[Bioc-devel] RareVariantVis failed

[Tomasz Stokowy]

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