[Bioc-devel] RareVariantVis failed

[Robert Castelo]

hi Tomasz,

regarding the warning caused by GenomicScores:

 > 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()'.

for this one just replace, the call:

scores(phastCons100way.UCSC.hg19, scores.only = TRUE, etc...

by

score(phastCons100way.UCSC.hg19, etc...

i.e., 'scores()' by 'score()' and remove 'scores.only=TRUE'.

 > Warning in gscores(object, ranges, ...) :
 >    assuming query ranges genome build is the one of the GScores object
 > (Genome Reference Consortium GRCh37).

here the 'genome' column in the sequence information ('seqinfo()') from 
the input ranges ranges is probably something like "hg19" or NA, while 
the one in the GScores object is "Genome Reference Consortium GRCh37". 
if you know both objects have positions over the same reference genome, 
you can forget about this warning. however, probably a warning is not 
necessary here, i'll replace it by a message and the warning will 
dissappear in a couple of days.

btw, i'm assuming we're talking here about the current 'development' 
branch of Bioconductor, i.e., GenomicScores version 1.3.21.

cheers,

robert.


On 04/03/2018 12:43 PM, Tomasz Stokowy wrote:
> 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,
> 

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550