search

rafalab / bumphunter

bumphunter
15 stars 14 forks source link

species() is defunct in Bioc 3.4 #11

Closed lcolladotor closed 7 years ago

lcolladotor commented 8 years ago

As seen at http://bioconductor.org/checkResults/devel/bioc-LATEST/bumphunter/zin1-checksrc.html today (June 27th), species() is defunct. 

Error: Calling species() on a TxDb object is defunct.  Please use organism()
  instead.

This causes bumphunter to fail R CMD check, and in turns breaks derfinder which uses bumphunter::matchGenes().

Best, Leo

lcolladotor commented 7 years ago

Fixed by https://github.com/rafalab/bumphunter/commit/2f31d42609977d68c1862b3b8478259547e9c187