[Bioc-devel] pandoc on celaya2

[Pages, Herve]

Hi package developers,

3 Bioconductor packages (ClusterJudge, KinSwingR, and YAPSA) are currently failing to build on celaya2 because of a pandoc-citeproc error that looks like:

    Error parsing references: Could not read as Int: "October"

See:

  https://bioconductor.org/checkResults/3.9/bioc-LATEST/ClusterJudge/celaya2-buildsrc.html
  https://bioconductor.org/checkResults/3.9/bioc-LATEST/KinSwingR/celaya2-buildsrc.html
  https://bioconductor.org/checkResults/3.9/bioc-LATEST/YAPSA/celaya2-buildsrc.html

This error seems to be due to a change in recent versions of pandoc (we use pandoc 2.5, the latest stable release, on celaya2). With this version, it looks like the month cannot be specified by its name anymore in the references section of a markdown document. For example, this

references:
  ...
  issued:
    month: October
    volume: 12
    year: 2002

is no longer valid. Replacing October with the number 10 seems to address the problem:

references:
  ...
  issued:
    month: 10
    volume: 12
    year: 2002


I'm not a pandoc user and I'm not following pandoc development so I don't know whether this is an intended change in pandoc or a regression.

Anyway: If your package fails to 'R CMD build' on celaya2 because of this pandoc-citeproc error, please take the time to fix it.

Keep in mind that all Bioconductor packages will need to pass 'R CMD build' and 'R CMD check' with no error in order to be included in the next Bioconductor release, scheduled for Tuesday April 30. Note that Bioconductor 3.9 will be based on R 3.6 (scheduled to be released on Friday April 26) so please make sure to use a recent version of R devel when testing/fixing your package.

See our release schedule:

  https://bioconductor.org/developers/release-schedule/

and this recent announcement on this list:

  https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014832.html

Thank you for your ongoing contribution to Bioconductor.

Cheers,

H.


--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org<mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319




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