[Bioc-devel] R: Problems with pandoc version

[Giovanni Micale]

Hi Pariksheet,
no problem.
The messages you sent refer to the previous version (0.99.12) of geneslator package and that problem was already fixed.
The report I sent refers to version 0.99.14, whose results appeared this morning.
Best,
Giovanni

-----Messaggio originale-----
Da: Nanda, Pariksheet <PAN79 using pitt.edu>
Inviato: mercoledì 2 settembre 2026 17:39
A: bioc-devel using r-project.org
Cc: Giovanni Micale <giovanni.micale using unict.it>
Oggetto: Re: Problems with pandoc version

[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://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/raw-results/nebbiolo2/checksrc-out.txt
[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://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/raw-results/nebbiolo2/checksrc-summary.dcf

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://aka.ms/LearnAboutSenderIdentification ]

Hello,
thanks for the quick reply.
Geneslator is among the data annotation packages:
https://bioconductor.org/checkResults/devel/data-annotation-LATEST/geneslator/

Here is the link to the page for more details about the last build:
https://bioconductor.org/checkResults/3.24/data-annotation-LATEST/geneslator/nebbiolo2-buildsrc.html

Best,
Giovanni


-----Messaggio originale-----
Da: Nanda, Pariksheet <PAN79 using pitt.edu>
Inviato: mercoledì 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://pandoc.org/releases.html#pandoc-2.8-2019-11-22
[2] https://bioconductor.org/checkResults/devel/bioc-LATEST/geneslator/
[3] https://bioconductor.org/checkResults/release/bioc-LATEST/geneslator/

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://aka.ms/LearnAboutSenderIdentification ]

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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