A package for 3D plot of epigenetic data

[jianhong]

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[bioc-issue-bot]

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]

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[bioc-issue-bot]

Dear Package contributor,

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

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

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[bioc-issue-bot]

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

[bioc-issue-bot]

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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: ed4e63d6d5877f949af90a7a0a874c05df532c8d

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

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Please see the build report for more details.

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[lshep]

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

[bioc-issue-bot]

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

[jianhong]

@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.

[bioc-issue-bot]

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,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

[jianhong]

@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.

[bioc-issue-bot]

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

[bioc-issue-bot]

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]

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

[bioc-issue-bot]

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[lshep]

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