poem

[RoseYuan]

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• Repository: https://github.com/RoseYuan/poem

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[bioc-issue-bot]

Hi @RoseYuan

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: poem
Title: POpulation-based Evaluation Metrics
Version: 0.99.1
Authors@R: c(
    person("Siyuan", "Luo", email="[email protected]", role=c("cre","aut"), comment=c(ORCID="0009-0007-6404-3244")),
    person("Pierre-Luc", "Germain", email="[email protected]", role=c("aut","ctb"),
 comment=c(ORCID="0000-0003-3418-4218")))
Description: Implements a set of (mostly external) evaluation metrics for comparing partitions, 
  fuzzy partitions, for evaluating the segregation of classes/clusters in embeddings or graphs, etc.
  Also includes metrics for comparing spatial data to ground truth labels and spatially visualizing 
  errors.
BugReports: https://github.com/RoseYuan/poem/issues
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
    R (>= 4.0)
Imports:
    aricode,
    BiocNeighbors,
    BiocParallel,
    bluster,
    clevr,
    clue,
    cluster,
    elsa,
    fclust,
    igraph,
    Matrix,
    mclustcomp,
    methods,
    sp,
    spdep,
    stats,
    utils
Suggests: 
    testthat (>= 3.0.0),
    BiocStyle,
    knitr,
    DT,
    dplyr,
    scico,
    cowplot,
    ggnetwork,
    ggplot2,
    tidyr
VignetteBuilder: knitr
biocViews: DimensionReduction, Clustering, GraphAndNetwork, Spatial
Config/testthat/edition: 3

[lshep]

Bioconductor would like a clean repository on our system. Please remove pkgdown and Dockerfiles from default branch until after it has been cloned onto out system.

Is there a way to include a Bioconductor specific example in the vignette to show how this would work practically into a workflow and show interoperability with a common Bioconductor object/analysis? Perhaps with a SpatialExperiment object

[plger]

Hi @lshep ,
I'm just curious about your comment that "Bioconductor would like a clean repository on our system." Does that mean you want it clean only for the submission?
I (like a lot of people I suppose) keep github and Bioc in sync for all my packages to facilitate maintenance, so that even if it was "clean" upon submission it's not anymore after it's been included. Is this considered an issue or not?
Thanks in advance,
Pierre-Luc

[lshep]

Meaning the version we have on git.bioconductor.org should not contain developmental extras. After submission you could still keep a separate branch that removes those items and restore a default branch (ie. a branch called devel that is in sync with bioconductor and everything on a main branch less those features)

[RoseYuan]

Hi @lshep,
We now have a clean devel branch as required, and we added a new vignette for our package titled "Working with SpatialExperiment" to show the interoperability with Bioconductor. Please let us know if you have further comments. Thanks.
Best regards,
Siyuan

[bioc-issue-bot]

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
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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): poem_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/poem 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: 39b4332db7e6ebcbb53b7ebd584489dd6b1a3966

[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): poem_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/poem 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: 692f5a30a4a8c4229b66fe0ed7f3a1521f98e564

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