clustSIGNAL

[PratibhaPanwar]

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

• Repository: https://github.com/SydneyBioX/clustSIGNAL

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
  general public.

• I have read the Bioconductor Package Submission
  instructions. My package is consistent with the Bioconductor
  Package Guidelines.

• I understand Bioconductor Package Naming Policy and acknowledge
  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.
  Passing these checks does not result in automatic acceptance. The
  package will then undergo a formal review and recommendations for
  acceptance regarding other Bioconductor standards will be addressed.

• My package addresses statistical or bioinformatic issues related
  to the analysis and comprehension of high throughput genomic data.

• I am committed to the long-term maintenance of my package. This
  includes monitoring the support site for issues that users may
  have, subscribing to the bioc-devel mailing list to stay aware
  of developments in the Bioconductor community, responding promptly
  to requests for updates from the Core team in response to changes in
  R or underlying software.

• I am familiar with the Bioconductor code of conduct and
  agree to abide by it.

I am familiar with the essential aspects of Bioconductor software
management, including:

• The 'devel' branch for new packages and features.
• The stable 'release' branch, made available every six
  months, for bug fixes.
• Bioconductor version control using Git
  (optionally via GitHub).

For questions/help about the submission process, including questions about
the output of the automatic reports generated by the SPB (Single Package
Builder), please use the #package-submission channel of our Community Slack.
Follow the link on the home page of the Bioconductor website to sign up.

[bioc-issue-bot]

Hi @PratibhaPanwar

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: clustSIGNAL
Type: Package
Title: clustSIGNAL: a spatial clustering method
Version: 0.99.0
Authors@R: c(
    person("Pratibha", "Panwar", email = "[email protected]", 
    role = c("cre", "aut", "ctb"), comment = c(ORCID = "0000-0002-7437-7084")),
    person("Boyi", "Guo", email = "[email protected]", role = "aut"),
    person("Haowen", "Zhao", email = "[email protected]", role = "aut"),
    person("Stephanie", "Hicks", email = "[email protected]", role = "aut"),
    person("Shila", "Ghazanfar", email = "[email protected]", 
    role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-7861-6997")))
Description: clustSIGNAL: clustering of Spatially Informed Gene expression with 
    Neighbourhood Adapted Learning. A tool for adaptively smoothing and clustering 
    gene expression data. clustSIGNAL uses entropy to measure heterogeneity of 
    cell neighbourhoods and performs a weighted, adaptive smoothing, where 
    homogeneous neighbourhoods are smoothed more and heterogeneous neighbourhoods 
    are smoothed less. This not only overcomes data sparsity but also incorporates 
    spatial context into the gene expression data. The resulting smoothed gene 
    expression data is used for clustering and could be used for other downstream 
    analyses.
License: GPL-2
Encoding: UTF-8
URL: https://sydneybiox.github.io/clustSIGNAL/
BugReports: https://github.com/sydneybiox/clustSIGNAL/issues
biocViews: Clustering, Software, GeneExpression, Spatial, Transcriptomics, SingleCell
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0), SpatialExperiment
Imports: BiocParallel,
    BiocNeighbors, 
    bluster, 
    scater,
    harmony,
    SingleCellExperiment,
    SummarizedExperiment,
    methods
Suggests: knitr,
    BiocStyle,
    aricode,
    cluster,
    distances,
    dplyr,
    ggplot2, 
    patchwork,
    scattermore
VignetteBuilder: knitr

[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
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]

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: "skipped, TIMEOUT".
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/clustSIGNAL to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

The timeout issue must be resolved before we will assign a reviewer.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 84fe799f52887d29d46a14ff4511bebd404a4e55

[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): clustSIGNAL_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/clustSIGNAL 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: a9d2100f921e34c125351177ee1ae953dcdd0db4

[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): clustSIGNAL_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/clustSIGNAL 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: b42066e69f877cf9120f4f507df01262bf0b35c2

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

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

[svalvaro]

Hey @PratibhaPanwar a couple of important notes:

1. Could you add some unit testing to your functions?
   This assures the robustness of your package. If you have never done so, you can read more about it here.
2. Add an “Installation” section that show to users how to download and load the package from Bioconductor.