search

cbielow / PTXQC

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
Other
42 stars 25 forks source link

Error with pandoc 2.12 #95

Closed jpfeuffer closed 10 months ago

jpfeuffer commented 3 years ago 
  pandoc: (TagClose "script") is not a TagOpen
  CallStack (from HasCallStack):
    error, called at src/Text/HTML/TagSoup/Type.hs:128:19 in tagsoup-0.14.8-5475800661a147b74c5702e44e2bf7ad3c7dd7de6abc3374f8bae019636b95cb:Text.HTML.TagSoup.Type
  Error: pandoc document conversion failed with error 1
  In addition: There were 19 warnings (use warnings() to see them)
  Execution halted

From: https://github.com/nf-core/proteomicslfq/pull/122/checks?check_run_id=2065895445 MzTab: https://gist.github.com/jpfeuffer/4dd842c09836d9718a3b40b911952a3f With the default template. Everything from conda.

I assume it is a regression in pandoc or an incompatibility of the new version with RMarkdown.

jpfeuffer commented 3 years ago

We had to downgrade pandoc.

Alxcho commented 3 years ago

Same, downgrading from pandoc 2.13 solved the issue.