[Bioc-devel] Incorrect warning about failing package built

[Johannes Griss]

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.Wokaty using sph.cuny.edu <mailto:Jennifer.Wokaty using 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-bounces using r-project.org
>     <mailto:bioc-devel-bounces using r-project.org>> on behalf of Johannes
>     Griss <johannes.griss using meduniwien.ac.at
>     <mailto:johannes.griss using meduniwien.ac.at>>
>     Sent: Thursday, February 1, 2024 3:18 PM
>     To: bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>
>     <bioc-devel using r-project.org <mailto:bioc-devel using 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$>>
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> 
>     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 using r-project.org <mailto:Bioc-devel using r-project.org> mailing list
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