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is no longer valid.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: hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>
Phone: (206) 667-5791
Fax: (206) 667-1319
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