[Bioc-devel] Incorrect warning about failing package built

Fri Feb 2 01:37:15 CET 2024

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.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$>> 
>>
>> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D&reserved=0 
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D&reserved=0><https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U$ 
>> <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 using r-project.org <mailto:Bioc-devel using r-project.org> mailing list
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>>
>>
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-- 
Hervé Pagès

Bioconductor Core Team
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