[Bioc-devel] Incorrect warning about failing package built

Fri Feb 2 08:52:10 CET 2024

Dear Hervé,

Thanks a lot for the explanation and clarification! Issue should be 
fixed by now.

Kind regards,

Johannes

Am 2024-02-02 01:37, schrieb Hervé Pagès:

> 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 
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> [1]<https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$ 
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> [4]>
> 
> 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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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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