dandelionR

[zktuong]

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[bioc-issue-bot]

Hi @zktuong

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: dandelionR
Title: Single-cell Immune Repertoire Trajectory Analysis in R
Version: 0.99.0
Authors@R:
    c(person(given="Jiawei", family="Yu", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0009-0005-9170-7881")),
      person(given="Nicholas", family="Borcherding", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0003-1427-6342")),
      person(given="Kelvin", family="Tuong", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6735-6808")))
Description: dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
biocViews: Software, ImmunoOncology, SingleCell
Collate:
    'check.R'
    'constructMarkovChain.R'
    'data.R'
    'determMultiscaleSpace.R'
    'terminalStateFromMarkovChain.R'
    'differentiationProbabilities.R'
    'filterCells.R'
    'getPbs.R'
    'projectProbability.R'
    'maxMinSampling.R'
    'minMaxScale.R'
    'markovProbability.R'
    'miloUmap.R'
    'projectPseudotimeToCell.R'
    'setupVdjPseudobulk.R'
    'splitCTgene.R'
    'vdjPseudobulk.R'
Imports:
    BiocGenerics,
    bluster,
    destiny, 
    igraph,
    MASS,
    Matrix,
    methods,
    miloR,
    purrr,
    rlang,
    S4Vectors,
    SingleCellExperiment,
    spam,
    stats,
    SummarizedExperiment,
    uwot
Suggests:
    BiocStyle,
    knitr,
    RColorBrewer,
    scater,
    scRepertoire,
    testthat
VignetteBuilder: knitr
URL: https://www.github.com/tuonglab/dandelionR/
BugReports: https://www.github.com/tuonglab/dandelionR/issues
Depends: 
    R (>= 4.4.0)

[lshep]

I currently cannot get the package to build for local testing

R CMD build dandelionR 
* checking for file 'dandelionR/DESCRIPTION' ... OK
* preparing 'dandelionR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette_from_scRepertoire.Rmd’ using rmarkdown

Quitting from lines 77-86 [unnamed-chunk-6] (vignette_from_scRepertoire.Rmd)
Error: processing vignette 'vignette_from_scRepertoire.Rmd' failed with diagnostics:
unused argument (filterNonproductive = TRUE)
--- failed re-building ‘vignette_from_scRepertoire.Rmd’

--- re-building ‘vignette_reproduce_original.rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Reproducing the original dandelion method/paper"", and the latter is "Reproducing the original dandelion method/paper". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘vignette_reproduce_original.rmd’

SUMMARY: processing the following file failed:
  ‘vignette_from_scRepertoire.Rmd’

Error: Vignette re-building failed.
Execution halted

[zktuong]

hi @lshep, i'm told that it should work – as the bioconcductor 3.20 release has that argument in scRepertoire: https://code.bioconductor.org/browse/scRepertoire/blob/RELEASE_3_20/R/combineContigs.R#L55

In anycase, we have since gona back to edit the vignette to exclude the argument filterNonproductive = TRUE as that was the default anyway.

[lshep]

Your package is building against devel not release_3_20 and that argument does not exist there https://code.bioconductor.org/browse/scRepertoire/blob/devel/R/combineContigs.R#L52 . Through this review process make sure you are testing against R-devel and Bioc devel (soon to be 3.21)

[zktuong]

ok thanks for that!

seems like the Bioc-devel version of scRepertoire is an outdated (different) version compared to the released version and that's causing the build to fail. i will work with @ncborcherding to resolve that first.

[zktuong]

Hi @lshep, we are ready for this to be reviewed again. our tests are passing when built against R-devel and Bioc-devel https://github.com/tuonglab/dandelionR/actions/runs/12441168543

[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.

On one or more platforms, the build results were: "ERROR".
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:
Linux (Ubuntu 24.04.1 LTS): dandelionR_0.99.0.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/dandelionR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 4f31e0fc66a85460216cef29b64e7f7f8b6e3ee4

[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.

On one or more platforms, the build results were: "ERROR".
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:
Linux (Ubuntu 24.04.1 LTS): dandelionR_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/dandelionR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1a94ac148261043e07fa5134e03a20b09b39e8ef

[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.

On one or more platforms, the build results were: "ERROR".
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:
Linux (Ubuntu 24.04.1 LTS): dandelionR_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/dandelionR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d1a41fd7b0c2cbc16f15c256e0ae820de30319ca

[bioc-issue-bot]

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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): dandelionR_0.99.3.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/dandelionR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5e64785d2a96a6f0bf183e2ee31f2e0fd7eb47c1

[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): dandelionR_0.99.4.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/dandelionR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.