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?
http://bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html
https://github.com/tstokowy/RareVariantVis
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 ->
match.names
I will be thankful for any suggestions.
Kind regards,
--
Tomasz Stokowy PhD
Department of Clinical Science
University of Bergen, Norway
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