[Bioc-devel] RareVariantVis failed
Tomasz Stokowy
tomasz.stokowy at k2.uib.no
Sun Apr 15 18:31:46 CEST 2018
Dear Robert,
Thank you for clarification. I updated package following your instructions
and committed changes to
https://github.com/tstokowy/RareVariantVis.
I will verify if the R CMD check goes through this time.
Kind regards,
--
Tomasz
On Tue, 03 Apr 2018 15:16:55 +0200, Robert Castelo
<robert.castelo at upf.edu> wrote:
> 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,
>>
>
--
Tomasz Stokowy
Department of Clinical Science
University of Bergen
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