[Bioc-devel] RareVariantVis failed

Tomasz Stokowy tomasz.stokowy at k2.uib.no
Tue Apr 3 12:43:30 CEST 2018

Dear bioc-devel,

My package RareVariantVis currently failed check because of examples  
warnings/error. I am not able to reproduce this on my system, despite  
updating R and Bioconductor.
It seems that recent changes in dependencies are causing this trouble.  
Should I go for useDevel() to solve this issues?


Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
   GRanges object contains 2 out-of-bound ranges located on sequence
   68559. Note that ranges located on a sequence whose length is unknown
   (NA) or on a circular sequence are not considered out-of-bound (use
   seqlengths() and isCircular() to get the lengths and circularity flags
   of the underlying sequences). You can use trim() to trim these ranges.
   See ?`trim,GenomicRanges-method` for more information.
Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,  
GRanges(seqnames = paste0("chr",  :
   The 'scores()' method has been deprecated and will become defunct in the  
next release version of Biocondcutor 3.8. Please use its replacement  
functions 'gscores()' and 'score()'.
Warning in gscores(object, ranges, ...) :
   assuming query ranges genome build is the one of the GScores object  
(Genome Reference Consortium GRCh37).
Error in match.names(clabs, nmi) : names do not match previous names
Calls: chromosomeVis ... eval -> eval -> eval -> rbind -> rbind ->  

I will be thankful for any suggestions.

Kind regards,

Tomasz Stokowy PhD
Department of Clinical Science
University of Bergen, Norway

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