[Bioc-devel] Problems with pandoc version

Wed Sep 2 18:04:31 CEST 2026

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

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
________________________________
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

________________________________________
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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