[Bioc-devel] OncoSimulR Timeout on kunpeng2 during vignette build

[Ramon Diaz-Uriarte]

Dear Lori,

Thanks a lot for the detailed clarification.

Best,

R.

On Tue, 21-April-2026, at 13:42:25, "Kern, Lori" <Lori.Shepherd using RoswellPark.org> wrote:
> We have identified an issue with the version of R that was being used on kunpeng2 which likely is related.  This can be ignored for now until we
> run an update.
>
> The build results/errors from this machine will not be evaluated when determining packages propagating to the next release. Your package will
> still be included.
>
> Lori Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> -------------------------------------------------------------------------------------------------------------------------
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ramon Diaz-Uriarte <rdiaz02 using gmail.com>
> Sent: Tuesday, April 21, 2026 7:37 AM
> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: [Bioc-devel] OncoSimulR Timeout on kunpeng2 during vignette build
>
> Dear All,
>
> A package I maintain, OncoSimulR, now on version 4.13.4,  is showing a TIMEOUT on kunpeng2
> (https://secure-web.cisco.com/1Eh8FxRUgzDCK8YQO9aEFtH0BUSGt5qXPn-nj4fUSB_-Fmr7sO6-n9Pl9s0Q8HhKbkWYEDZFXcMKkArym_BungjnA7JcOaVJEMFwXK5RdhMi-GfRZdRnrbmEDjMOWqEvOIuvarEcRY2RqDmH4Lh_cylBBD_hSULQU1EChGwKyCZ3GG1VW3DOOVdcQez5osJeTTW4lGW286AyVOaJAa2rb8YI52argSk_g_ToslDxhf1tdW7UbFHopG6t4ULHuWlbjufjmcBMH1fKYOrdxSg97XNr3Gj3n9XcyMaNMQVBiD5dph16MHwVV_9ioDaw9s0Gs/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FOncoSimulR%2F),
> apparently during the vignette build process
> (https://secure-web.cisco.com/1wC-QitpATgzZLg-OA4Yqk8kDdDqtZ85t1eoOogdoDG39pNkmH_xx8xzqT9EXe6e3gFjL8shxF9559wAQoBn_WfxaNR_k_3aF1t9GtSqb492Zu8SY6MGhss9vTMp3VxPNqgcDKNdNz57JVMzSj8pjZ8aNselyDXxMn4fVx9VRdgnUcQZJBh2UQKAqynzk4OLjRo9-BkaTunIz86d3-CsHun_6oA9b4PMYlWa4Abc7tqz1IJoA1io92b6Wo_iaJ5TblF1Vf0cdouQOrMcXRoL1Cj9zgEQ8l3PARJ9eFzoapnK2a23NJCBpIw84Rh4mAf6-/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FOncoSimulR%2Fkunpeng2-buildsrc.html).
>
>
> I do not understand what is happening, nor how to debug this, since al the logs show is
>
> * checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
> * preparing ‘OncoSimulR’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> * creating vignettes ...
>
> The package does not seem to show this issue in  the (supported) platforms in R universe
> (https://secure-web.cisco.com/1ED6QCe2u7X_1AcLT5ewiDKMSEzO4Phzv36sjGvM5hmYg40cfLmN3pmB4sbmrEc6dUs3ENrbLklaeQAiTA_6_TzhxULCOlORyGyldt6NhWZDO429UCvUrf5QnLdqSOiLOtpV3xuIMls9MHbouX1D7hJxcwobF2Fx3zyQdh01eeJqrKIx_JJe18YPDj9j1d_mRb1gT485p2joeEtIOzyjzigHJH276OGdkFhztAKXOyqijpw7_2EWIKM5uVl3Ez3kUYsfrEFGE_WNmmytK8Il1kPk_4df3YCCvSAPR46sVvB9c6JRZom3qhEYAIRodmizj/https%3A%2F%2Fbioc.r-universe.dev%2FOncoSimulR%23checktable).
>
>
> I've noticed there are at least some other packages with a similar pattern: they seem to build and check OK on all platforms, but timeout on
> vignette build on kunpeng2. Is there anything I should do?
>
> Best,
>
> R.

--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-31
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 using gmail.com
       r.diaz using uam.es
       ramon.diaz using iib.uam.es

https://ligarto.org/rdiaz