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CCPlotR #3116

Closed Sarah145 closed 12 months ago

Sarah145 commented 1 year 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 1 year ago

Hi @Sarah145

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: CCPlotR
Title: Plots For Visualising Cell-Cell Interactions
Version: 0.99.1
Authors@R: c(
    person("Sarah", "Ennis", email = "ennissarah94@gmail.com", role = c("aut", "cre"), 
 comment = c(ORCID = "0000-0001-6100-8573")),
    person("Pilib", "Ó Broin", email = "p.obroin@universityofgalway.ie", role = c("aut")),
    person("Eva", "Szegezdi", email = "eva.szegezdi@universityofgalway.ie", role = c("aut")))
Description: CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc. 
Imports:
    plyr,
    tidyr,
    dplyr,
    ggplot2,
    forcats,
    ggraph,
    igraph,
    scatterpie,
    circlize,
    ComplexHeatmap,
    tibble,
    grid,
    ggbump,
    stringr,
    ggtext,
    ggh4x,
    patchwork,
    RColorBrewer,
    scales,
    viridis,
    grDevices,
    graphics,
    stats
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle
VignetteBuilder: knitr
biocViews: SingleCell, Network, Visualization, CellBiology, SystemsBiology
bioc-issue-bot commented 1 year 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 1 year 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: "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 Bioconductor Build System: macOS 12.6.5 Monterey: CCPlotR_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): CCPlotR_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/CCPlotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 420a947ee81fd1438dd572ead296dee6b6e3ec7a

Sarah145 commented 1 year ago

Hi, The ERROR was due to me not being subscribed to the bioc-devel mailing list. I had subscribed with a different email address but have subscribed with the correct one now too so the ERROR should be resolved.

bioc-issue-bot commented 1 year 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): CCPlotR_0.99.2.tar.gz macOS 12.6.5 Monterey: CCPlotR_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/CCPlotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

ococrook commented 1 year ago

Hi

Sorry for the delay. I thought I had already posted a review! I think the package is very good and useful! My main comment is the suitability for Bioconuductor. I realise the packages intended use is to be quite generic but it's not clear how it's meant to integrate within the wider ecosystem. That doesn't mean it shouldn't be a Bioconductor package, I just need to be convinced.

Please check through the build report carefully, there are a few things in there that can be straightforwardly handled such as setting laxydata to FALSE - unless you need it to be true for some reason?

I think the package would also benifit from unit tests.

The vignette can't be name UserGuide this is too generic for a Bioconductor package.

Function arguments with no default should be checked for validty - else I get error messages I cant debug very easily.

You will also need bioconductor install instructions in the readme and vignette. Remember to set the eval = FALSE

Thanks¬

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b84f80262720cc1f0e0a6dea96791ff4384d2d45

bioc-issue-bot commented 1 year 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): CCPlotR_0.99.3.tar.gz macOS 12.6.5 Monterey: CCPlotR_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/CCPlotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sarah145 commented 1 year ago

Hi,

Thanks for taking the time to review the package and for the helpful suggestions! I've addressed each of your points below:

Thanks again for the input and please let me know if any more changes are required!

ococrook commented 1 year ago

Thank you!

bioc-issue-bot commented 1 year 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.

lshep commented 12 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/Sarah145.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("CCPlotR"). The package 'landing page' will be created at

https://bioconductor.org/packages/CCPlotR

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.