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BioGA #3315

Closed danymukesha closed 2 weeks ago

danymukesha commented 4 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 4 months ago

Hi @danymukesha

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:

Type: Package
Package: BioGA
Title: Bioinformatics Genetic Algorithm (BioGA)
Version: 0.99.0
Authors@R: 
    person("Dany", "Mukesha", , "danymukesha@gmail.com", 
  role = c("aut", "cre"),
 comment = c(ORCID = "0009-0001-9514-751X"))
Description: Genetic algorithm are a class of optimization algorithms
    inspired by the process of natural selection and genetics. This
    package allows users to analyze and optimize high throughput genomic
    data using genetic algorithms.  The functions provided are implemented
    in C++ for improved speed and efficiency, with an easy-to-use
    interface for use within R.
License: MIT + file LICENSE
URL: https://danymukesha.github.io/BioGA/
BugReports: https://github.com/danymukesha/BioGA/issues
Imports:
    ggplot2,
    graphics,
    Rcpp,
    sessioninfo
Suggests: 
    knitr,
    rmarkdown
LinkingTo: 
    Rcpp
VignetteBuilder: 
    knitr
biocViews: ExperimentalDesign, Technology
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
lshep commented 4 months ago

Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and show interoperability with a common Bioconductor class

danymukesha commented 3 months ago

I made the changes asked above. Could you review the updates please?

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.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): BioGA_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/BioGA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 3 months ago

Please add any needed dependency to the DESCRIPTION of your package in Suggest field.

danymukesha commented 3 months ago

I pushed the modifications. Could you please check if everything is alright?

lshep commented 3 months ago

Please see previous post https://github.com/Bioconductor/Contributions/issues/3315#issuecomment-2012229816 You will need to push your changes to git.bioconductor.org to trigger a new build

danymukesha commented 3 months ago

I already committed the modification to bioconductor

lshep commented 3 months ago

You need to do a version bump so that a new build is triggered.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: dc08dd462e584d960a3b39acaf4e59d656dbb093

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.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): BioGA_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/BioGA 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 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 322682aa3945187b4a628d027da2f4fe2c4c7726

bioc-issue-bot commented 2 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.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): BioGA_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/BioGA 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 months ago

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

jianhong commented 2 months ago

Could you please fix the error first? Thank you.

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 711726625985f724c5358e761838521cff6c5226

bioc-issue-bot commented 2 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): BioGA_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/BioGA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

danymukesha commented 2 months ago

Could you please fix the error first? Thank you.

@jianhong , I fixed the error

jianhong commented 2 months ago

Package 'BioGA' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

The DESCRIPTION file

jianhong commented 1 month ago

Just wanted to check in to see if we may expect any updates soon? Otherwise, I will close this issue.

danymukesha commented 1 month ago

I will be workin the issue this week. Thank you for reminding!

bioc-issue-bot commented 1 month ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 864ba147b7766f319263d9ddcf189f7258a70f04

bioc-issue-bot commented 1 month 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): BioGA_0.99.4.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/BioGA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

danymukesha commented 1 month ago

@jianhong I pushed the updates to fix the issues you mentioned.

Could you please check if everything is alright?

jianhong commented 1 month ago

Sure I will do that soon.Best!Your sincerely,Jianhong OuOn May 28, 2024, at 12:40 PM, Dany Mukesha @.***> wrote: @jianhong I pushed the updates to fix the issues you mentioned. Could you please check if everything is alright?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

jianhong commented 3 weeks ago

Almost there.

The DESCRIPTION file

bioc-issue-bot commented 3 weeks ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 037f6cb3b14c64d6ae92c1d0feee0ce8cb04bf34

bioc-issue-bot commented 3 weeks 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): BioGA_0.99.6.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/BioGA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

danymukesha commented 3 weeks ago

Almost there.

The DESCRIPTION file

  • [ ] Important: R version should be no less than 4.4

    Documentation

  • [ ] Note: Will it be better to add the authors and date in the vignettes?

@jianhong thank you for the review.

I just did the modifications you asked. Could you please check if everything is alright?

bioc-issue-bot commented 3 weeks 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 weeks 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/danymukesha.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("BioGA"). The package 'landing page' will be created at

https://bioconductor.org/packages/BioGA

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.