FAQ on package development

What should I do if I see the Error in doc_parse_raw error in Travis report?

Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html,  : 
  Opening and ending tag mismatch: expr line x and equal_assign [y]

This error is due to the use of = assignments in the file. A quick way to fix them is to run styler::style_file("<FILENAME>"). Note this will change the coding style of all codes in the file.

What should I do if I see the file link in package does not exist and so has been treated as a topic warning in Bioconductor check report?

Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYxQneR/R.INSTALL2c6428e173c3/celda/man/bestLogLikelihood.Rd:22: file link 'altExp' in package 'SingleCellExperiment' does not exist and so has been treated as a topic

This is a Windows system specific warning. Quick fix: use \link{altExp} instead of \link[SingleCellExperiment]{altExp} in Roxygen2 documentation.