[Bioc-devel] RareVariantVis failed

Tue Apr 17 17:30:17 CEST 2018

Output of git remote -v seems to be ok:

Tomaszs-MacBook-Pro:RareVariantVis tomaszstokowy$ git remote -v
origin https://github.com/tstokowy/RareVariantVis.git (fetch)
origin https://github.com/tstokowy/RareVariantVis.git (push)
upstream git at git.bioconductor.org:packages/RareVariantVis.git (fetch)
upstream git at git.bioconductor.org:packages/RareVariantVis.git (push)

According to push instructions I should do
git push upstream master

Is that right?

--
Tomasz

On Tue, 17 Apr 2018 17:25:42 +0200, Shepherd, Lori  
<Lori.Shepherd at roswellpark.org> wrote:

>
> You need to push the changes to the git.bioconductor.org server.
>
>
> What is the result of
> `git remote -v`
>
>
> You should have set up the upstream remote to point the the Bioconductor  
> git server where you will also have to push changes.
> See the following help page:
>
>
>
>
> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
>
>
>
>
>
> 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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Tomasz Stokowy
Department of Clinical Science
University of Bergen