[Bioc-devel] RareVariantVis failed
tomasz.stokowy at k2.uib.no
Tue Apr 17 17:20:33 CEST 2018
I updated my package to version 2.7.1 following instructions from Robert
Unfortunately, check still reports error on version 2.7.0
What should I do to have my git updated version checked?
On Sun, 15 Apr 2018 18:31:46 +0200, Tomasz Stokowy
<tomasz.stokowy at k2.uib.no> wrote:
> Dear Robert,
> Thank you for clarification. I updated package following your
> instructions and committed changes to
> I will verify if the R CMD check goes through this time.
> Kind regards,
> 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
>> > 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...
>> 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
>> > (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.
>> 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?
>>> 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
>>> (NA) or on a circular sequence are not considered out-of-bound (use
>>> seqlengths() and isCircular() to get the lengths and circularity
>>> of the underlying sequences). You can use trim() to trim these
>>> 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,
Department of Clinical Science
University of Bergen
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