[Bioc-devel] RareVariantVis failed

Tue Apr 17 17:45:54 CEST 2018

I just checked and it is indeed updated on the git.bioconductor.org server.  So you should be all set.

The version number in the build report should be updated either tomorrow or thur to indicate it is building the new 2.7.1 version of the package.

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

If you didn't want to wait until the build report coming out to check that the version was updated -  you could create a temporary directory and clone the repository from the git server -

git clone git at git.bioconductor.org:packages/RareVariantVis.git

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 11:39:59 AM
To: bioc-devel at r-project.org; Shepherd, Lori
Subject: Re: [Bioc-devel] RareVariantVis failed

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

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--
Tomasz Stokowy
Department of Clinical Science
University of Bergen

--
Tomasz Stokowy
Department of Clinical Science
University of Bergen

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