Closed kuwisdelu closed 1 year 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
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Dear Package contributor,
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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
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Remember: if you submitted your package after July 7th, 2020,
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@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.
?CardinalIO
.Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: 3f65bcc142fb558546882c12df8882329b0449d8
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.
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
@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
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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