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.sheph...@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.stok...@k2.uib.no>
Sent: Tuesday, April 17, 2018 11:30:17 AM
To: bioc-devel@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
g...@git.bioconductor.org:packages/RareVariantVis.git (fetch)upstream
g...@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.sheph...@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-boun...@r-project.org> on behalf of Tomasz
Stokowy <tomasz.stok...@k2.uib.no>
Sent: Tuesday, April 17, 2018 11:20:33 AM
To: bioc-devel@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.stok...@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.cast...@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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