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epistack #2362

Closed gdevailly closed 2 years ago

gdevailly commented 3 years 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 3 years ago

Hi @gdevailly

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: epistack
Title: Heatmaps of Stack Profiles from Epigenetic Signals
Version: 0.99.0
Authors@R: 
    c(
    person("SACI", "Safia", email = "safiasaci1995@gmail.com", role = "aut"),
    person("DEVAILLY", "Guillaume",
        email = "gdevailly@hotmail.com", role = "cre"))
Description: The epistack package main objective is the visualizations of
    stacks of genomic tracks (such as, but not restricted to, ChIP-seq,
    ATAC-seq, DNA methyation or genomic conservation data)
    centered at genomic regions of interest.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Imports: 
    GenomicRanges,
    BiocGenerics,
    S4Vectors,
    IRanges,
    viridisLite,
    graphics,
    plotrix,
    grDevices,
    stats
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Depends: 
    R (>= 4.0)
Suggests: 
    testthat (>= 3.0.0),
    BiocStyle,
    knitr,
    rmarkdown,
    EnrichedHeatmap,
    biomaRt,
    rtracklayer,
    covr,
    vdiffr,
    magick
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: RNASeq, Preprocessing, ChIPSeq, GeneExpression
bioc-issue-bot commented 3 years 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 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/epistack to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: abc39f0da38bb2b72ec5dd1ee896808cf5d181ca

bioc-issue-bot commented 2 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/epistack to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 2 years ago

a few minor comments:

NEWS.md

README

vignette

Please make the above changes. When ready please trigger a new build report by pushing a version bump and comment back here you are ready for a re-review.

Thank you

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7fd24008c9bcfacd78241514092bff30ef8fa69b

bioc-issue-bot commented 2 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/epistack to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

gdevailly commented 2 years ago

NEWS.md

README

vignette

package refactoring

Thanks for your time and comments 👍.

lshep commented 2 years ago

I do think a refactoring to allow for use of SummarizedExperiment would also be helpful -- since you are still currently relying on another major Bioconductor class structure with GenomicRanges, I will feel comfortable accepting the package as it but would strongly suggest moving forward with the idea of also making it compatible with SummarizedExperiment (or since GenomicRanges was utilized maybe a RangedSummarizedExperiment) during the next development cycle (3.15) -- Cheers,

bioc-issue-bot commented 2 years 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 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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/gdevailly.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("epistack"). The package 'landing page' will be created at

https://bioconductor.org/packages/epistack

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.