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bugsigdbr #2200

Closed jwokaty closed 3 years ago

jwokaty commented 3 years ago

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

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bioc-issue-bot commented 3 years ago

Hi @jwokaty

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: bugsigdbr
Version: 0.99.0
Title: R-side access to published microbial signatures from BugSigDB
Authors@R: c(
    person(given = "Ludwig",
 family = "Geistlinger",
 role = c("aut", "cre"),
 email = "ludwig_geistlinger@hms.harvard.edu"),
    person(given = "Levi",
 family = "Waldron",
 role = "aut",
 email = "lwaldron.research@gmail.com"),
    person(given = "Jennifer",
 family = "Wokaty",
 role = "aut",
 email = "jennifer.wokaty@sph.cuny.edu")
    )
Description: Utilities for accessing microbiome signature data from bugsigdb.org
    and creating plain text signatures.
URL: https://github.com/waldronlab/bugsigdbr
BugReports: https://github.com/waldronlab/bugsigdbr/issues
Depends: R (>= 4.0.0)
Imports:
    BiocFileCache,
    readr,
    plyr
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
License: GPL (>= 3)
VignetteBuilder: knitr
LazyData: true
biocViews: GeneSetEnrichment, Metagenomics, Microbiome
Encoding: UTF-8
RoxygenNote: 7.1.1
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: "skipped, 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/bugsigdbr 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 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 86b5a53c5ccb4a2267aedf1b9fb020d36278f8a1

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.

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

vjcitn commented 3 years ago

Sorry for delay in review. BiocCheck produces

 [2] "Update R version dependency from 4.0.0 to 4.1."                                                                                                                                    
 [3] "Consider adding these automatically suggested biocViews: DataImport"                                                                                                               
 [4] "License 'GPL (>= 3)' unknown; licenses cannot restrict use"                                                                                                                        
 [5] " Avoid 1:...; use seq_len() or seq_along()"                                                                                                                                        
 [6] " Avoid the use of 'paste' in condition signals"                                                                                                                                    
 [7] "Consider adding runnable examples to the following man pages which document exported objects:"  

can these be addressed?

vjcitn commented 3 years ago

@jwokaty just want to make sure this is on your radar screen. It would be nice to clean up the BiocCheck events unless there are sound reasons not to. If you need a hand with events [5]-[7] let me know.

jwokaty commented 3 years ago

@vjcitn Thank you. I will work on these today.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: bc7f85a1d9272d5fe6fbac3ec3f909bd648d3b4c

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.

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/bugsigdbr 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 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fee71f209f0c1e28e83ed409503dbef6a0b9b312

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.

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/bugsigdbr 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 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 3 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/jwokaty.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("bugsigdbr"). The package 'landing page' will be created at

https://bioconductor.org/packages/bugsigdbr

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.