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CardinalIO #3110

Closed kuwisdelu closed 10 months ago

kuwisdelu commented 11 months ago

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

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 11 months ago

Hi @kuwisdelu

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: CardinalIO
Type: Package
Title: Read and write mass spectrometry imaging files
Version: 0.99.0
Date: 2023-8-12
Authors@R: person("Kylie Ariel", "Bemis",
    email = "k.bemis@northeastern.edu",
    role = c("aut", "cre"))
Description: Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.
License: Artistic-2.0
Depends: R (>= 4.3), matter, ontologyIndex
Imports: methods, S4Vectors, stats, utils, tools
Suggests: BiocStyle, testthat, knitr, rmarkdown
VignetteBuilder: knitr
biocViews: Software, Infrastructure, DataImport,
    MassSpectrometry, ImagingMassSpectrometry
URL: http://www.cardinalmsi.org
BugReports: https://github.com/kuwisdelu/CardinalIO/issues
bioc-issue-bot commented 11 months ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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 commented 11 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): CardinalIO_0.99.0.tar.gz macOS 12.6.5 Monterey: CardinalIO_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 git@git.bioconductor.org:packages/CardinalIO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 11 months ago

@kuwisdelu - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

NAMESPACE

Data

Man pages

R code

Best, Kayla

bioc-issue-bot commented 11 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3f65bcc142fb558546882c12df8882329b0449d8

bioc-issue-bot commented 11 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): CardinalIO_0.99.1.tar.gz macOS 12.6.5 Monterey: CardinalIO_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/CardinalIO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kuwisdelu commented 11 months ago

Thank you for the initial review!

@kuwisdelu - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

  • [ ] SUGGESTION: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")'.
  • [ ] SUGGESTION: Consider adding these automatically suggested biocViews: Preprocessing, DimensionReduction

The package does not perform pre-processing or dimension reduction, so I have not added them, nor do I currently have an ORCID iD.

NAMESPACE

  • [ ] SUGGESTION: Generally 'importFrom()' is encouraged over importing an entire package. However, if there are many functions from a single package, 'import()' can be acceptable.

I used importFrom() where I was only using a few functions, and import() where I was using more functions and it seems more convenient/appropriate. I left this as-is.

Data

  • [ ] REQUIRED: Data included in the 'inst/extdata/' directory requires documentation in an 'inst/script/' directory. The scripts in this directory can vary. Most importantly a related script must be present that clearly documents how the data was generated and source information. It should include source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data.

I did not initially include this as the files were directly downloaded as official examples of the imzML format without any additional processing, as documented in ?exampleImzMLFile.

However, I've now added "manifest.md" to inst/script to satisfy this requirement, which lists the files and where they were originally downloaded from.

Man pages

  • [ ] SUGGESTION: We encourage having a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?CardinalIO.

I have added this.

R code

  • [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 93 lines that are > 80 characters long.
  • [ ] SUGGESTION: For formatting reasons, consider 4 spaces instead of tabs. There are 1206 lines that contain tabs.

I generally try to keep lines around ~80 characters, but some lines would be made more awkward/less readable if shortened, and some lines are pre-formatted XML templates. Lastly, I have a strong preference for tabs.

Best, Kayla

I have made the changes where required and considered all suggestions.

Thank you.

-Kylie

Kayla-Morrell commented 11 months ago

@kuwisdelu - Thank you for making the necessary changes. I have reviewed everything and it all looks good. I'm more than happy to accept the package.

Best, Kayla

bioc-issue-bot commented 11 months ago

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

kuwisdelu commented 11 months ago

Thank you!

lshep commented 10 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/kuwisdelu.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

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("CardinalIO"). The package 'landing page' will be created at

https://bioconductor.org/packages/CardinalIO

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.