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

[Kern, Lori]

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 Aut�noma 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

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