在 github 上的 README.md 包中允许徽章但在 CRAN 版本中不允许徽章的解决方法

Question

R CMD check packagename_0.1.1.tar.gz --as-cran produces a WARNING if badges are present in README.md . This causes consequences like travis CI to fail (since it treats warnings as errors)

Is there a workaround to get the check to pass without removing the badges?

Here is an example of the WARNING I see

* checking top-level files ... WARNING
Conversion of ‘README.md’ failed:
pandoc: Could not fetch https://www.r-pkg.org/badges/version/bigrquery
TlsExceptionHostPort (HandshakeFailed (Error_Misc "user error (unexpected type received. expecting handshake and got: Alert [(AlertLevel_Fatal,HandshakeFailure)])")) "www.r-pkg.org" 443

Related: pandoc: Could not fetch http://www.r-pkg.org/badges/version/package TlsExceptionHostPort (HandshakeFailed

Answer 1

This is a workaround to embed (static) badges in pages. They do not auto-update. The purpose is to avoid offline derived errors.

Take a look at readme files in: https://gitlab.com/ferroao/idiogramFISH . This also handles errors while installing with devtools in windows, a process that does not have online connectivity (see vignette index.Rmd). Look at DESCRIPTION also if you want to see dependencies and vignette builders.

Generate the .md from the .Rmd (Rmarkdown).

Answer 2

Months on, I discovered the problem. When I installed anaconda, it changed the version of pandoc my system used - which pandoc should return something like /usr/local/bin/pandoc (and not like /Users/st/anaconda3/bin/pandoc ).

In my case, I edited by .bash_profile to exclude ananconda, closed and reopened the terminal and everything worked. (I also reinstalled pandoc from here , but I don't think that had anything to do with fixing it - it did show me the default installation location though)