Re: [Bioc-devel] RareVariantVis failed
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 g...@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
Sent: Tuesday, April 17, 2018 11:39:59 AM
To: bioc-devel@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
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
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
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 on behalf of Tomasz Stokowy
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
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
> 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 referen
Re: [Bioc-devel] RareVariantVis failed
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
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
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 on behalf of Tomasz Stokowy
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
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
> 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) :
>>>
Re: [Bioc-devel] RareVariantVis failed
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 on behalf of Tomasz Stokowy
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
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
> 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()'.
>
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
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
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
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 on behalf of Tomasz
Stokowy
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
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
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
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
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 on behalf of Tomasz
Stokowy
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
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
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 d
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
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
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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Re: [Bioc-devel] RareVariantVis failed
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
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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Re: [Bioc-devel] RareVariantVis failed
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,
--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
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[Bioc-devel] RareVariantVis failed
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 PhD
Department of Clinical Science
University of Bergen, Norway
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