[Bioc-devel] RareVariantVis failed

Tue Apr 17 17:39:59 CEST 2018

Ok, I pushed to upstream master. Where could I check that version "to be  
checked" was updated to 2.7.1?

--
Tomasz

On Tue, 17 Apr 2018 17:35:18 +0200, Shepherd, Lori  
<Lori.Shepherd at roswellpark.org> wrote:

>
> Yes that is correct.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>From: Tomasz Stokowy <tomasz.stokowy at k2.uib.no>
> Sent: Tuesday, April 17, 2018 11:30:17 AM
> To: bioc-devel at r-project.org; Shepherd, Lori
> Subject: Re: [Bioc-devel] RareVariantVis failed
> 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

-- 
Tomasz Stokowy
Department of Clinical Science
University of Bergen