[Bioc-devel] Regarding package parati: Bioc 3.24 builders use Pandoc 2.7.3 but rmarkdown 2.32 requires >= 2.8

[Kern, Lori]

Please see previous posts.  There are several over the last few days including this one
https://stat.ethz.ch/pipermail/bioc-devel/2026-September/021507.html


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 Jinyi Che <chejinyi777 using gmail.com>
Sent: Friday, September 4, 2026 2:22 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Regarding package parati: Bioc 3.24 builders use Pandoc 2.7.3 but rmarkdown 2.32 requires >= 2.8

Dear Bioconductor Team,

I'm writing regarding the error reported for my package 'parati'.

parati 1.1.0 now fails during R CMD build on both nebbiolo2 and lconway.
The vignette error is:

  pandoc version 2.8 or higher is required and was not found

Both node-info pages report Pandoc 2.7.3, while both builders installed
rmarkdown 2.32 on 2026-09-01. rmarkdown 2.32 raised its minimum Pandoc
version from 1.14 to 2.8. This appears to be a builder image mismatch,
not a package-specific failure.

nebbiolo2 log:
https://secure-web.cisco.com/1kGfSXQLSUsUn98TVbzZifz7VMXsBv4IapJCIbGnttIX62e1gwwMEgQEttJo3iUgK7aVhLJfJl6o-qnkzS5Ma_VN1QZqVeHtnrrt72nGopefNszw-t5Qh1DvBXvuTuC99H5LgEeIcwEf7NZofnJKvs1SZsjD9xMbkCIk3uCCQIWMJFqL2Voja-DeVQO0rBJDSl6sJNNBQZhNC-X51Xez333xqJBkeyL63U-6K4QJgpEuoj2XIbBq9ae0zHYXdnu_yHRQcNunqEv5T7aqQDcqMG-JsF-WNc1Xt3fbQgkxECFaJMM8fcMu0iLhUptO-2xMl/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.24%2Fbioc-LATEST%2Fparati%2Fnebbiolo2-buildsrc.html

lconway log:
https://secure-web.cisco.com/1tmvkQ9edkIiDUvBcMSroaFNjIssHE6PjQWYOIB6K9QZlExO_2bfUVJjv4ZtIcTF4xP3wHyEm6yBgSuqa4Yf-tgV9ygBGvc9-iTkJUgqugaJtpo-uLWHJ5YYIOGpTvIQsIBIGAYAyM6E5x6-42mtVrbJndtqG9bq1HkdarLQeMy3ZXj27ccchzCL4uppa-TUUO9Px7UwjY9q3Ht6BzNhqZKvP_JLwoYovYx4gjPA3wLHHbHoSay2vf_4Vio_FAr1dWWdPgF8_ApwAydo-lWaafTWMSbbl4X6SqpLwLfsZfjL8sOaaFgZu6DuOu77L2VeM/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.24%2Fbioc-LATEST%2Fparati%2Flconway-buildsrc.html

Could you please help to check the issue and inform me of the next steps?
Thanks!

best
jinyi

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