By default, after agglomeration it was possible that there were duplicated rownames. --> duplicated rownames caused a warning in plotRowTree --> since now agglomerateByRank returns unique rownames, there was no warning --> checks were still expecting warning --> checks fail
To fix the checks, I modified them so that ununique rownames are returned after agglomerating step (make_unique = FALSE)
(master branch's checks are ok, because mia had the commit just a short time ago)
This fixes the checks
https://bioconductor.org/checkResults/devel/bioc-LATEST/miaViz/nebbiolo2-checksrc.html
By default, after agglomeration it was possible that there were duplicated rownames. --> duplicated rownames caused a warning in plotRowTree --> since now agglomerateByRank returns unique rownames, there was no warning --> checks were still expecting warning --> checks fail
To fix the checks, I modified them so that ununique rownames are returned after agglomerating step (make_unique = FALSE)
(master branch's checks are ok, because mia had the commit just a short time ago)