LTLA commented 3 years ago

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

Repository: https://github.com/LTLA/TrajectoryUtils

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bioc-issue-bot commented 3 years ago

Hi @LTLA

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: TrajectoryUtils
Version: 0.99.0
Date: 2020-12-11
Title: Single-Cell Trajectory Analysis Utilities
Description: 
    Implements low-level utilities for single-cell trajectory analysis,
    primarily intended for re-use inside higher-level packages.
    Include a function to create a cluster-level minimum spanning tree
    and data structures to hold pseudotime inference results.
Authors@R: 
    c(
        person("Aaron", "Lun", role=c("aut", "cre"), email="infinite.monkeys.with.keyboards@gmail.com"),
        person("Kelly", "Street", role="aut")
    )
License: GPL-3
biocViews: GeneExpression, SingleCell
Depends:
    SingleCellExperiment
Imports:
    methods,
    stats,
    Matrix,
    igraph,
    S4Vectors,
    SummarizedExperiment
Suggests:
    BiocNeighbors,
    DelayedArray,
    DelayedMatrixStats,
    BiocParallel,
    testthat,
    knitr,
    BiocStyle,
    rmarkdown
VignetteBuilder: knitr
RoxygenNote: 7.1.1

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". 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. This link will be active for 21 days.

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

LiNk-NY commented 3 years ago

Hi Aaron, @LTLA Thanks for your submission. Please see the short review below. Best, Marcel

TrajectoryUtils #1865

DESCRIPTION

Add BugReports and URL fields pointing to GitHub locations.

NAMESPACE

Looks good.

vignettes

Looks good.

R

You may not need to deprecate argument use since the package has not been released (in .create_cluster_mst).
Avoid nested for loops if possible in splitByBranches.

tests

Tests look extensive.

LTLA commented 3 years ago

Add BugReports and URL fields pointing to GitHub locations.

Done.

You may not need to deprecate argument use since the package has not been released (in .create_cluster_mst).

This is present because the function was transferred from TSCAN and I was planning to just reexport it from this package; in that sense, the argument is deprecated if we consider the continuity of that function's history.

Avoid nested for loops if possible in splitByBranches.

I don't think the alternative solutions are much better for the current approach. A cleaner algorithm would be to recurse through the graph but that will require some extra coding.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c22aa89c4942ac7aa0f3b473c490ee06c72faa03

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". 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. This link will be active for 21 days.

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

LiNk-NY commented 3 years ago

Hi Aaron, @LTLA Thanks for updating the DESCRIPTION file. The package looks ready to go. Best, Marcel

bioc-issue-bot commented 3 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

mtmorgan commented 3 years ago

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