[Bioc-devel] RareVariantVis failed

[Shepherd, Lori]

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

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