Re: [Bioc-devel] Ask for help to debug the error on riesling1

[Hervé Pagès]

Hi Jianhong,

Memory leaks and other memory errors are bugs in native code that often 
exist on all platforms but typically manifest themselves in different 
ways depending on the platform where it runs. Running your code thru a 
tool like Valgrind should reveal these problems even if you do this on a 
non-Windows machine. See

https://bioconductor.org/developers/how-to/c-debugging/
for more information.

Best,
H.


On 4/6/21 6:46 AM, Jianhong Ou, Ph.D. wrote:

Hi,

The trackViewer package got error on Windows Server since version 1.27.4. I am 
totally lost to figure it out by myself. The current error message listed in 
building system is:


* creating vignettes ... ERROR
--- re-building 'changeTracksStyles.Rmd' using rmarkdown
--- finished re-building 'changeTracksStyles.Rmd'

--- re-building 'dandelionPlot.Rmd' using rmarkdown
--- finished re-building 'dandelionPlot.Rmd'

--- re-building 'lollipopPlot.Rmd' using rmarkdown
--- finished re-building 'lollipopPlot.Rmd'

--- re-building 'plotInteractionData.Rmd' using rmarkdown

I suppose this is a memory leak error. But I don't have windows server to 
repeat the error. What is the best way to fix the issue? Thank you in advance 
for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] EXTERNAL: Re: Best practice use pkgdown, docker with Bioconductor

[Marcel Ramos]

Thank you Jianhong for the clean solution.

I would encourage Alan to check out the biocthis::use_bioc_github_action
to set up the Docker build and pkgdown.

Best,

Marcel

On 4/6/21 12:48 PM, Jianhong Ou, Ph.D. wrote:
> Hi Alan,
>
> Here is my solution: https://github.com/jianhong/HMMtBroadPeak/tree/staging. 
> Hope this help.
>
> You may want to add one more step after check and before pkgdown to push to 
> your dockerhub by:
>
> - name: push to docker
> - uses: docker/build-push-action@v1
>  with:
>username: ${{ secrets.DOCKER_USERNAME }}
>password: ${{ secrets.DOCKER_TOKEN }}
>repository: your/docker/path
>tag_with_ref: true
>tag_with_sha: true
>tags: latest
> [https://avatars.githubusercontent.com/u/5640707?s=400=4]
> jianhong/HMMtBroadPeak
> call broad peak by a modified Baum_Welch algorithm that supports 
> multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak
> github.com
> 
>
> 
> From: Bioc-devel  on behalf of Murphy, Alan 
> E 
> Sent: Tuesday, April 6, 2021 10:24 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
>
> Hi all,
>
> I'm working on the development of 
> (EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$
>  ] and have a question regarding a reviewer note. My package currently uses 
> pkgdown to create a website through the master branch. I also create and push 
> a new docker image from the main branch when the package successfully builds 
> on travis.
>
> My reviewer has asked to remove the related files 
> _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any 
> issues with these external configurations and Bioconductor. My reviewer has 
> suggested to put these in another branch. It's not clear to me how best to do 
> this? Ideally, if they are in a separate branch, is there a way to run them 
> once there is an update and successful build on the master branch? If this 
> isn't possible, is there a way to avoid manually duplicating new changes in 
> the master branch in this separate branch and instead, just push the changes 
> from master to this separate branch and trigger pkgdown and docker build that 
> way? Sorry, I realise this last part more so relates to github commands but I 
> was thinking someone else has probably already foudn a way around this issue.
>
> Kind regards,
> Alan.
>
> Alan Murphy
> Bioinformatician
> Neurogenomics lab
> UK Dementia Research Institute
> Imperial College London
>
>  [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPX4panddY$
>
>   [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263



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Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

[Murphy, Alan E]

Thank you all for your suggestions! Can anyone from the Bioconductor team 
comment on whether David's approach to use the .Rbuildignore file is valid for 
submission to Bioconductor? Obviously, this will would the least work so if 
possible, I would like to use this.

Kind regards,
Alan.

From: David Jimenez-Morales 
Sent: 06 April 2021 17:53
To: Andris Jankevics 
Cc: Murphy, Alan E ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor


This email from biodavi...@gmail.com originates from outside Imperial. Do not 
click on links and attachments unless you recognise the sender. If you trust 
the sender, add them to your safe senders 
list to disable email stamping 
for this address.



Hi there,

What about including the "_pkgdown.yml" file in the ".Rbuildignore" file? Would 
this somehow help "avoiding any issues with these external configurations and 
Bioconductor"?

Thanks
David

On Tue, Apr 6, 2021 at 5:05 AM Andris Jankevics 
mailto:a.jankev...@bham.ac.uk>> wrote:
Haven't used this, but I think you could use Github Action to merge master 
branch in the branch for pkgdown whenever changes on master are made.

https://github.com/marketplace/actions/merge-branch

BW,
Andris

-Original Message-
From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> On 
Behalf Of Murphy, Alan E
Sent: 06 April 2021 16:24
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi all,

I'm working on the development of (EWCE)[https://github.com/NathanSkene/EWCE] 
and have a question regarding a reviewer note. My package currently uses 
pkgdown to create a website through the master branch. I also create and push a 
new docker image from the main branch when the package successfully builds on 
travis.

My reviewer has asked to remove the related files 
_pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues 
with these external configurations and Bioconductor. My reviewer has suggested 
to put these in another branch. It's not clear to me how best to do this? 
Ideally, if they are in a separate branch, is there a way to run them once 
there is an update and successful build on the master branch? If this isn't 
possible, is there a way to avoid manually duplicating new changes in the 
master branch in this separate branch and instead, just push the changes from 
master to this separate branch and trigger pkgdown and docker build that way? 
Sorry, I realise this last part more so relates to github commands but I was 
thinking someone else has probably already foudn a way around this issue.

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

[David Jimenez-Morales]

Hi there,

What about including the "_pkgdown.yml" file in the ".Rbuildignore" file?
Would this somehow help "avoiding any issues with these external
configurations and Bioconductor"?

Thanks
David

On Tue, Apr 6, 2021 at 5:05 AM Andris Jankevics 
wrote:

> Haven't used this, but I think you could use Github Action to merge master
> branch in the branch for pkgdown whenever changes on master are made.
>
> https://github.com/marketplace/actions/merge-branch
>
> BW,
> Andris
>
> -Original Message-
> From: Bioc-devel  On Behalf Of Murphy,
> Alan E
> Sent: 06 April 2021 16:24
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
>
> Hi all,
>
> I'm working on the development of (EWCE)[
> https://github.com/NathanSkene/EWCE] and have a question regarding a
> reviewer note. My package currently uses pkgdown to create a website
> through the master branch. I also create and push a new docker image from
> the main branch when the package successfully builds on travis.
>
> My reviewer has asked to remove the related files
> _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any
> issues with these external configurations and Bioconductor. My reviewer has
> suggested to put these in another branch. It's not clear to me how best to
> do this? Ideally, if they are in a separate branch, is there a way to run
> them once there is an update and successful build on the master branch? If
> this isn't possible, is there a way to avoid manually duplicating new
> changes in the master branch in this separate branch and instead, just push
> the changes from master to this separate branch and trigger pkgdown and
> docker build that way? Sorry, I realise this last part more so relates to
> github commands but I was thinking someone else has probably already foudn
> a way around this issue.
>
> Kind regards,
> Alan.
>
> Alan Murphy
> Bioinformatician
> Neurogenomics lab
> UK Dementia Research Institute
> Imperial College London
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
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>

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Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

[Jianhong Ou, Ph.D.]

Hi Alan,

Here is my solution: https://github.com/jianhong/HMMtBroadPeak/tree/staging. 
Hope this help.

You may want to add one more step after check and before pkgdown to push to 
your dockerhub by:

- name: push to docker
- uses: docker/build-push-action@v1
with:
  username: ${{ secrets.DOCKER_USERNAME }}
  password: ${{ secrets.DOCKER_TOKEN }}
  repository: your/docker/path
  tag_with_ref: true
  tag_with_sha: true
  tags: latest
[https://avatars.githubusercontent.com/u/5640707?s=400=4]
jianhong/HMMtBroadPeak
call broad peak by a modified Baum_Welch algorithm that supports 
multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak
github.com



From: Bioc-devel  on behalf of Murphy, Alan E 

Sent: Tuesday, April 6, 2021 10:24 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi all,

I'm working on the development of 
(EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$
 ] and have a question regarding a reviewer note. My package currently uses 
pkgdown to create a website through the master branch. I also create and push a 
new docker image from the main branch when the package successfully builds on 
travis.

My reviewer has asked to remove the related files 
_pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues 
with these external configurations and Bioconductor. My reviewer has suggested 
to put these in another branch. It's not clear to me how best to do this? 
Ideally, if they are in a separate branch, is there a way to run them once 
there is an update and successful build on the master branch? If this isn't 
possible, is there a way to avoid manually duplicating new changes in the 
master branch in this separate branch and instead, just push the changes from 
master to this separate branch and trigger pkgdown and docker build that way? 
Sorry, I realise this last part more so relates to github commands but I was 
thinking someone else has probably already foudn a way around this issue.

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

[Andris Jankevics]

Haven't used this, but I think you could use Github Action to merge master 
branch in the branch for pkgdown whenever changes on master are made.

https://github.com/marketplace/actions/merge-branch

BW,
Andris

-Original Message-
From: Bioc-devel  On Behalf Of Murphy, Alan E
Sent: 06 April 2021 16:24
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi all,

I'm working on the development of (EWCE)[https://github.com/NathanSkene/EWCE] 
and have a question regarding a reviewer note. My package currently uses 
pkgdown to create a website through the master branch. I also create and push a 
new docker image from the main branch when the package successfully builds on 
travis.

My reviewer has asked to remove the related files 
_pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues 
with these external configurations and Bioconductor. My reviewer has suggested 
to put these in another branch. It's not clear to me how best to do this? 
Ideally, if they are in a separate branch, is there a way to run them once 
there is an update and successful build on the master branch? If this isn't 
possible, is there a way to avoid manually duplicating new changes in the 
master branch in this separate branch and instead, just push the changes from 
master to this separate branch and trigger pkgdown and docker build that way? 
Sorry, I realise this last part more so relates to github commands but I was 
thinking someone else has probably already foudn a way around this issue.

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

[[alternative HTML version deleted]]

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[Bioc-devel] Best practice use pkgdown, docker with Bioconductor

[Murphy, Alan E]

Hi all,

I'm working on the development of (EWCE)[https://github.com/NathanSkene/EWCE] 
and have a question regarding a reviewer note. My package currently uses 
pkgdown to create a website through the master branch. I also create and push a 
new docker image from the main branch when the package successfully builds on 
travis.

My reviewer has asked to remove the related files 
_pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues 
with these external configurations and Bioconductor. My reviewer has suggested 
to put these in another branch. It's not clear to me how best to do this? 
Ideally, if they are in a separate branch, is there a way to run them once 
there is an update and successful build on the master branch? If this isn't 
possible, is there a way to avoid manually duplicating new changes in the 
master branch in this separate branch and instead, just push the changes from 
master to this separate branch and trigger pkgdown and docker build that way? 
Sorry, I realise this last part more so relates to github commands but I was 
thinking someone else has probably already foudn a way around this issue.

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

[[alternative HTML version deleted]]

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[Bioc-devel] Ask for help to debug the error on riesling1

[Jianhong Ou, Ph.D.]

Hi,

The trackViewer package got error on Windows Server since version 1.27.4. I am 
totally lost to figure it out by myself. The current error message listed in 
building system is:


* creating vignettes ... ERROR
--- re-building 'changeTracksStyles.Rmd' using rmarkdown
--- finished re-building 'changeTracksStyles.Rmd'

--- re-building 'dandelionPlot.Rmd' using rmarkdown
--- finished re-building 'dandelionPlot.Rmd'

--- re-building 'lollipopPlot.Rmd' using rmarkdown
--- finished re-building 'lollipopPlot.Rmd'

--- re-building 'plotInteractionData.Rmd' using rmarkdown

I suppose this is a memory leak error. But I don't have windows server to 
repeat the error. What is the best way to fix the issue? Thank you in advance 
for your help.


Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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Re: [Bioc-devel] non-subsettable GRanges object

[Oleksii Nikolaienko]

Thanks very much, Hervé, I indeed never noticed the wrong number of
elements in my objects.

Best regards,
Oleksii

On Tue, 6 Apr 2021 at 02:10, Hervé Pagès  wrote:

> This is fixed in S4Vectors 0.29.13:
>
> https://github.com/Bioconductor/S4Vectors/commit/6d79932910af9618465d5f932df5864d0a270e11
>
> This new version of S4Vectors should propagate to the build machines and
> become available via BiocManager::install() in the next 48h or so.
>
> Cheers,
> H.
>
> On 4/5/21 3:40 PM, Hervé Pagès wrote:
> > Hi Oleksii,
> >
> > It looks like we have a long-standing bug in the rbind() method for
> > DataFrame objects that is somehow surfacing now. Here is a simple
> example:
> >
> >library(IRanges)
> >DF1 <- DataFrame(A=I(list(11:12, 21:23)))
> >DF2 <- DataFrame(A=IntegerList(31:34, 41:45, 51:56))
> >DF3 <- rbind(DF1, DF2)
> >DF3
> ># DataFrame with 3 rows and 1 column
> >#A
> >#   
> ># 1  11,12
> ># 2   21,22,23
> ># 3 31,32,33,...,41,42,43,...,51,52,53,...
> >
> > This result is wrong. We observe this in release and devel.
> >
> > If you look at the mcols of the GRanges object returned by getAMR() in
> > your code below, you'll see that it's actually an invalid DataFrame
> > object (its first column has 23 elements but 22 are expected). This is a
> > consequence of the above bug. Even though the bug has existed for a long
> > time, somehow it was not affecting your code. However this changed
> > recently because of some minor refactoring of the rbind() method for
> > DataFrame objects that I made a few days ago in S4Vectors.
> >
> > I'm working on a fix and will let you know when it's ready.
> >
> > Cheers,
> > H.
> >
> >
> > On 4/5/21 1:12 PM, Oleksii Nikolaienko wrote:
> >> Dear Bioc team,
> >> my package has started to fail during the build check (
> >> http://bioconductor.org/checkResults/devel/bioc-LATEST/ramr/). I tried
> to
> >> figure out why and it appears that I somehow make GRanges object
> >> non-subsettable. Could anyone from "GenomicRanges" developers look at my
> >> issue and advise me on a solution, please?
> >>
> >> To reproduce:
> >>
> >> library(ramr)
> >> data(ramr)
> >> amrs <- getAMR(ramr.data, ramr.samples, ramr.method="beta", min.cpgs=5,
> >> merge.window=1000, qval.cutoff=1e-3, cores=2)
> >> # this works:
> >> class(amrs)
> >> amrs
> >> # error:
> >> amrs[2]
> >> # suddenly works again:
> >> GRangesList(amrs)[[1]][2]
> >>
> >>
> >> Best regards,
> >> Oleksii
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>

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