[Bioc-devel] Problems with pandoc version
Andres Wokaty
Andre@@Wok@ty @end|ng |rom @ph@cuny@edu
Wed Sep 2 18:31:12 CEST 2026
If you were just notified today of package errors and didn't push any recent changes to your packages, it's likely a problem with the builder. Yesterday a new version of rmarkdown was published on CRAN that requires that we update pandoc. I will update the builders so we'll see some improvements on the next build. Thanks for your patience.
Andres Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Nalin Arora <naa4050 using med.cornell.edu>
Sent: Wednesday, September 2, 2026 12:04 PM
To: Andres Wokaty <Andres.Wokaty using sph.cuny.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>; Nanda, Pariksheet <PAN79 using pitt.edu>
Cc: Giovanni Micale <giovanni.micale using unict.it>
Subject: Re: Problems with pandoc version
I am maintainer of DAssemble and I also just got notified of the same issue being discussed in the thread.
Attaching the link of the issue: https://bioconductor.org/checkResults/3.24/bioc-LATEST/DAssemble/nebbiolo2-buildsrc.html<https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.24/bioc-LATEST/DAssemble/nebbiolo2-buildsrc.html__;!!LRXxDv2l!VP2g2zxy6WhWlucrUxHEe8CvSH2rgGfAEXXcVbghGIzXORc9yVjd6OZe_XbGADFcD_dgAXAcplOcajce-jN53bOByWjQx6k$>
Is it an issue in Nebbiolo or something related to the package?
Nalin Arora
Research Assistant
Mallick Lab
Weill Cornell Medicine
Biostatistics and Epidemiology
425 East 61st Street
New York, NY 10065
T: 5138081026
naa4050 using med.cornell.edu
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Andres Wokaty via Bioc-devel <bioc-devel using r-project.org>
Date: Wednesday, 2 September 2026 at 11:49 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>; Nanda, Pariksheet <PAN79 using pitt.edu>
Cc: Giovanni Micale <giovanni.micale using unict.it>
Subject: Re: [Bioc-devel] Problems with pandoc version
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Thanks for raising this. I'll look at the builds.
Andres Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
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From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Nanda, Pariksheet via Bioc-devel <bioc-devel using r-project.org>
Sent: Wednesday, September 2, 2026 11:39 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Giovanni Micale <giovanni.micale using unict.it>
Subject: Re: [Bioc-devel] Problems with pandoc version
* External Sender - Proceed Cautiously with Links and Attachments. *
[Sorry, accidentally posted off list]
Hi Giovanni,
Ah, my mistake. Thank you for pointing me to the annotation package tree. So if I click on the "raw results" and go to the directory containing more of the output [1], I actually see further messages about the vignette being okay (?!) but a different failure in your unit tests [3]. I would expect that a vignette not building shouldn't impact the unit tests. Looks like this happened at 5-6 in the morning [4] (US Eastern time?) and maybe someone on the Bioconductor infrastructure team could check into the system logs, etc. for nebbiolo2.
[1] https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/raw-results/nebbiolo2/checksrc-out.txt__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIsCMovDJg$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/raw-results/nebbiolo2/checksrc-out.txt__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIsCMovDJg$>
[2] Excerpt:
[...]
* checking files in ��vignettes�� ... OK
[...]
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
[3] Excerpt:
* checking tests ...
Running ��testthat.R��
ERROR
Running the tests in ��tests/testthat.R�� failed.
Last 13 lines of output:
7. ����KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
8. ����httr::GET(url)
9. ����httr:::handle_url(handle, url, ...)
10. ����httr::handle_find(url)
11. ����httr:::handle_name(url)
12. ����httr::build_url(parse_url(url)[c("scheme", "hostname", "port")])
13. �� ����base::stopifnot(is.url(url))
14. �� ����httr:::is.url(url)
15. ����httr::parse_url(url)
16. ����base::stopifnot(length(url) == 1)
[ FAIL 22 | WARN 0 | SKIP 0 | PASS 34 ]
Error:
! Test failures.
Execution halted
[4] https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/raw-results/nebbiolo2/checksrc-summary.dcf__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIsCqOjZFw$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/raw-results/nebbiolo2/checksrc-summary.dcf__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIsCqOjZFw$>
Pariksheet
________________________________________
From: Giovanni Micale <giovanni.micale using unict.it>
Sent: Wednesday, September 2, 2026 11:19 AM
To: Nanda, Pariksheet
Subject: R: Problems with pandoc version
[You don't often get email from giovanni.micale using unict.it. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvkaKytoA$<https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvkaKytoA$> ]
Hello,
thanks for the quick reply.
Geneslator is among the data annotation packages:
https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIuberSoKw$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIuberSoKw$>
Here is the link to the page for more details about the last build:
https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.24/data-annotation-LATEST/geneslator/nebbiolo2-buildsrc.html__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvey-E1bw$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.24/data-annotation-LATEST/geneslator/nebbiolo2-buildsrc.html__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvey-E1bw$>
Best,
Giovanni
-----Messaggio originale-----
Da: Nanda, Pariksheet <PAN79 using pitt.edu>
Inviato: mercoled�� 2 settembre 2026 17:14
A: Giovanni Micale <giovanni.micale using unict.it>
Oggetto: Re: Problems with pandoc version
Hello Giovanni,
Pandoc 2.8 is about 6 years old [1] so I imagine the specificity around the version may be a red herring and that the system dependency for pandoc itself may not be available on whatever machine in the build pool your package was running on. I can't seem to find your package in the build logs [2,3] and was wondering if you could post a link to more details of the build to better understand the build environment, machine, timestamps, etc.?
[1] https://urldefense.com/v3/__https://pandoc.org/releases.html*pandoc-2.8-2019-11-22__;Iw!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIuTxYqfhA$<https://urldefense.com/v3/__https://pandoc.org/releases.html*pandoc-2.8-2019-11-22__;Iw!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIuTxYqfhA$>
[2] https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/geneslator/__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvHpJyB3w$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/geneslator/__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvHpJyB3w$>
[3] https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/geneslator/__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvvoXZTCg$<https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/geneslator/__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvvoXZTCg$>
Pariksheet
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From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Giovanni Micale <giovanni.micale using unict.it>
Sent: Wednesday, September 2, 2026 10:18 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Problems with pandoc version
[You don't often get email from giovanni.micale using unict.it. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvkaKytoA$<https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!LRXxDv2l!XPSdOL_9bu3mHKycOy3KQIoUgMIvuPWs8xk99zaps-JjXk5d1JpgoXTCnBdFkaAGn2o-5ONOfaQ0Zkj0tH-EnqxfhIvkaKytoA$> ]
Hello,
I'm Giovanni Micale, one of the authors of geneslator annotation data package (part of devel version 3.24).
I noticed that last build failed with the following error, that seems to be unrelated to the correct functioning of the package.
* checking for file 'geneslator/DESCRIPTION' ... OK
* preparing 'geneslator':
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building 'geneslator.Rmd' using rmarkdown
Error: processing vignette 'geneslator.Rmd' failed with diagnostics:
pandoc version 2.8 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'geneslator.Rmd'
SUMMARY: processing the following file failed:
'geneslator.Rmd'
Error: Vignette re-building failed.
Execution halted
Many other annotation data packages failed with a similar error.
Best,
Giovanni.
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