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raerdata #3160

Closed kriemo closed 8 months ago

kriemo commented 9 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]'

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

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 commented 9 months ago

Hi @kriemo

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: raerdata
Title: A collection of datasets for use with raer package
Version: 0.99.2
Description: raerdata is an ExperimentHub package that
  provides a collection of files useful for demostrating
  functionality in the raer package. Datasets include 
  10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome
  and RNA-seq data. Additionally 
  databases of human and mouse RNA editing sites are provided.
Authors@R:
    person(given = "Kent",
   family = "Riemondy",
   role = c("aut", "cre"),
   comment = c(ORCID = "0000-0003-0750-1273"),
   email = "kent.riemondy@cuanschutz.edu")
License: MIT + file LICENSE
Imports: 
  ExperimentHub, 
  Rsamtools, 
  SingleCellExperiment, 
  rtracklayer, 
  GenomicRanges,
  BiocGenerics
Suggests: rmarkdown, knitr, BiocStyle
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Encoding: UTF-8
biocViews: SingleCellData, SequencingData, RNASeqData, ExperimentHub, PackageTypeData, ExpressionData
BugReports: https://github.com/rnabioco/raerdata/issues
URL: https://github.com/rnabioco/raerdata
bioc-issue-bot commented 9 months ago

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 commented 9 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): raerdata_0.99.2.tar.gz macOS 12.6.5 Monterey: raerdata_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/raerdata to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kriemo commented 9 months ago

AdditionalPackage: https://github.com/rnabioco/raer

bioc-issue-bot commented 9 months ago

Hi @kriemo, Thanks for submitting your additional package: https://github.com/rnabioco/raer. We are taking a quick look at it and you will hear back from us soon.

bioc-issue-bot commented 9 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 9 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.

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 Bioconductor Build System: macOS 12.6.5 Monterey: raer_0.99.14.tar.gz Linux (Ubuntu 22.04.2 LTS): raer_0.99.14.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/raer to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kriemo commented 9 months ago

Regarding the R CMD CHECK checking compiled code ... WARNING seen on the package builds. This warning arises from the use of Rhtslib, which includes source code with sprintf usage. From my understanding this is an expected warning, and is found with all packages that use Rhtslib (https://bioconductor.org/checkResults/3.18/bioc-LATEST/Rhtslib/ ).

bioc-issue-bot commented 9 months ago

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

Kayla-Morrell commented 9 months ago

@kriemo - 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. Keep in mind that the deadline to accept new packages into the Bioconductor 3.18 release is 10/18. Any packages accepted after this date will be included in the next release.

NAMESPACE

Vignette

Unit tests

R code

Best, Kayla

kriemo commented 9 months ago

@Kayla-Morrell. Many thanks for the review. I have one quick question before I begin addressing the comments. Is the review in reference to both submitted packages or just the experiment data raerdata package?

Thanks, Kent

Kayla-Morrell commented 9 months ago

@kriemo - I'm so sorry I missed the additional package line! This would be a review for just raerdata. If you want to work on addressing that review I can work on getting a review together for rear and have it posted shortly.

Best, Kayla

kriemo commented 9 months ago

ok great, thank you.

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8fab809fe2d49f69fe8746652f8ae512b84ca0d4

bioc-issue-bot commented 9 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): raerdata_0.99.3.tar.gz macOS 12.6.5 Monterey: raerdata_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/raerdata to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kriemo commented 9 months ago

I've made the requested changes to the raerdata package and fixed most of the suggested formatting notes

NAMESPACE

I have replaced all imports with importFrom()

Vignette

I have added an Introduction section with some additional details

I have added an Installation section

Unit tests

I have added unit tests to ensure that the package functions return the expected experimentHub resources

R code

I have reduced the number of lines > 80 characters down to 2 documentation lines, which reference URLs

I have fixed this formatting issue

Kayla-Morrell commented 8 months ago

@kriemo - Below is my review for raer. I'll work on re-reviewing raerdata while you work on addressing these points.

Data

Vignette

Man pages

R code

Best, Kayla

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f0b45380e6b76ed3dd0cd946f33cf7a88e71c9a9

bioc-issue-bot commented 8 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.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): raer_0.99.15.tar.gz macOS 12.6.5 Monterey: raer_0.99.15.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/raer to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kriemo commented 8 months ago

@Kayla-Morrell Many thanks for your prompt review of the raer package. I believe I have addressed your comments, with the exception of the request to remove the man/figures directory, which I justify in the notes below. The WARNING from the single package builder is the same warning related to the use of Rhtslib in the package that I mentioned previously in the issue.

Data

I have moved the README from inst/extdata to inst/scripts and updated the README text. I copied the corresponding scripts from raerdata referenced in the README into inst/scripts and kept only code relevant for making the files present in the inst/extdata directory.

Vignette

I have modified the code to make it executable (lines 183 - 203)

I have added this section (lines 35 - 43)

I have made the sessionInfo an entry in the table of contents and removed the html that made the content a hidden code chunk.

Man pages

- [ ] REQUIRED: The figures/ directory does not belong in man/. I would suggest moving this directory to inst/figures/.

I would like to request an exemption to this required change. The image files included in man/figures are referenced as part of the documentation for the package (?raer) and used by the pkgdown documentation site for the package. The man/figures directory is a standard directory that is supported by CRAN, and the suggested location for images used in the documentation. https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Figures

The man/figures directory is also currently used by many Bioconductor packages that use pkgdown for their documentation: (e.g. results from a BioC code search for packages that reference an man/figures/logo.png file)

I have moved the illustrator file (raer-logo.ai) to inst/misc as this is not necessary for pkgdown or the R documentation.

R code

I have reduced the number of lines > 80 from 323 lines to 70 lines. Most of the remaining lines > 80 characters are in .Rd documentation files.

I have reduced the number of line indents not multiples of 4 spaces from 217 lines to 115 lines. Most of the remaining problematic lines idents are in .Rd documentation files.

Kayla-Morrell commented 8 months ago

@kriemo - Thank you for making all the necessary changes. I have re-reviewed both raer and raerdata and everything looks good. I'm more than happy to accept the packages.

Best, Kayla

bioc-issue-bot commented 8 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.

kriemo commented 8 months ago

Great, thank you so much for all of your help!

lshep commented 8 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/kriemo.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("raerdata"). The package 'landing page' will be created at

https://bioconductor.org/packages/raerdata

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.

lshep commented 8 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/kriemo.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("raer"). The package 'landing page' will be created at

https://bioconductor.org/packages/raer

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.