Just to clarify: we build the vignettes on all platforms, via 'R CMD build'. However when a package contains more than one vignette like here, keep in mind that 'R CMD build' evaluates them all in the same R session. This "feature" can help a vignette succeed even if it's broken. For example if ReactomeGSA got loaded by a previous vignette then evaluation of reanalysing-public-data.Rmd would still succeed even though it doesn't do 'library(ReactomeGSA)'.
To complicate things even more, it could be that the order in which vignettes are evaluated is platform-dependent. This could explain why a vignette succeeds on one platform and not the other. Best, H. On 2/1/24 13:30, Johannes Griss wrote: > Hi, > > Thanks a lot for the quick reply! > > Vignette is already fixed and committed. > > Kind regards, > Johannes > > On 01.02.24 22:24, Martin Grigorov wrote: >> Hi, >> >> On Thu, 1 Feb 2024 at 23:05, Jennifer Wokaty >> <jennifer.wok...@sph.cuny.edu <mailto:jennifer.wok...@sph.cuny.edu>> >> wrote: >> >> 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. >> >> >> I will take a look early next week! >> >> Martin >> >> >> >> 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 <bioc-devel-boun...@r-project.org >> <mailto:bioc-devel-boun...@r-project.org>> on behalf of Johannes >> Griss <johannes.gr...@meduniwien.ac.at >> <mailto:johannes.gr...@meduniwien.ac.at>> >> Sent: Thursday, February 1, 2024 3:18 PM >> To: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> >> <bioc-devel@r-project.org <mailto: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&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200958363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=tbYEx3lk0V%2BBLNUdbLHtclDpeGm9sq5W7Tv9lK%2BnNx8%3D&reserved=0 >> >> <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&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200958363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=tbYEx3lk0V%2BBLNUdbLHtclDpeGm9sq5W7Tv9lK%2BnNx8%3D&reserved=0><https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$ >> >> <https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$>> >> >> >> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D&reserved=0 >> >> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D&reserved=0><https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U$ >> >> <https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U$>> >> >> >> >> On release we have no errors or warnings at all, on devel, >> everything is >> fine in two instances while the others seem to have issues that >> we will >> look into. >> >> Is there anything I can do to fix that? >> >> Kind regards, >> Johannes >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200977608%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=0x4xNPvAHnkGyUcEz4PVIOM8eCVTEWNpNUOkskspUEQ%3D&reserved=0 >> >> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200977608%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=0x4xNPvAHnkGyUcEz4PVIOM8eCVTEWNpNUOkskspUEQ%3D&reserved=0><https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$ >> >> <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 <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
