[Bioc-devel] RareVariantVis failed

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Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Tomasz  
Stokowy <tomasz.stokowy at k2.uib.no>
Sent: Tuesday, April 17, 2018 11:20:33 AM
To: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] RareVariantVis failed

Dear Bioc-devel,

I updated my package to version 2.7.1 following instructions from Robert
(https://github.com/tstokowy/RareVariantVis).
Unfortunately, check still reports error on version 2.7.0

https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html

What should I do to have my git updated version checked?

--
Tomasz Stokowy



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
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