[Bioc-devel] Build error - Latex environment in vignettes

Jennifer Wokaty Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu
Mon Feb 27 23:19:48 CET 2023

Hi Sergi,

I agree these are due to newer pandoc versions on these machines. I'm going make sure both linux and both macs use the same versions this week so we get consistent results.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Sergio Picart Armada <sergi.picart using upc.edu>
Sent: Sunday, February 26, 2023 3:38 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Build error - Latex environment in vignettes

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Dear bioc-devel list,

I am the maintainer of the FELLA package. I got some BUILD errors related
to the LaTeX environments:

Release: error only on lconway
<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_FELLA_lconway-2Dbuildsrc.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=SZC3cdDF3FAwwp3w0YNtiJgKxdcbNSGJhvWXgM_alRVi9A4Efgp7PjfMKlfEIXPF&s=7rnUtLpHW3am2NIjFmW92rBw__T2ZgbjBTj6u637lMM&e= >

* creating vignettes ... ERROR

--- re-building �musmusculus.Rmd� using rmarkdown

! LaTeX Error: Environment cslreferences undefined.

Devel: error only on nebbiolo1
<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_FELLA_nebbiolo1-2Dbuildsrc.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=SZC3cdDF3FAwwp3w0YNtiJgKxdcbNSGJhvWXgM_alRVi9A4Efgp7PjfMKlfEIXPF&s=IkRNxO5WoxQuxSU3DvkGmDDOWYM85o5MD7W6goHeCtE&e= >

* creating vignettes ... ERROR

--- re-building �musmusculus.Rmd� using rmarkdown

! LaTeX Error: Environment CSLReferences undefined.

I suspect the pandoc version on the testing machines may have something to
do with it. What is strange, this only happens in the macOS machine
(release) and linux (devel), in two different vignettes. Any
recommendations on how to handle this?

Thank you


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