYlAvyHVs6i_WdoX$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Missing Java on Windows Development Machine palomino4
Hi Michael, Java is installed on the devel windows builder Palomino4 in the same way it is installed on the release 3.17 Windows builder. I think https://code.bioconductor.org/browse/rRDP/blob/devel/R/RDP.R#L63 assumes that JAVA_HOME is set, but it is not set on these builders. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Hahsler, Michael Sent: Tuesday, September 26, 2023 9:40 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Missing Java on Windows Development Machine palomino4 * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi, It looks like Java is not installed on palomino4 (https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fpalomino4-NodeInfo.html__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Ilyt-zEJW%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=mqeiSpnP7G7m6jesTYLcYpih%2BcL1AYwiAmTMZFg3Hck%3D=0 ). RDP interfaced by rRDP is a Java application. Package rRDP specifies: SystemRequirements: Java JDK 1.4 or higher It now fails on the Windows test server (Development): https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FrRDP%2F__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il4DjcClu%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=r9OvDPFH1%2Fw9Jfx2brWFYYULUvr%2FzM5VkVOWh%2FeDprI%3D=0<https://urldefense.com/v3/__https://www.bioconductor.org/checkResults/devel/bioc-LATEST/rRDP/__;!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il4DjcClu$> Bioconductor Core Team, please install a JDK on the machine or let me know if it is intentionally unavailable on that machine. Best regards, Michael -- Michael Hahsler Associate Professor mhahs...@smu.edu<mailto:mhahs...@smu.edu> Department of Computer Science Bobby B. Lyle School of Engineering Southern Methodist University Dallas, TX 75205, USA Click here for more information (office hours, etc.)<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmichael.hahsler.net%2F__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il1L4pTD8%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=VYetsgIOn28Ihv9xvgKmTjHUcOHurfCLhKQA0Eq0Bm8%3D=0 > From: Rainer Johannes Sent: Tuesday, September 26, 2023 1:02 AM To: Hahsler, Michael Cc: bioconductorcoret...@gmail.com Subject: Package "rRDP" failing on Bioconductor devel You don't often get email from johannes.rai...@eurac.edu. Learn why this is important<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il6RxcsNr%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=9Xc2pcLzslWjCmKJXLGhhmwenj7ZWahbrKjlrg09sZ4%3D=0 > Dear package maintainer, your package "rRDP" is currently failing on the Bioconductor devel branch (error for R CMD build on Windows; build report from 2023-09-24). Please have a look into this and fix the issue. From the error message it seems that java is missing on that build machine. Eventually get in contact with the Bioconductor core team for help. Please use the Bioconductor developer mailing list if you need any help (also from Bioconductor core) or have any questions. Thank you, Johannes Rainer Johannes Rainer, PhD Eurac Research Institute for Biomedicine Via A.-Volta 21, I-39100 Bolzano, Italy email: johannes.rai...@eurac.edu github: jorainer mastodon: jorai...@fosstodon.org [[alternative HTML version deleted]]
[Bioc-devel] Bioconductor project proposals for Outreachy internships by 9/29
Bioconductor is participating in the Outreachy internship program for the December 2023 - March 2024 cohort. Outreachy's goal is to support people from groups underrepresented in the technology industry. Interns will work remotely with mentors from our community. We are seeking mentors from the Bioconductor community to propose projects that Outreachy interns can work on during their internship. Projects must be open source and can include programming, research, design, event planning, UX, data science, and more. The deadline to submit projects is next week on Sept. 29, 2023 at 4 pm UTC. Visit https://www.outreachy.org/communities/cfp/bioconductor/ to submit a project. Mentors FAQ: https://www.outreachy.org/mentor/mentor-faq<https://www.outreachy.org/mentor/mentor-faq/> Full details about the Outreachy program and the internship timeline can be found on the Call for Participation page on the Outreachy website: https://www.outreachy.org/communities/cfp/. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] YAPSA failed on the release branch
Both release and devel show the same error. I'm able to reproduce the error when attempting R CMD INSTALL YAPSA in the Bioconductor docker container (https://www.bioconductor.org/help/docker/). I recommend using it to troubleshoot this error. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Zuguang Gu Sent: Saturday, September 16, 2023 12:41 AM To: bioc-devel Subject: [Bioc-devel] YAPSA failed on the release branch * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi Bioc, The YAPSA package failed on the release branch: ** installing vignettes Warning in file(con, "w") : cannot open file 'F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-YAPSA/00new/YAPSA/doc/index.html': No such file or directory Error in file(con, "w") : cannot open the connection ERROR: installing vignettes failed * removing 'F:/biocbuild/bbs-3.17-bioc/R/library/YAPSA' https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FYAPSA%2Fpalomino3-install.html__%3B!!PxiZbSOawA!ICPPZ7IJXfgBIf1HVv6WEokN6qSCFn0uR0CJ8iWnUfWl4TTfsQK7EEGjYbN0eLz8miT0QLn_nzkHk0Q5PkbTwKerhzw%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Ca888324fa64c4d7a4fbd08dbb66f56eb%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638304361561054701%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=BWUf3mhca%2BdwmIDW%2B7GX7Sx5otycrPcGbZhhkOmP9oc%3D=0<https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/YAPSA/palomino3-install.html__;!!PxiZbSOawA!ICPPZ7IJXfgBIf1HVv6WEokN6qSCFn0uR0CJ8iWnUfWl4TTfsQK7EEGjYbN0eLz8miT0QLn_nzkHk0Q5PkbTwKerhzw$> According to the error message, I cannot see how the error occurred. YAPSA passed all the tests on my local machine and also on CRAN win-builder. I guess it might due to the configurations on the building server side? YAPSA passed all tests on devel and the two versions are basically identical. Thanks! Zuguang [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!ICPPZ7IJXfgBIf1HVv6WEokN6qSCFn0uR0CJ8iWnUfWl4TTfsQK7EEGjYbN0eLz8miT0QLn_nzkHk0Q5PkbTSA5OCDw%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Ca888324fa64c4d7a4fbd08dbb66f56eb%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638304361561054701%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=C7gWNIpY9CM3j2haVK6d01c2j1UjAEfuf6kbNSVygFk%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!ICPPZ7IJXfgBIf1HVv6WEokN6qSCFn0uR0CJ8iWnUfWl4TTfsQK7EEGjYbN0eLz8miT0QLn_nzkHk0Q5PkbTSA5OCDw$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] synaptome.db check error
Hi Anatoly, I see we got a few of these on the most recent build. No action is needed as the Bioconductor build system will remove the lock files on the next run next Wednesday. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Anatoly Sorokin Sent: Friday, September 1, 2023 6:34 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] synaptome.db check error * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Dear all, I've found a strange error on *nebbiolo2 <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.18%2Fdata-annotation-LATEST%2Fnebbiolo2-NodeInfo.html__%3B!!PxiZbSOawA!OxBOK7v_etZ8bAv-qRxlhci8I2O9RM1QCBFcLfhFFOwov1NvgVB9VmnJfPhHzMCVFo-5mitDjaEDAFDKYYbLP1u8YQ%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Ca796973f07ed49411b7808dbaad73b31%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638291613648265413%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=v%2BwY9PvGaH64mEpbJowtFOTerNW1EJaQPaOPYmtoLPU%3D=0 >* check server for our package synaptome.db: * installing to library �/home/biocbuild/bbs-3.18-bioc/R/site-library� ERROR: failed to lock directory �/home/biocbuild/bbs-3.18-bioc/R/site-library� for modifying Try removing �/home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-metaboliteIDmapping� What should I do to get rid of it? Cheers, Anatoly [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!OxBOK7v_etZ8bAv-qRxlhci8I2O9RM1QCBFcLfhFFOwov1NvgVB9VmnJfPhHzMCVFo-5mitDjaEDAFDKYYYaT7wrwQ%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Ca796973f07ed49411b7808dbaad73b31%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638291613648265413%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ShBv%2BwHsevzYnjtPL%2FFd%2BKC6714XqYagqXvvam4BOg4%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!OxBOK7v_etZ8bAv-qRxlhci8I2O9RM1QCBFcLfhFFOwov1NvgVB9VmnJfPhHzMCVFo-5mitDjaEDAFDKYYYaT7wrwQ$> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Seeking Outreachy internship project proposals
Bioconductor is participating in the Outreachy internship program for the December 2023 - March 2024 cohort. Outreachy's goal is to support people from groups underrepresented in the technology industry. Interns will work remotely with mentors from our community. We are seeking mentors from the Bioconductor community to propose projects that Outreachy interns can work on during their internship. Projects should be open source and can include programming, research, design, event planning, UX, data science, and more. The deadline to submit projects is Sept. 29, 2023 at 4 pm UTC. Visit https://www.outreachy.org/communities/cfp/bioconductor/ to submit a project. Outreachy will also host a live talk on August 22 at 4PM UTC on their YouTube channel at https://www.youtube.com/@outreachyinternships. I also gave a short talk about mentoring with Outreachy and in particular preparing the proposal during Bioc2023's Outreachy Birds of a Feather. If you want help crafting your project proposal, you're welcome to reach out to me via email or the Bioconductor Slack. Mentors should read the mentor FAQ: https://www.outreachy.org/mentor/mentor-faq<https://www.outreachy.org/mentor/mentor-faq/> Full details about the Outreachy program and the internship timeline can be found on the Call for Participation page on the Outreachy website: https://www.outreachy.org/communities/cfp/ Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] rfaRm package
Hi Lara, Today, I tried R CMD build on your package on our Linux release builder and got the following: ~/bbs-3.17-bioc/R/bin/R CMD build rfaRm * checking for file ‘rfaRm/DESCRIPTION’ ... OK * preparing ‘rfaRm’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘rfaRm.Rmd’ using rmarkdown Quitting from lines 74-83 [unnamed-chunk-3] (rfaRm.Rmd) Error: processing vignette 'rfaRm.Rmd' failed with diagnostics: Timeout was reached: [rfam.org] SSL connection timeout --- failed re-building ‘rfaRm.Rmd’ SUMMARY: processing the following file failed: ‘rfaRm.Rmd’ Error: Vignette re-building failed. Execution halted However, I see that it actually passed the build today on that same machine but failed on R CMD check, so it's possible that that the problem is intermittent due to connection issues. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Selles Vidal, Lara Sent: Monday, June 19, 2023 9:37 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] rfaRm package * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Dear all, My rfaRm package has been giving TIMEOUT in the build results on all plaforms recently. I have been tried to debug the issue, but I am unable to reproduce the problem locally. The build report only seems to indicate that it times out while building vignettes (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_rfaRm_merida1-2Dbuildsrc.html=DwIFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=qTwdJxyJM_TNb3T9s_tfKmSX0e7aNvkVIBXATnsYJRaFl9_9IE9R7tqCSRJcDRJH=VhKun5uNWjqnt5WsUNKIC1Z6vYVC3LnChzZWpGFvQfg= ). Would there be any way to specifically find out at which point of building the vignette the timing out is taking place? Thanks a lot in advance! Best wishes, Lara ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=qTwdJxyJM_TNb3T9s_tfKmSX0e7aNvkVIBXATnsYJRaFl9_9IE9R7tqCSRJcDRJH=KEVTPqjo3zFZDhjjgKDTI9MkdA4cXZZdcbDxUojcQ_k= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Single Package Build Machines Update
Hi, The build machines used for single package submissions will be updated today so they will be temporarily unavailable until 1pm. Thanks for your understanding. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Adding package to long tests
Hi Nils, Thanks for your email. There was a configuration on our end with the mac builder, merida1. I ran the last report without it, so we can see that imcRtools is now on the report: https://bioconductor.org/checkResults/3.17/bioc-longtests-LATEST/. The report generated on Saturday will include the mac builder. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Nils Eling Sent: Monday, June 5, 2023 5:28 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Adding package to long tests * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi all, I'm trying to add my package (imcRtools) to use long tests as explained here: https://urldefense.proofpoint.com/v2/url?u=https-3A__contributions.bioconductor.org_long-2Dtests.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=XbylC5b9IgGsf9vJ1fVmehLoCF40sU1f9yjtTXnFrOwDNt1JdGnj2B1JxDo6lPpG=3hu4AG0g1nBMN-4QtQklDkUTnWLFFjrYHu2a-KZPhXk= This is to avoid a time out on MacOS for the current release. I have pushed the changes roughly 2 weeks ago but don't see it added to the long tests report (https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2Dlongtests-2DLATEST_=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=XbylC5b9IgGsf9vJ1fVmehLoCF40sU1f9yjtTXnFrOwDNt1JdGnj2B1JxDo6lPpG=Gccl_6EVqo4CV1BTkdXTbHRscMFWuREuyfyobQeCqas= ) The release code for the package is at: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BodenmillerGroup_imcRtools_tree_RELEASE-5F3-5F17=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=XbylC5b9IgGsf9vJ1fVmehLoCF40sU1f9yjtTXnFrOwDNt1JdGnj2B1JxDo6lPpG=mU0SzXYpVJuys4UiFhJST0ILAlCpcfFT4AWG-VS5IyQ= I would appreciate any hints on what I would need to do to get it added. Best, Nils [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=XbylC5b9IgGsf9vJ1fVmehLoCF40sU1f9yjtTXnFrOwDNt1JdGnj2B1JxDo6lPpG=rtC3dAQXLszQv9FdmJ0kVZECAOFWqRZNO1ypg4tiIkg= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package "rmspc" failing on Bioconductor devel
Hi Meriem, We had .NET 5.0 on those machines, which I've updated to 6.0. You should see the errors clear up tomorrow or Thursday. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Meriem Bahda Sent: Thursday, May 25, 2023 9:32 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Package "rmspc" failing on Bioconductor devel * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Dear Community, I have submitted a recent version of the package rmspc to Bioconductor recently, in order to upgrade it. A prerequisite for the rmspc package is .NET 6.0. Before installing the rmspc package, the program .NET 6.0. should already be installed on the user's computer. I recently received an email saying that the package didn't pass the platform build check for the host *nebbiolo2* , *palomino4* and *lconway* . I believe this error may have occurred because .NET 6.0 isn't installed on these platforms. Thank you for your help! -- *Meriem BAHDA* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=2uirUJFRQwNMbNX8n9aSKkM4CyDAk6XJIBj_ln8v24kpQn49x7HraG55jLuZKd_H=E5CJKDLa6sWjGyJ8ooCnbccn1EmDyX_2M_H_pyT_6Bo= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] _R_CHECK_SUGGESTS_ONLY_ reinstated on release
On May 10th, we reinstated _R_CHECK_SUGGESTS_ONLY_ to identify missing package dependencies on the 3.17 release Linux builder, so you may notice more errors in CHECK from the build report. The flag was temporarily removed it was added very close to the release, but it will remain part of the builds going forward. The error can be resolved by adding the missing dependency to Suggests in the DESCRIPTION file. You can read the original announcement at https://stat.ethz.ch/pipermail/bioc-devel/2023-March/019555.html. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Version Bumped Packages for Mac Intel and Mac Silicon binaries with bad dynamic links
As a result of some Mac Intel and Mac Silicon binaries for 3.17 and 3.18 not linking correctly to the dynamic libraries as reported at https://support.bioconductor.org/p/9151097/ and on the community Slack, we've corrected the linking on the builders and bumped versions for affected packages listed below so that their binaries may be rebuilt correctly. The new binaries should be available from Wednesday 1pm ET. If you are a maintainer of one of the affected packages, please remember to pull from git.bioconductor.org before doing work on the corresponding branch. Additionally, thanks to Herve, we can also see that links are corrected at the end of the build bin step of the report under 'Fixing paths to dynamic libraries.' 3.17 BANDITS BASiCS BDMMAcorrect BPRMeth BUSpaRse BUSseq BayesSpace CGEN CNAnorm COMPASS CelliD DEScan2 DESeq2 DNAcopy DegNorm DifferentialRegulation FRASER GGPA GRENITS GeneSelectMMD GeneticsPed HDTD LEA Linnorm MSstats NuPoP OUTRIDER SAIGEgds SC3 SIMLR SNPRelate affyPLM bambu bandle bayNorm ccImpute celda chromVAR densvis distinct edgeR enhancerHomologSearch epigraHMM epistasisGA genefilter glmGamPoi graper iClusterPlus iPath impute oligo pRoloc preprocessCore qpgraph sSNAPPY scGPS scde scmap scran scuttle signeR 3.18 BPRMeth CGEN CNAnorm COMPASS DNAcopy GGPA GRENITS GeneSelectMMD GeneticsPed GeoDiff HDTD LEA Linnorm MSstats NuPoP SAIGEgds SIMLR SNPRelate affyPLM densvis edgeR genefilter graper iClusterPlus impute preprocessCore Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Windows build error
Hi, cfTools will be still be included in 3.17. I don't see the error relating to conda on today's build report. We don't directly manage conda on the builders and allow basilisk to handle it. I can try clearing the cache on the 3.17 Windows builder this week to see if that helps. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of RAN HU Sent: Thursday, April 20, 2023 2:58 PM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Windows build error ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear BioC team, I wonder if this error is caused by your Windows environment. Or is there anything I can do to fix it? If this Windows build error is not solved, will cfTools still be included in the 3.17 release version? Thanks in advance! Best, Ran On Tue, Apr 18, 2023 at 4:46 PM RAN HU wrote: > Hi all, > > My package cfTools has recently been accepted. I just found that there is > a build error on Windows: Multiple platform build/check report for BioC > 3.17 - BUILD results for cfTools on palomino3 (bioconductor.org) > <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.17_bioc-2DLATEST_cfTools_palomino3-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=a5vg0H-TJG4KeZppnKMuNeJ5EAUERiCoGcYn3fd9i4oH62Nu-WzHwN2s1gQRetTh=KOoT4OpK2XZLs9HelMrfHFQOnn7jiUQUwZZVoZ4tUPE= > >, > citing: > > ==> WARNING: A newer version of conda exists. <== > current version: 4.12.0 > latest version: 23.3.1 > > Please update conda by running > > $ conda update -n base -c defaults conda > > Quitting from lines 160-162 (cfTools-vignette.Rmd) > Error: processing vignette 'cfTools-vignette.Rmd' failed with diagnostics: > cannot open the connection > --- failed re-building 'cfTools-vignette.Rmd' > > How can I fix this? > > Many thanks, > Ran > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=a5vg0H-TJG4KeZppnKMuNeJ5EAUERiCoGcYn3fd9i4oH62Nu-WzHwN2s1gQRetTh=4oEXxb6o1UOPRQN9_MJMGMQ62vRBiormcIAeeXONNUU= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] /home/biocbuild/bbs-3.17-bioc/R/bin/R: not found
Hi, I am updating the Linux builder with a newer version of R. I'll try to provide a notice for future updates to avoid confusion. I should be finished about 1 PM ET. Thanks for your patience. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Arek G�adki Sent: Monday, April 17, 2023 12:24 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] /home/biocbuild/bbs-3.17-bioc/R/bin/R: not found ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi, There seems to be an issue with the R binary on Linux environment. Link to the build report: https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_gDRstyle-5Fbuildreport-5F20230417121012.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=MfBk18NYA_9OOVWLvgfMlBJ-G4YFBDtNqfG_UMC3I6KlIYpJhiu6LSpehcJGDJJ0=cSFppEyXa30G4mcUuIfwtp8tBqLb0bWpqlTv7_tD4tg= Thanks in advance for your help. Best, Arek [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=MfBk18NYA_9OOVWLvgfMlBJ-G4YFBDtNqfG_UMC3I6KlIYpJhiu6LSpehcJGDJJ0=NxCoiqXbMJUd1fxcW-u6yypAi2ZwAVBlE2MX_VP9kqM= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problem in merida1
Hi Jose, Thanks for your message. I just noticed this issue. I'm working on a fix now that I hope will resolve the issue later this week. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Jos� Luiz Rybarczyk Filho Sent: Tuesday, April 11, 2023 1:29 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Problem in merida1 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi! I got this error in merida1: ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib not found! How can I fix this? Jos� Luiz [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=LtEik0l8FjhTW9lgsTVVx08o7xtMFg5M8deIi1tyf-iP1gnph8UM38LsJ6FZN48O=cothix6qVFqDoKRaqrDtbkUIk9OWTCQ8NYgyvsEdoIA= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Push changes to release branch
Yes, you should make changes on release as well. You can read more about how to do this at https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel. Chapter 21 Git Version Control | Bioconductor Packages: Development, Maintenance, and Peer Review<https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel> The Bioconductor project is maintained in a Git source control system. Package maintainers update their packages by pushing changes to their git repositories. This chapter contains several... contributions.bioconductor.org Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of matine rb Sent: Monday, March 27, 2023 4:09 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Push changes to release branch ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi Bioc-team, I am the maintainer of the HPiP package. The package showed a problem last couple of weeks and I have already committed changes to the devel branch. The package is fine now without any errors or warnings in the devel branch. My question is do I need to commit those changes to the release branch as well? Thank you, Matineh Rahmatbakhsh [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=D2WeHerUr5ukjRs0NRwlI4HrTjcP3vJxAWQfMelwQVFoYANfTcOqxGnVBNeyEDZa=AHzZRZ8bAXjrSnFmX0IKwCo1F26mp2TcctP3G7MawxU= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] _R_CHECK_SUGGESTS_ONLY=true
On March 29, we'll add _R_CHECK_SUGGESTS_ONLY=true to our devel 3.17 Linux builder to detect missing package dependencies. You can read more about the motivation behind the issue at https://github.com/Bioconductor/BBS/issues/248. If you notice after March 29 that one of your packages is failing R CMD check, consider adding this line to your Renviron.bioc. To reproduce the error, you will need to have a site-library directory in your R home directory, so you'll have to reinstall R and make the site-library before you see the error. To resolve the error, you should identify the missing dependency and add it to Suggests in the DESCRIPTION file. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] "Graphics API version mismatch": Devel package check on macOS failing
Hi Sarvesh, Thanks for reporting the issue. I had to reinstall ragg on merida1. The errors should clear up on tomorrow's build report. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Sarvesh Nikumbh Sent: Monday, March 27, 2023 6:38 AM To: Bioc-devel Subject: [Bioc-devel] "Graphics API version mismatch": Devel package check on macOS failing ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi, I see some devel packages (including my package seqArchRplus <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_seqArchRplus_merida1-2Dchecksrc.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=ggn1h-dsCKMBHaoRwp6mcKa2AIM03HJlij6V-qa_MUwNsUJD00AFSKCOMmdygyzR=4h6KuBHeiVZMgiOmbYJ7PxHDin7WVu9nN9QeQTa_5AI= >) failing on macOS due to "Graphics API version mismatch". The R-devel announcement here <https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_r-2Ddevel_NEWS.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=ggn1h-dsCKMBHaoRwp6mcKa2AIM03HJlij6V-qa_MUwNsUJD00AFSKCOMmdygyzR=qk0nGu1AnN1M9omHNRw6xFYxci0zx7OfQ_XwtfDcyiY= > has the following note under the Graphics head, which is probably the cause of this error (as a similar error was caused on an earlier occasion) GRAPHICS - The graphics engine version, R_GE_version, has been bumped to 16 and so packages that provide graphics devices should be reinstalled. I believe re-installing Cairo on the build machine should be helpful here? Please let us know if there is anything that developers can/should do. Thanks and best wishes, Sarvesh -- thanks! -Sarvesh Q: Why is this email five sentences or less? A: https://urldefense.proofpoint.com/v2/url?u=http-3A__five.sentenc.es=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=ggn1h-dsCKMBHaoRwp6mcKa2AIM03HJlij6V-qa_MUwNsUJD00AFSKCOMmdygyzR=NXMmahHRv0JVjF3zZ8Uwa0vPEwR4MCb6pPw65KgG-fc= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=ggn1h-dsCKMBHaoRwp6mcKa2AIM03HJlij6V-qa_MUwNsUJD00AFSKCOMmdygyzR=kVzzufJoan0T_Gj9ee-szh22IFQ9L0BLj9RBVSPVdbU= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Packages failing on macOS build system - recent updates to the build system?
Johannes, Thanks for reporting this. It should improve in the next build report. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Rainer Johannes Sent: Monday, March 20, 2023 6:44 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Packages failing on macOS build system - recent updates to the build system? ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear Bioc core, after checking some build reports for a set of packages it seems that many are failing due some recent updates with the macOS builder. The common theme seems to be that for these packages (CRAN) dependencies "magick" and "rsvg" are not available on macOS. Just wanted to give a heads up to please look maybe into this. cheers, jo --- Johannes Rainer, PhD Eurac Research Institute for Biomedicine Via A.-Volta 21, I-39100 Bolzano, Italy email: johannes.rai...@eurac.edu github: jorainer mastodon: jorai...@fosstodon.org [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=NM3U9HAHfVzAWpSuLY4aJgQr9DebXN7zAPBYE0J2YpsKnE8oCitCeoWzRwrpiX5L=hqPoWN-D6jh3kIFn41OlxO-XMf-Np2PVx_oMgDMgE2Q= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Fwd: TDbasedUFE problems reported in the Multiple platform build/check report for BioC 3.17
Hi Tag, Yes, I have been trying to resolve issues with Pandoc on our build machines. I know this affected your build report and others. Since you're going through a package review, you'll likely see this resolved sooner on the single package report. For anyone who is looking at the build reports, it will be resolved on Wednesday's report. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Y-h. Taguchi Sent: Tuesday, March 7, 2023 8:10 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Fwd: TDbasedUFE problems reported in the Multiple platform build/check report for BioC 3.17 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear People, Although I have received the following error message, it might not be because of my side The reasons why I thinks so are 1) The error is >Could not find executable pandoc-citeproc This means that the system that tries to build is missing pandoc. 2) many other packages receive the same error. Here are some examples Multiple platform build/check report for BioC 3.17 - BUILD results for BG2 on nebbiolo1 (bioconductor.org) <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_BG2_nebbiolo1-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2=rTl4QTHfTCVAk4tF1Hqn3gF7kVaEd1aqokt_PDyL26Y= > Multiple platform build/check report for BioC 3.17 - BUILD results for planttfhunter on nebbiolo1 (bioconductor.org) <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_planttfhunter_nebbiolo1-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2=hgAyDMpoNzjzUXOAGfYsLp0AW2f-ip7-8wMfCq36IgU= > Multiple platform build/check report for BioC 3.17 - BUILD results for MetaPhOR on nebbiolo1 (bioconductor.org) <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_MetaPhOR_nebbiolo1-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2=dEtwOE6mblSAZVbAJzRpgZjL0APrTbDjlU9GS16eCk8= > 3) I did not commit anything since it has passed the build test last time. Is it possible for you to check if your system that performs build is OK or not? Yours, tag. -- Forwarded message - From: Date: 2023$BG/(B3$B7n(B7$BF|(B($B2P(B) 2:06 Subject: TDbasedUFE problems reported in the Multiple platform build/check report for BioC 3.17 To: [This is an automatically generated email. Please don't reply.] Hi TDbasedUFE maintainer, According to the Multiple platform build/check report for BioC 3.17, the TDbasedUFE package has the following problem(s): o ERROR for 'R CMD build' on nebbiolo1. See the details here: https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.17_bioc-2DLATEST_TDbasedUFE_nebbiolo1-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2=NgRAs3gpRQ7oz-bAocvNL3Ic7-gy2-r1QUX8ewU_Gec= Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_help_mailing-2Dlist_=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=I5Sw5JzBx8K6loFZY3AYVvZX8IfWJ4Au7Hsa65WUiOgfwprbceTNkissdG8hk5f2=AKZXRPLkd_Tjy6IDLooexFjIdbZVb0Vz5LvUdeaFrOY= (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscr
Re: [Bioc-devel] seqArchRplus build error on Linux
Hi Sarvesh, The error should go away on tomorrow's build report. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Sarvesh Nikumbh Sent: Monday, March 6, 2023 6:15 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] seqArchRplus build error on Linux ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi Bioc-team, I get this build error for my package seqArchRplus on Linux/nebbiolo1. --- re-building �seqArchRplus.Rmd� using rmarkdown Error running filter pandoc-citeproc: Could not find executable pandoc-citeproc Error: processing vignette 'seqArchRplus.Rmd' failed with diagnostics: pandoc document conversion failed with error 83 --- failed re-building �seqArchRplus.Rmd� SUMMARY: processing the following file failed: �seqArchRplus.Rmd� I checked the mailing-list and see that this may be due to changing versions of pandoc on some machines. I understand that the team is working on it, and this should go away in a few days? Please let me know if there is something to be done on my end. Thanks and best wishes, Sarvesh -- thanks! -Sarvesh Q: Why is this email five sentences or less? A: https://urldefense.proofpoint.com/v2/url?u=http-3A__five.sentenc.es=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=99kNM8tSnTn_l2Ivt9sYFB8aZ_2zW1x3g_BmShhDjsmn_wiFj84_LJ-IgMVjdLx6=Hu2ZabY8ptsoxQ0OJPImjTxZ-GbhIFe2n3q0JMrdDGw= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=99kNM8tSnTn_l2Ivt9sYFB8aZ_2zW1x3g_BmShhDjsmn_wiFj84_LJ-IgMVjdLx6=-cwPg_qYWeiljycV7Un_e2NszCGGOzzzqZv-fda7r3c= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] libsbml and libxml2 on palomino3 BBS
Hi Ahmed, Thanks for your email. LIB_XML2 should point to C:\libxml2. The path for LIBSBML_PATH is correct and they exist. Since the builds started today, I will make the change tomorrow so that we'll see effect on the Saturday build report. We can troubleshoot the LIBSBML_PATH next. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Ahmed Mohamed Sent: Monday, February 27, 2023 6:11 PM To: bioc-devel Subject: [Bioc-devel] libsbml and libxml2 on palomino3 BBS ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** I'm encountering issues when building my package NetPathMiner on palomino3 ( https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_NetPathMiner_palomino3-2Dchecksrc.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=_qCS3QgxrpFRR9gDVfqzwdSz3y95bJB7-IWrQcHa9hokg9o6Ar-YHbyMj6kuQCZ6=2C7FjRtxvK8D2hdUVtAMkl9GTq17VzEKVt7PlWD0SgM= ). The package depends on system libraries libxml2 and libsbml. So far, I've been using `LIB_XML2` and `LIBSBML_PATH` as previously advised by Bioconductor maintainers. I've noticed lately that NetPathMiner is having trouble finding these packages. *First libxml2,* looking at the log below (output from configure.win), I can see `LIB_XML2` is pointing to `C:/LIB_XML2/`. Is this correct? Looking at the setup scripts ( https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_BBS_blob_master_utils_setup-2Dwin.ps1=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=_qCS3QgxrpFRR9gDVfqzwdSz3y95bJB7-IWrQcHa9hokg9o6Ar-YHbyMj6kuQCZ6=ImDz0ymb5uXiCKQxOyxPdS2nG1FoUt_FrDGjFcQksNI= ), I think it should point to `c:\libxml2`. ** Command: g++ -std=gnu++14 -o xml_test.out xml_test.cpp -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include -IC:/LIB_XML2/x64/include/libxml2 -LC:/LIB_XML2/x64/lib -lxml2 -lws2_32 For *libsbml*, `LIBSBML_PATH` correctly points to `C:/libsbml/`, and NetPathMiner can find the headers needed, but it fails to link against the library (error below). This can be either the binaries are not at `C:/libsbml/x64/bin` or they have been compiled with a different compiler. C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: F:\biocbuild\bbs-3.17-bioc\tmp\cc9H7H7o.o:sbml_test.cpp:(.text+0x20): undefined reference to `SBMLDocument::getModel()' collect2.exe: error: ld returned 1 exit status Many thanks in advance for your help. Cheers, Ahmed. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=_qCS3QgxrpFRR9gDVfqzwdSz3y95bJB7-IWrQcHa9hokg9o6Ar-YHbyMj6kuQCZ6=_A7pxXenVErQP0qAhQr9pc_i7OxJkkaVFWfjDzZgE6A= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Openssl is not available in netConnectHttps for importing remote BigWig files
Hi Leo,
I discussed this with Herve who noticed that you're running rtracklayer on an
M1 Mac, so he looked at
https://bioconductor.org/checkResults/3.16/bioc-mac-arm64-LATEST/rtracklayer/kjohnson-buildbin.html.
It's linking to the static libraries for libssl.a and libcrypto.a so that it
can be used on machine without these libraries according to the following line
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o
rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o
R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o
chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o
ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o
ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o
ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o
ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o
ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o
ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o
ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o
ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o
ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread
/opt/homebrew/Cellar/openssl@3/3.0.5/lib/libssl.a
/opt/homebrew/Cellar/openssl@3/3.0.5/lib/libcrypto.a
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
We have not made any recent changes to these binaries but these are the first
ones we made available for M1 Macs.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Leonardo
Collado Torres
Sent: Thursday, February 23, 2023 2:48 PM
To: Bioc-devel
Subject: [Bioc-devel] Openssl is not available in netConnectHttps for importing
remote BigWig files
***ATTENTION: This email came from an external source. Do not open attachments
or click on links from unknown senders or unexpected emails.***
Hi Bioc-devel,
recount had been failing in recent months at bioc-release and
bioc-devel. I finally had the time to dive into it, and eventually
that led to an error on rtracklayer that I reported at
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lawremi_rtracklayer_issues_83=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_=B-a7fuBFTYUWc0FdqCGxVp5IX_asMYsRZ1BAQeYsXmI=
. Michael Lawrence
noticed that my R session information didn't show openssl being
loaded. In a message there, Michael speculated that maybe a change in
how the rtracklayer binaries were being built by Bioconductor could be
the source of the issue.
Here's a small reprex for the error:
library("GenomicRanges")
library("rtracklayer")
range <- GRanges(seqnames = "chrY", ranges = IRanges(1, 57227415))
rtracklayer::import("https://urldefense.proofpoint.com/v2/url?u=http-3A__sciserver.org_public-2Ddata_recount2_data_SRP002001_bw_mean-5FSRP002001.bw=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_=F0oFWXFFxsylMqc00YZ05rFgLzkkocPevscWyQc=
",
selection = reduce(range), as = "RleList")
And here's the error output:
Error in seqinfo(con) : UCSC library operation failed
In addition: Warning message:
In seqinfo(con) :
No openssl available in netConnectHttps for sciserver.org : 443
> traceback()
7: seqinfo(con)
6: seqinfo(con)
5: .local(con, format, text, ...)
4: import(FileForFormat(con), ...)
3: import(FileForFormat(con), ...)
2:
rtracklayer::import("https://urldefense.proofpoint.com/v2/url?u=http-3A__sciserver.org_public-2Ddata_recount2_data_SRP002001_bw_mean-5FSRP002001.bw=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_=F0oFWXFFxsylMqc00YZ05rFgLzkkocPevscWyQc=
",
selection = reduce(range), as = "RleList")
1:
rtracklayer::import("https://urldefense.proofpoint.com/v2/url?u=http-3A__sciserver.org_public-2Ddata_recount2_data_SRP002001_bw_mean-5FSRP002001.bw=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_=F0oFWXFFxsylMqc00YZ05rFgLzkkocPevscWyQc=
",
selection = reduce(range), as = "RleList")
> packageVersion("rtracklayer")
[1] �1.58.0�
I'm not sure what else I can do to help. As noted at
https://urldefense.
Re: [Bioc-devel] Build error - Latex environment in vignettes
Hi Sergi, I agree these are due to newer pandoc versions on these machines. I'm going make sure both linux and both macs use the same versions this week so we get consistent results. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Sergio Picart Armada Sent: Sunday, February 26, 2023 3:38 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Build error - Latex environment in vignettes ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear bioc-devel list, I am the maintainer of the FELLA package. I got some BUILD errors related to the LaTeX environments: Release: error only on lconway <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_FELLA_lconway-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=SZC3cdDF3FAwwp3w0YNtiJgKxdcbNSGJhvWXgM_alRVi9A4Efgp7PjfMKlfEIXPF=7rnUtLpHW3am2NIjFmW92rBw__T2ZgbjBTj6u637lMM= > * creating vignettes ... ERROR --- re-building �musmusculus.Rmd� using rmarkdown ! LaTeX Error: Environment cslreferences undefined. Devel: error only on nebbiolo1 <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_FELLA_nebbiolo1-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=SZC3cdDF3FAwwp3w0YNtiJgKxdcbNSGJhvWXgM_alRVi9A4Efgp7PjfMKlfEIXPF=IkRNxO5WoxQuxSU3DvkGmDDOWYM85o5MD7W6goHeCtE= > * creating vignettes ... ERROR --- re-building �musmusculus.Rmd� using rmarkdown ! LaTeX Error: Environment CSLReferences undefined. I suspect the pandoc version on the testing machines may have something to do with it. What is strange, this only happens in the macOS machine (release) and linux (devel), in two different vignettes. Any recommendations on how to handle this? Thank you Sergi [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=SZC3cdDF3FAwwp3w0YNtiJgKxdcbNSGJhvWXgM_alRVi9A4Efgp7PjfMKlfEIXPF=Wj1QQnjw002k-fRGntmA9DTn_GZR9I98p8CSIzuP-TQ= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Java version on merida1?
These are the results for merida1:
merida1$ java --version
openjdk 18.0.1.1 2022-04-22
OpenJDK Runtime Environment (build 18.0.1.1+2-6)
OpenJDK 64-Bit Server VM (build 18.0.1.1+2-6, mixed mode, sharing)
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Shraddha Pai
Sent: Wednesday, February 22, 2023 1:20 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Java version on merida1?
***ATTENTION: This email came from an external source. Do not open attachments
or click on links from unknown senders or unexpected emails.***
Hello BioC community,
What�s the Java version installed on Merida1?
I have a package failing build specifically on that macOS machine (has worked
with older versions of BioC) and I suspect it�s got a newer version of Java,
but want to rule out other possibilities.
Thanks,Shraddha
--
Shraddha Pai, PhD
Principal Investigator
Adaptive Oncology
Assistant Professor
Department of Medical Biophysics
University of Toronto
shraddha@oicr.on.ca<mailto:shraddha@oicr.on.ca>
Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
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Re: [Bioc-devel] Package "rmspc" failing on Bioconductor devel
Using the mailing list or the #bioc-builds channel on the community slack are good ways to reach out to the Bioconductor core team. I'll look into the dotnet issues for rmspc. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Meriem Bahda Sent: Sunday, January 22, 2023 6:06 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Package "rmspc" failing on Bioconductor devel ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear Community, I have submitted a recent version of the package rmspc to Bioconductor recently, in order to upgrade it. A prerequisite for the rmspc package is .NET 6.0. Before installing the rmspc package, the program .NET 6.0. should already be installed on the user's computer. I recently received an email saying that the package didn't pass the platform build check for the host *nebbiolo1*, *palomino3* and *merida1*. I believe this error may have occurred because .NET 6.0 isn't installed on these platforms. Do you know who I should contact about this issue? Thank you! -- *Meriem BAHDA* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=RkAeJ7s4baKaPd3cIWElUK_d1dX2hXbGTbdXd_IlDpV3MZlC0fRmIvQrcj8kB0TR=oac21zxfx9Vk9cYzPVvQ0emQOYUOYhn3RyYMEp6_6Io= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Maftools not working on Mac therefore package not passing macOS checks
Graciela, Thanks for the link to the issues using 3.16 on a Mac. It helped me to see there's a gfortran issue on our Mac I needed to fix but it will need time to propagate. I anticipate it will be resolved by next week. Regarding your package, I echo Marcel's response that you should go ahead and submit. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Graciela Uria Regojo Sent: Tuesday, January 17, 2023 9:14 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Maftools not working on Mac therefore package not passing macOS checks ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hello, I�m working on a new R package for bioconductor and my packages uses maftools::read.maf function. All R CMD checks for ubuntu and windows are fine but I get an error on macOS related to a general problem that is going on now with installing maftools and subsequently DNAcopy in Mac. It seems like the problem is related to gcc, fortran and clang not being compatible: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_PoisonAlien_maftools_issues_886=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=HKWmjrORz07tMPph7OgPJtPftCQusyv9KxeIlFO0TabSX4U9QihALwrYRfRAl0FL=5nh14p_6rDsz5Xrc2CW8TLQPppT47sC3EPaOkIxPn3c= <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_PoisonAlien_maftools_issues_886=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=HKWmjrORz07tMPph7OgPJtPftCQusyv9KxeIlFO0TabSX4U9QihALwrYRfRAl0FL=5nh14p_6rDsz5Xrc2CW8TLQPppT47sC3EPaOkIxPn3c= > which is why my package is failing the check on macOS. This should be fixed I hope, my question is if I can contribute my package to bioconductor even though I have this problem at the moment of macOS failing my check (maftools should be fixed soon) Thank you for your help [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=HKWmjrORz07tMPph7OgPJtPftCQusyv9KxeIlFO0TabSX4U9QihALwrYRfRAl0FL=kV932g8NgcvdrFBPGFbRIdrR1ifTu6Sic3V-zOy3WE0= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] official bioconductor link to the package
Hi Anna, If your package was recently accepted around the holidays, it should be processed by the end of the week. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Anna Pa��nkov� Sent: Monday, January 2, 2023 3:26 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] official bioconductor link to the package ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear developers, I want to ask how long does it take to have an official Bioconductor link to the package after adding to Bioconductor nightly builds. I have found it should be after max 48 hours. I cannot find the link to my IntOMICS package ( https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_2744=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=eB6xLkg-94n01QQj2u6Bf9uc-vq6jbHl_kiv5UUpvRpdkzonXaGa7YhlE1GNC98n=DLsjogKlnDxg9vempKioyWqFCjIdYhiD2DUhdcr1jmI= ). Am I wrong, and do I have to wait longer? Best wishes, Anna [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=eB6xLkg-94n01QQj2u6Bf9uc-vq6jbHl_kiv5UUpvRpdkzonXaGa7YhlE1GNC98n=NsxI-jc7Icer90C8qQb73R5IygTWvtavz4S3DST3PmM= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] package PloGO2 error on Windows build advice
Hi Dana, Hope you had a great holiday. I updated MiKTex and was able to build PloGO2 manually on palomino4. Let's check the build report tomorrow and see if the error is cleared up. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPS Bioconductor Core Team From: Bioc-devel on behalf of Dana Pascovici Sent: Thursday, November 24, 2022 11:05 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] package PloGO2 error on Windows build advice ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi, I was wondering if you can offer any advice for fixing a current error for our package PloGO2 - it is there only on Windows release build and has not been there before. https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_PloGO2_palomino4-2Dbuildsrc.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=XpIJlU-quMrtDr3lXRBshZrZ0oRayN3AUzBSIMqnpFqcm3ghGLwcNxI6rpf8wprZ=2EybUrneevAGrVW5eV4990cnYCTrCBnoYqGuJtFBcFU= The first issue seems to be as below: texify: major issue: So far, you have not checked for updates as a MiKTeX user. Any advice would be appreciate - and happy Thanksgiving btw, don't expect any responses for a while! Kind regards, Dana [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=XpIJlU-quMrtDr3lXRBshZrZ0oRayN3AUzBSIMqnpFqcm3ghGLwcNxI6rpf8wprZ=pSfwLfE7rS7WiLJM4psAJAyv-J-38y6vTXk87sW7zsQ= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Failed to locate 'texi2pdf' - Windows build error
Hi Pedro, I don't see these issues on today's build report, so they may have been resolved. If you see the issue again, let us know. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPS Bioconductor Core Team From: Bioc-devel on behalf of Pedro Madrigal Sent: Friday, November 25, 2022 4:09 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Failed to locate 'texi2pdf' - Windows build error ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear Bioc-Devel I have a couple of packages (CexoR, fCCAC) failing the Windows-build due to Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) : running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033 Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", : running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "CexoR.tex" ' had status 1033 Error: processing vignette 'CexoR.Rnw' failed with diagnostics: Failed to locate 'texi2pdf' output file 'CexoR.pdf' for vignette with name 'CexoR' and engine 'utils::Sweave'. The following files exist in working directory 'F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmpkf5YYz\Rbuild42143e2f6b79\CexoR\vignettes': 'CexoR.Rnw' (6938 bytes), 'CexoR.tex' (14846 bytes) --- failed re-building 'CexoR.Rnw' I think this is happening in other packages as well. Could please provide advice? Best wishes, Pedro -- Dr Pedro Madrigal Senior Bioinformatician, Gene Expression Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, United Kingdom [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=-FclmDt0uLHmAGUyQ2qFlSCNHEss7xxExR__ih3WtQ-vrQgJo-UMIfJE-sWPsIir=vlTkawNFotVv7kwME8ZtWVxqEpYGFN8R1AzFRIelo-w= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] palomino4 CHECK error "permission denied" msqrob2
Thanks for your email. I'll look into this. From: Bioc-devel on behalf of vandenbulcke stijn Sent: Friday, October 28, 2022 9:29 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] palomino4 CHECK error "permission denied" msqrob2 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear All, On the palomino4 host the check for msqrob2 returns the following error ( https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_msqrob2_palomino4-2Dchecksrc.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=HNeyisXM7SP-moqvWWnaXru04ziiE1kXfXFE43gC6oe4eq79u7VxKHBWxpknrTwU=F79QOTCx_p3FTiKuMas7dkAWWqpkE84sGvg3QWSDqZY= ) * checking examples ...Warning in file(con, "r") : cannot open file 'msqrob2-Ex.Rout': Permission denied Error in file(con, "r") : cannot open the connection Execution halted I am however not able to reproduce this, and it works on the other hosts. Would anyone know the cause of this issue? Thanks in advance Stijn [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=HNeyisXM7SP-moqvWWnaXru04ziiE1kXfXFE43gC6oe4eq79u7VxKHBWxpknrTwU=Zu4D5KpYLpfevsh0dKoPEj2D7gj0t842cfe8ODlO_9k= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Increase version of system dependency?
Hi Sarvesh, I've installed packaging on our devel Windows builder. We should see the issue resolved in the next build report. Jen From: Bioc-devel on behalf of Sarvesh Nikumbh Sent: Thursday, October 20, 2022 12:08 PM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Increase version of system dependency? ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi bioc team, Could you please install the Python module 'packaging' on palomino4? I have pushed the updated SystemRequirements yesterday. Linux and macOS seem to be fine. Thanks in advance. Best wishes, Sarvesh On Wed, 19 Oct 2022 at 02:36, Herv� Pag�s wrote: > Hi Sarvesh, > > All I see is that seqArchR fails on palomino4 because Python module > 'packaging' is not available on that machine. > > The module seems to be available on the other builders though so no > problem there. > > Anyways if your package depends on that module (and it seems that it > does, via the inst/python/perform_nmf.py script), then you need to list > the module in your SystemRequirements. > > Then we'll make sure to install the module on all the builders. > > Thanks, > > H. > > > On 18/10/2022 09:31, Sarvesh Nikumbh wrote: > > Hi bioc team, > > > > My package seqArchR though does not error in any way, but can spit out > > numerous warnings (originally from Python/scikit-learn which is a > > dependency) depending on the version of scikit-learn available. This > fills > > the output to the extent that it is unreadable. The cause for this is the > > deprecation/future version warning in NMF/scikitlearn > > < > https://urldefense.proofpoint.com/v2/url?u=https-3A__scikit-2Dlearn.org_stable_modules_generated_sklearn.decomposition.NMF.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=DzxNJLg1ADaS3XDof9AnhKWeOBenp1DvnG6qt37swGk= > > > > which is forced, so I cannot suppress it. > > > > I pushed a fix for this in the devel version -- where, instead of > > increasing the dependency version, I check the module version using > > packaging module from setuptools and appropriately make the python > function > > call. But this gives an error on the Windows build machine, and is fine > on > > Linux/macOS. > > See > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.16_bioc-2DLATEST_seqArchR_palomino4-2Dchecksrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=yJdY-LnSsA0-Xfh47DYFXIxLFxWOy8gQEQu4BiIwBA0= > > > > I expected that setuptools will be available on all machines, because the > > previous alternative, distutils, is available with vanilla python, but is > > not recommended. > > > > Would you suggest having setuptools in the SystemRequirements or using > > distutils? > > Or simply depending on higher version of scikit-learn (the latest 1.2) -- > > which is the root cause of this issue anyway. > > > > Thanks and best, > >Sarvesh > > > -- > Herv� Pag�s > > Bioconductor Core Team > hpages.on.git...@gmail.com > > -- thanks! -Sarvesh Q: Why is this email five sentences or less? A: https://urldefense.proofpoint.com/v2/url?u=http-3A__five.sentenc.es=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=tINaCsEcKRF4gJ2k-iW6J1n_Rsucc632G8xtz784wnI= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=CNOml7Ibm5f1NLsQePoNZeV9smJCxNRI5nNd8D2JVp0= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Package "rmspc" failing on Bioconductor devel
Hi Meriem, .NET 6.0 was installed on lconway, so I removed it and replaced it with .NET 5.0; however, I noticed that 5.0 is no longer supported by Microsoft, which now suggests .NET 6.0. The new version also supports Mac ARM64 whereas 5.0 does not. You may want to consider upgrading your package to work with .NET 6.0 in the future. Jennifer Wokaty they/them Bioconductor Core Team CUNY SPH From: Bioc-devel on behalf of Meriem Bahda Sent: Wednesday, September 28, 2022 11:48:47 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Package "rmspc" failing on Bioconductor devel ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear Community, I have submitted the package rmspc to Bioconductor in July 2021. A prerequisite for the rmspc package is .NET 5.0. Before installing the rmspc package, the program .NET 5.0. should already be installed on the user's computer. The Bioconductor team added .NET to their builders and the package was accepted in August 2021. A few days ago, I received an email saying that the package didn't pass the platform build check for the host *lconway*. I believe this error may have occured because .NET isn't installed in *lconway*. Who should I contact regarding this issue? Thank you! -- *Meriem BAHDA* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=s-YswEW41gROI8S_wD_AX8ZJ9expf9K1dhkMcgPz-YBzSrjmjQvxbj5-vFs8sTQm=iEHJAsIE5FHCWx16GXGObcDffUdDbMPYtzkjYge7CXo= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] broken DOI link for SINGLe package
Hi Rocio, Thanks for bringing this to our attention. I've fixed the DOI for SINGLe. Jennifer Wokaty they/them Bioconductor Core Team CUNY SPH From: Bioc-devel on behalf of Rocio Espada via Bioc-devel Sent: Wednesday, September 28, 2022 7:51 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] broken DOI link for SINGLe package ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi, The DOI link for the package SINGLe (which I uploaded to bioconductor) is not working. Do you know how I can fix this? This is the link to the package (that does work): https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_release_bioc_html_single.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=7FmOGwG3w09AwysDnb8Mkoe_nOk8KtlEkHCXFNrJMN4s-f0d4JllRph-pHuaRrJm=LcpRgSrxEqBnuWyGR3u5fnNwC1rP1Jc5_LkPoFIlWRQ= and this is the DOI's link included there, that does not work: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_doi-3A10.18129_B9.bioc.single=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=7FmOGwG3w09AwysDnb8Mkoe_nOk8KtlEkHCXFNrJMN4s-f0d4JllRph-pHuaRrJm=rGiIvVYCzEeKC19nlsEiMeiUG6regDYdLlnGssZaAUk= Thanks in advance, Rocio ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=7FmOGwG3w09AwysDnb8Mkoe_nOk8KtlEkHCXFNrJMN4s-f0d4JllRph-pHuaRrJm=ZaHIHKKE-ygIG-8YOPNB2sgJOYdaeVQQcAXxuVK0kos= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Mac ARM64 binaries available
Mac ARM64 binaries are now available. You can view the build report at https://bioconductor.org/checkResults/3.16/bioc-mac-arm64-LATEST/. To make use of these binaries * Install R-4.2.1-arm64.pkg from CRAN at https://cran.r-project.org/bin/macosx/ * Install BiocManager as usual * Use BiocManager::install() as usual Note: BiocManager::install() will automatically pick the new arm64 binaries so you should no longer need Xcode. Jennifer Wokaty they/them Bioconductor Core Team CUNY SPH [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Question on package update and version bump
Hi, They will be updated when the builds finish today. (The report is updated but we still need to propagate the new windows and mac binaries.) Devel builders run everyday except Sunday and there's a new build report for release Monday, Wednesday, and Friday. I updated R on the devel builders on Friday so some of them didn't complete Saturday's run to update the build report, which sometimes happens with a fresh install of R and may have added some confusion. Jennifer Wokaty they/them Bioconductor Core Team CUNY SPH From: Bioc-devel on behalf of Jiping Wang Sent: Monday, June 6, 2022 7:46:14 AM To: Anestis Gkanogiannis; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Question on package update and version bump ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Thanks. I noticed the source package of DegNorm has been updated to 1.7.1, but the windows and macosx version is still 1.7.0. Also when will the changes be updated in the release version, which is currently 1.6.0? From: Anestis Gkanogiannis Date: Monday, June 6, 2022 at 6:30 AM To: Jiping Wang , bioc-devel@r-project.org Subject: RE: [Bioc-devel] Question on package update and version bump Hi, I see DegNorm version 1.7.1 here https://urldefense.com/v3/__https://bioconductor.org/packages/devel/bioc/html/DegNorm.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvTnYY_Do$<https://urldefense.com/v3/__https:/bioconductor.org/packages/devel/bioc/html/DegNorm.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvTnYY_Do$> and build report here https://urldefense.com/v3/__http://bioconductor.org/checkResults/devel/bioc-LATEST/DegNorm/__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvUjVapyY$<https://urldefense.com/v3/__http:/bioconductor.org/checkResults/devel/bioc-LATEST/DegNorm/__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvUjVapyY$> Best regards, Anestis Gkanogiannis, PhD -- https://urldefense.com/v3/__https://linkedin.com/in/anestis-gkanogiannis__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvlATDOCE$<https://urldefense.com/v3/__https:/linkedin.com/in/anestis-gkanogiannis__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvlATDOCE$> https://urldefense.com/v3/__https://github.com/gkanogiannis__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvT2SWuJw$<https://urldefense.com/v3/__https:/github.com/gkanogiannis__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvT2SWuJw$> https://urldefense.com/v3/__https://www.gkanogiannis.com__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvMZFUuT0$<https://urldefense.com/v3/__https:/www.gkanogiannis.com__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvMZFUuT0$> -Original Message- From: Bioc-devel On Behalf Of Jiping Wang Sent: 06 June 2022 13:21 To: bioc-devel@r-project.org Subject: [Bioc-devel] Question on package update and version bump Hi, I am writing to inquire the process of package update and version bump. I submitted updated package DegNorm with a version bump to 1.7.1 last Thursday and wonder about the status of it. My understanding is that usually I should receive an email notice about the status of it. See the help information from https://urldefense.com/v3/__https://contributions.bioconductor.org/git-version-control.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvgo9AdBk$<https://urldefense.com/v3/__https:/contributions.bioconductor.org/git-version-control.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvgo9AdBk$> But I didn�t receive email notices. When I went to the https://urldefense.com/v3/__https://github.com/Bioconductor/Contributions/issues/__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvydOjXeo$<https://urldefense.com/v3/__https:/github.com/Bioconductor/Contributions/issues/__;!!Dq0X2DkFhyF93HkjWTBQKhk!T5uT_ynlcPqd_mYaeaniCBm7xo_qKJc9_guu3MqRGGOOSXhoDa6DuBkr96a67Dth3V9n3M2j-qdnz9AhXcjvydOjXeo$> I didn�t find my package listed there? Is there anything wrong? Or the procedures have been changed? In addition, my understanding is that my push is t
Re: [Bioc-devel] error on riesling1 but not on palomino3
Hi Oleksii, Although it's marked as failing on the devel package page when viewing the short report, if you click on the long report (top right), it's only because of the errors on Riesling. I can confirm that that the issues on Riesling are not a problem for the next Bioconductor release as we will only be looking for errors on Palomino3 (as well as Nebbiolo1 and Merida1). This machine has the new R tool chain for R that we must use going forward for the Windows builds. ? Jennifer Wokaty Bioconductor Core Team From: Oleksii Nikolaienko Sent: Thursday, February 24, 2022 5:05 AM To: Jennifer Wokaty Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] error on riesling1 but not on palomino3 Thanks Jennifer, I tried to fix it and now ran into another (known?) issue because of lack of proper support for "snprintf". I would like to disregard this error, but could you please confirm that it won't be a problem for a coming Bioc release? Package is marked as failing its build on the dev package page... Best, Oleksii On Wed, 23 Feb 2022 at 15:14, Jennifer Wokaty mailto:jennifer.wok...@sph.cuny.edu>> wrote: Hi Oleksii, Palomino3, which has the new UCRT toolchain to allow native support of UTF-8 and non-European languages, will replace Riesling1 soon, so please disregard the error on Riesling1, which is only running for historical reference. We're also working on a way to help troubleshoot issues related to Windows environments. Jennifer Wokaty Bioconductor Core Team From: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> on behalf of Oleksii Nikolaienko mailto:oleksii.nikolaie...@gmail.com>> Sent: Wednesday, February 23, 2022 4:44 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Subject: [Bioc-devel] error on riesling1 but not on palomino3 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear Bioc team, my package (epiallleleR) currently fails tests on riesling1, but not on the other hosts. Wrong results are produced by compiled c++ code, and at the moment I don't understand why. I can see that both Windows hosts use GCC 8.3.0, but the compiler flags are different. I don't have access to Windows, but I wasn't able to reproduce this error on my Linux with GCC 7.5.0 when tried to set "-fno-reorder-blocks-and-partition" in my Makevars, or did "pkgbuild::with_debug(devtools::check())". What are the other differences between riesling1 and palomino3? Is, for example, sizeof(int)<4? And what can I do to debug it if I don't have Windows around? Best regards, Oleksii [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=B6xvuxERd0zSWbao7oo7byBakBmrV9_gcBwdPoQjWfU=CaWbJnskDbCqNtl0c7wj_FQLs6tJcb5PktYg_0E9h10= [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in the Multiple platform build/check report for BioC 3.15
Hi Meriem, Thanks for reporting this issue. I've installed .NET 5.0 on nebbiolo1 and confirmed that I can build rmspc; however, the error may still show up on the build report Friday because we've already started building packages. So it should pass on the build report after that. Jennifer Wokaty Bioconductor Core Team From: Bioc-devel on behalf of Meriem Bahda Sent: Thursday, January 13, 2022 1:02 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Error in the Multiple platform build/check report for BioC 3.15 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear Community, I have submitted the package rmspc to Bioconductor in July 2021. A prerequisite for the rmspc package is .NET 5.0. Before installing the rmspc package, the program .NET 5.0. should already be installed on the user's computer. The Bioconductor team added .NET to their builders and the package was accepted in August. A few days ago, I received an email saying that the package didn't pass the platform build check for the host nebbiolo1. I believe this error occurs because .NET isn't installed in nebbiolo1. Who should I contact regarding this issue? Thank you! -- *Meriem BAHDA* [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=Bj7JnpjDFmcgLxghlL3of9dMqaEAcmL6obJVnWg9xxc=AdQGi5QbP21WkT8BtIX4iv6NBYbjiBZPFH7F5HPH3V4= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] release of new version of package
You can follow https://bioconductor.org/developers/how-to/git/push-to-github-bioc/ to push to both Github and Bioconductor repositories. Jennifer Wokaty Bioconductor Core Team From: Bioc-devel on behalf of Emanuela Iovino Sent: Monday, December 20, 2021 9:32 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] release of new version of package ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hello everyone I'm the developer and the maintainer of Bioconductor package uncoverappLib . I recently added some features to package and I would like to know how update to Biocondunctor . Do I follow new package workflow ? (https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_new-2Dpackage-2Dworkflow_=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=_T1pQgpLd2kgnSc5zaY1UKAWWfDuYDS_1IJBgtpyekI=EMX3UXnvQCEwiG3EL1wy0AqyKKj2BfzyWgxCh_MhkYE= ). Many thanks in advance Emanuela Iovino PhD Student in Data Science and Computation Division of Medical Genetics Dept. Medical and Surgical Sciences - DIMEC University of Bologna Pol.S.Orsola-Malpighi, via Massarenti 9, [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=_T1pQgpLd2kgnSc5zaY1UKAWWfDuYDS_1IJBgtpyekI=NjL7oQGio__Yum0kfJ8FzCTeX7BG7Ox0jkBeuaAe6ZQ= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ReactomeGSA - SSL Certificate Error on MacOS build
Hi Johannes, We've updated the certificates on the release Mac builder yesterday, so we should see these issues clear up on the next release build report Friday. Jennifer Wokaty Bioconductor Core Team From: Bioc-devel on behalf of Johannes Griss Sent: Thursday, October 14, 2021 4:48 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] ReactomeGSA - SSL Certificate Error on MacOS build ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Hi everyone, My package "ReactomeGSA" is currently not building on MacOS due to a presumably expired SSL certificate. The certificate was expired for a few days, but we renewed it already a few weeks ago. It seems, that the build system is not fetching the new certificate. On all other build systems, this was not an issue. Is there anything I can do to fix this? Thanks a lot for the help! Kind regards, Johannes ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=IAwQeL3ZwYPC-UPj1PaXyO-ozUdzx6PzGvqZ5TFHL30=eRRX5w0jOGftTZq9BhefCu9wDIor4wPo6mpjAeVgt14= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] python or python3 support in Linux
Hi Zheng, The builders all have Python installed, but how you access it depends on the OS: for Mac and Linux, use `python3` and for Windows, use `python`. The issue we see in Rbowtie2's build error is related to the lines 432 invisible(.callbinary(lang = "python", 433 bin1 = "bowtie2-build", 434 args1 = paste(argvs,collapse = " "))) 505 .callbinary(lang = "python", bin1 = "bowtie2-build", args1 = "-h") You should check for the the OS to determine how you should call Python, for example using `.Platform$OS.type`. The reason it isn't also failing on Mac is that `python` exists, but it's Python 2, which we no longer support and will likely be removed in the future. Jennifer Wokaty (they/them) Bioconductor Core Team From: Bioc-devel on behalf of Zheng Wei via Bioc-devel Sent: Wednesday, September 29, 2021 7:41 PM To: bioc-devel Subject: [Bioc-devel] python or python3 support in Linux ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear all, I have tested python (Rbowtie2 version 1.15.3) and python3 (Rbowtie2 version 1.15.4). Both of the building results are the same: The python or python3 can not be found in Linux Server. Both versions of python works in Windows and Mac. Could anyone check the Linux server? Thanks, Zheng Wei [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=K-mtn5mmpV1uK5I2LdIYSH9b3jdmVt48zFt_99tAY_Y=dPAvPdhxs9B1UBoTz21iMxVK2eVephlN-roX1mFkH3E= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] python support
Zheng, I talked to Herve about your issue as well as the build machines. You should use `python` for Windows and `python3` for Linux and Mac. Jennifer Wokaty Bioconductor Core Team Waldron Lab CUNY Graduate School of Public Health and Health Policy From: Jennifer Wokaty Sent: Thursday, September 23, 2021 9:55 AM To: Zheng Wei Cc: Bioc-devel Subject: Re: [Bioc-devel] python support Hi Zheng, The Linux builders only have python3 available with no symlink to python due to the deprecation of Python 2. One way this could be solved is by referencing python3 instead of python. I believe the other machines might have Python 2 available, which is why the results are inconsistent, but Bioconductor no longer supports Python 2. Jennifer Wokaty Bioconductor Core Team Waldron Lab CUNY Graduate School of Public Health and Health Policy From: Bioc-devel on behalf of Zheng Wei via Bioc-devel Sent: Thursday, September 23, 2021 7:36 AM To: bioc-devel Subject: [Bioc-devel] python support ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** Dear all, I'm the maintainer of package RBowtie2. Some scripts of Bowtie2 need to be supported by python. RBowtie2 passes the checking and building in Windows and MacOS but fails in Linux because python can not be found in Linux server. How to solve this problem? Here is the result: http://bioconductor.org/checkResults/devel/bioc-LATEST/Rbowtie2/nebbiolo2-buildsrc.html Thanks, Zheng Wei [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
