tpSVG

[boyiguo1]

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[bioc-issue-bot]

Hi @boyiguo1

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: tpSVG
Title: Thin plate models to detect spatially variable genes 
Version: 0.99.1
Authors@R: c(
    person("Boyi", "Guo",
 email = "boyi.guo.work@gmail.com",
 role = c("aut", "cre"),
 comment = c(ORCID = "0000-0003-2950-2349")),
    person("Lukas M.", "Weber", 
 email = "lukas.weber.edu@gmail.com", 
 role = c("ctb"), 
 comment = c(ORCID = "0000-0002-3282-1730")), 
    person("Stephanie C.", "Hicks", 
 email = "shicks19@jhu.edu", 
 role = c("aut"), 
 comment = c(ORCID = "0000-0002-7858-0231")))
Description: The goal of `tpSVG` is to detect and visualize spatial variation in
  the gene expression for spatially resolved transcriptomics data analysis.
  Specifically, `tpSVG` introduces a family of count-based models, with 
  generalizable parametric assumptions such as Poisson distribution or 
  negative binomial distribution. In addition, comparing to currently 
  available count-based model for spatially resolved data analysis, the 
  `tpSVG` models improves computational time, and hence greatly improves 
  the applicability of count-based models in SRT data analysis. 
License: MIT + file LICENSE
URL: https://github.com/boyiguo1/tpSVG
BugReports: https://github.com/boyiguo1/tpSVG/issues
biocViews: 
    Spatial, 
    Transcriptomics, 
    GeneExpression, 
    Software
Encoding: UTF-8
Depends: 
    mgcv,
    R (>= 4.3)
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports: 
    BiocParallel,
    MatrixGenerics,
    methods,
    SingleCellExperiment,
    SpatialExperiment,
    stats,
    SummarizedExperiment
Suggests: 
    BiocStyle,
    knitr,
    nnSVG,
    rmarkdown,
    scran,
    scuttle,
    STexampleData,
    escheR,
    ggpubr,
    colorspace,
    BumpyMatrix
VignetteBuilder: knitr

[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:
macOS 12.7.1 Monterey: tpSVG_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
git@git.bioconductor.org:packages/tpSVG 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: cab1ae81cd4c0103f810541fcaed9ca9c8fb7e5c

[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: "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.

The following are build products from R CMD build on the Single Package Builder:
macOS 12.7.1 Monterey: tpSVG_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
git@git.bioconductor.org:packages/tpSVG 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: ced12821ad5e3c81701fd5e76f91cbcf5677240e

[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: "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.

The following are build products from R CMD build on the Single Package Builder:
macOS 12.7.1 Monterey: tpSVG_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
git@git.bioconductor.org:packages/tpSVG to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[boyiguo1]

@lshep I apologize for tagging you. I believe the the package builder warning is a false positive.

In the previous two build reports build report for 0.99.2 and build report for 0.99.3, an outstanding warning message in Check is associated with bioconductor software dependencies.

• Checking for Bioconductor software dependencies...
  * WARNING: No Bioconductor dependencies detected; consider a CRAN
  submission.

IMO, the package depends on SpatialExperiment either via "Imports"(0.99.2) or "Depends" (0.99.3).

If this is a false positive, I'm happy to create a issue and document it in BiocCheck. Otherwise, I would appreciate any of your input.

Thank you so much!

Best,
Boyi

[lshep]

Yes please open an issue on BiocCheck if you think it is a false positive. It was recently added this past week and may need some tweaking.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 89ee5a39a31fbebce2c309cbf8c86204ea873c1a

[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:
macOS 12.7.1 Monterey: tpSVG_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
git@git.bioconductor.org:packages/tpSVG 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: 2669bc63c6c8d436c4fa06c0de04efe536bf8a87

[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: "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.

The following are build products from R CMD build on the Single Package Builder:
macOS 12.7.1 Monterey: tpSVG_0.99.5.tar.gz
Linux (Ubuntu 22.04.2 LTS): tpSVG_0.99.5.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
git@git.bioconductor.org:packages/tpSVG 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: 267763f2dcf82b8ba786e06c0cbdc5b3db3b6f4d

[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:
macOS 12.7.1 Monterey: tpSVG_0.99.6.tar.gz
Linux (Ubuntu 22.04.2 LTS): tpSVG_0.99.6.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
git@git.bioconductor.org:packages/tpSVG to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[boyiguo1]

Hi,

I wonder if there is a timeline for when the peer-review would be starting. I would be extremely grateful for this information so that I could plan for manuscript submission, etc.

I understand that there are a lot unseen efforts going on, and I really appreciate all!

Sincerely,
Boyi

[lshep]

We try to look and moderate once a week or every other week. I will look at assigning a reviewer likely later today or tomorrow at the latest. Sorry for the inconvenience.

[boyiguo1]

Got it. Thanks for sharing this information with me. It is very helpful for me to plan for other efforts.

I really appreciate the Bioconductor team for the responsiveness and huge efforts putting into to running and maintaining a such valuable community!!!

[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.

[lshep]

We strongly advise adding unit tests to check whether the function is behaving as expected.
In your intro_to_tpSVG could you expand the intro to provide comparisons to existing packages like nnSVG on how this package differs.

[boyiguo1]

Sounds great! I think I would be able to do that. I'm looking for about 3-week-ish turnaround time for the unit tests and comparison, if this is okay.

[lshep]

yes. thank you.

[lshep]

also completely optionally but considering the second vignette is so short it might be worth just adding as a supplemental section at the end of the intro vignette

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 10989b91cb7757018ae55a84623ed1b3d984bbe5

[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 22.04.3 LTS): tpSVG_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
git@git.bioconductor.org:packages/tpSVG to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[boyiguo1]

@lshep Thanks for your patience! I've addressed the previous comments via a recent PR (boyiguo1/tpSVG#14)

We strongly advise adding unit tests to check whether the function is behaving as expected.

I've initiated some unit tests to check if the error prevention for arguments.

In your intro_to_tpSVG could you expand the intro to provide comparisons to existing packages like nnSVG on how this package differs.

I've added the a paragraph in the vignette explains the innovation of our package, tpSVG, which provides a scalable and flexible framework to model count data instead of log-transformed count. A specific example is given comparing the gene ranking from nnSVG (modeling log-transformed gene counts with Gaussian process model ) and from tpSVG (modeling gene counts with thin plate regression spline), which results different inference results.

also completely optionally but considering the second vignette is so short it might be worth just adding as a supplemental section at the end of the intro vignette

I have placed the shorter vignette to the end of the intro vignette.

Thank you very much!

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

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community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

[lshep]

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https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("tpSVG"). The package 'landing page' will be created at

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If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.