New ExperimentHub package "JohnsonKinaseData"

fgeier commented 3 months ago

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

Repository: https://github.com/fgeier/JohnsonKinaseData

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bioc-issue-bot commented 3 months ago

Hi @fgeier

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: JohnsonKinaseData
Title: Kinase PWMs based on data published by Johnson et al. 2023  (doi:10.1038/s41586-022-05575-3)
Version: 0.99.0
Date: 2023-09-19
Authors@R:
    person("Florian", "Geier", , "florian.geier@unibas.ch", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-9076-9264"))
Description: The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine kinases originally published in Johnson et al. 2023. It includes gene annotation for each kinase PWM and PWM matching scores for a set of 85603 curated human phosphosites which can be used to map a PWM score to its percentile rank. The package also includes basic functionality to score user provided phosphosites. 
License: MIT + file LICENSE
URL: https://github.com/fgeier/JohnsonKinaseData/
BugReports: https://support.bioconductor.org/t/JohnsonKinaseData
Imports: 
    ExperimentHub,
    BiocParallel, 
    checkmate, 
    dplyr, 
    stats, 
    stringr, 
    tidyr,
    purrr,
    utils
Suggests:
    knitr,
    BiocStyle,
    ExperimentHubData,
    testthat (>= 3.0.0),
    rmarkdown
biocViews: ExperimentHub, Homo_sapiens_Data, Proteome
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Config/testthat/edition: 3

bioc-issue-bot commented 3 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 3 months ago

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): JohnsonKinaseData_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/JohnsonKinaseData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 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 2 months ago

@fgeier - Thank you for submitting this package. I have looked everything over and have no proposed changes. Therefore I'm more than happy to accept the package as is.

Best, Kayla

bioc-issue-bot commented 2 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.

lshep commented 2 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/fgeier.keys is not empty), then no further steps are required. Otherwise, do the following:

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

https://bioconductor.org/packages/JohnsonKinaseData

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.

Bioconductor / Contributions

New ExperimentHub package "JohnsonKinaseData" #3354