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A package for 3D plot of epigenetic data #3534

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jianhong opened this issue Sep 1, 2024 · 18 comments
Closed
10 tasks done

A package for 3D plot of epigenetic data #3534

jianhong opened this issue Sep 1, 2024 · 18 comments
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3a. accepted will be ingested into Bioconductor daily builder for distribution OK

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@jianhong
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jianhong commented Sep 1, 2024

Update the following URL to point to the GitHub repository of
the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

  • I understand that by submitting my package to Bioconductor,
    the package source and all review commentary are visible to the
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    instructions. My package is consistent with the Bioconductor
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    Bioconductor may retain use of package name.

  • I understand that a minimum requirement for package acceptance
    is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS.
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  • My package addresses statistical or bioinformatic issues related
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Hi @jianhong

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: geomeTriD
Type: Package
Title: A R/Bioconductor package for interactive 3D plot of epigenetic data or
  single cell data
Version: 0.99.0
Authors@R: c(person(given="Jianhong", family="Ou", email="[email protected]", 
        role=c("aut", "cre"), comment=c(ORCID="0000-0002-8652-2488")))
Description: geomeTriD (Three Dimensional Geometry Package) 
  create interactive 3D plots using the GL library with the 'three.js' 
  visualization library (https://threejs.org) or the rgl library.
  In addition to creating interactive 3D plots, the application also generates 
  simplified models in 2D.
  These 2D models provide a more straightforward visual representation,
  making it easier to analyze and interpret the data quickly.
  This functionality ensures that users have access to both detailed 
  three-dimensional visualizations and more accessible two-dimensional views,
  catering to various analytical needs.
License: MIT + file LICENSE
Depends: R (>= 4.4.0)
Imports:
  BiocGenerics,
  GenomeInfoDb,
  GenomicRanges,
  graphics,
  grDevices,
  grid,
  htmlwidgets,
  igraph,
  InteractionSet,
  IRanges,
  MASS,
  Matrix,
  methods,
  plotrix,
  rgl,
  rjson,
  S4Vectors,
  scales,
  stats,
  trackViewer
Suggests: 
  RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
  manipulateWidget, shiny,
  BiocStyle, knitr, rmarkdown,
  testthat
biocViews: Visualization
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Encoding: UTF-8
URL: https://github.com/jianhong/geomeTriD
BugReports: https://github.com/jianhong/geomeTriD/issues

@bioc-issue-bot bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Sep 1, 2024
@lshep lshep added the pre-check passed pre-review performed and ready to be added to git label Sep 4, 2024
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Your package has been added to git.bioconductor.org to continue the
pre-review process. A build report will be posted shortly. Please
fix any ERROR and WARNING in the build report before a reviewer is
assigned or provide a justification on why you feel the ERROR or
WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting
up remotes to push to git.bioconductor.org. All changes should be
pushed to git.bioconductor.org moving forward. It is required to push a
version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org
access. To manage keys and future access you may want to active your
Bioconductor Git Credentials Account

@bioc-issue-bot bioc-issue-bot added pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean and removed 1. awaiting moderation submitted and waiting clearance to access resources pre-check passed pre-review performed and ready to be added to git labels Sep 4, 2024
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Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ABNORMAL".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
ERROR before build products produced.

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/geomeTriD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: ecf6d1abc5ce84fab3d03d56dd0e4d14e93fd089

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Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): geomeTriD_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/geomeTriD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@bioc-issue-bot bioc-issue-bot added OK and removed ABNORMAL labels Sep 4, 2024
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Received a valid push on git.bioconductor.org; starting a build for commit id: ed4e63d6d5877f949af90a7a0a874c05df532c8d

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Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): geomeTriD_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/geomeTriD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@lshep lshep added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean labels Sep 11, 2024
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A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

@lshep
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lshep commented Oct 4, 2024

I apologize for the delay.

In extdata there are several files. in inst/script there is only scripts that
indicate how 4DNFI1UEG1HD.feature.gr.rds and pbmc_small.3d.rds. Can you please
have a file of text, pseudo code, or code that explains the other files included
and any relevant licensing information.

Is there a separate license or information on what the threejs is licensed
under. I think it is important to list that information too.

Could you please include a package man page so that if a naive user does
?geomeTriD there is some direction on how to start.

When I try to run the vignette,

## create threeJsGeometry objects
list3d <- view3dStructure(obj,
  feature.gr = feature.gr,
  renderer = "none"
)
## plot the data
threeJsViewer(list3d)

creates an empty graphic window and opens a browser that says file not found?
This seems true for most of the plotting through the first half of the
vignette. eventually some plots show but many do not. is there more set up or
configuration that needs to be done? See screenshot

Screenshot from 2024-10-04 11-32-23

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Received a valid push on git.bioconductor.org; starting a build for commit id: 7023790c55f0d6b6e8f667fe0c8f96add40f8b7a

@jianhong
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jianhong commented Oct 4, 2024

@lshep Thank you for the review. Could you please double check if the issue is caused by snap installing discussed here? Could you please try to relocated the tmp folder in your ${HOME}/.Renviron file and retry the plot? Let me know if it does not work.

Jianhong.

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Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): geomeTriD_0.99.6.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/geomeTriD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@jianhong
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jianhong commented Oct 4, 2024

@lshep
This update may contain multiple bug fix.
And according your comments, I add a md file to list all the file information and saved it at extdata/filelist.md.
Additional items were added into the LICENSE file. The full documentation of license is listed in LICENSE.md file.
Let me know if I missed anything.

Jianhong.

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Received a valid push on git.bioconductor.org; starting a build for commit id: fa63871e7f3c2935f34739ea97995a051fd5f77a

@bioc-issue-bot
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Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): geomeTriD_0.99.7.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/geomeTriD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@lshep
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lshep commented Oct 11, 2024

Thank you that worked and all looks good. I would consider mentioning this firefox bug somewhere in the documentation in case others are using it. I fixed it by changing the default to chrome that I also had installed but others might not have that option

@lshep lshep added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Oct 11, 2024
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Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

@lshep
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lshep commented Oct 11, 2024

The default branch of your GitHub repository has been added to Bioconductor's
git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/jianhong.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("geomeTriD"). The package 'landing page' will be created at

https://bioconductor.org/packages/geomeTriD

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

@lshep lshep closed this as completed Oct 11, 2024
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