Re: [Bioc-devel] RareVariantVis failed

2018-04-17 Thread Tomasz Stokowy 
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 circu

Re: [Bioc-devel] RareVariantVis failed

2018-04-17 Thread Tomasz Stokowy 


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 i

Re: [Bioc-devel] RareVariantVis failed

2018-04-15 Thread Tomasz Stokowy 

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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[Bioc-devel] RareVariantVis failed

2018-04-03 Thread Tomasz Stokowy 

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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Re: [Bioc-devel] Hsapiens in bioconductor

2017-09-14 Thread Tomasz Stokowy 

Dear Herve,

Your solution worked out, no 'R CMD check' warning.

--
Tomasz

On Thu, 14 Sep 2017 18:09:44 +0200,   
wrote:



Hi Tomasz,
The name of the BSgenome object defined in a BSgenome data package
is the name of the package itself. Hsapiens is just an convenient
"alias" for the long name. So you could do:
importFrom(BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19)
importFrom(BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38)
and there should be no more 'R CMD check' warning.
Then you need to use the long name in your code to refer to the object.
Hope this help,
H.


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[Bioc-devel] Hsapiens in bioconductor

2017-09-14 Thread Tomasz Stokowy 

Dear bioc-devel,

I would like to import Hsapiens objects from both
BSgenome.Hsapiens.UCSC.hg19
and
BSgenome.Hsapiens.UCSC.hg38

this is currently handled in the namespace of my package by

import(BSgenome.Hsapiens.UCSC.hg19)
import(BSgenome.Hsapiens.UCSC.hg38)

I get warning (because I assign two different genomes to Hsapiens  
variable):
Warning: replacing previous import ‘BSgenome.Hsapiens.UCSC.hg19::Hsapiens’  
by ‘BSgenome.Hsapiens.UCSC.hg38::Hsapiens’ when loading ‘RareVariantVis’


Could you suggest how to avoid this warning? I would like to use both hg19  
and hg38 references in my package.


Packages are listed in my Description file under Imports:. Furthermore, I  
use them as BSgenome.Hsapiens.UCSC.hg38::Hsapiens in my code.


Kind regards,

--
Tomasz Stokowy Phd
Senior Engineer
Department of Clinical Science
University of Bergen, Norway

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