BioGA

[danymukesha]

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

• Repository: https://github.com/danymukesha/BioGA

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[bioc-issue-bot]

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]

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]

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

[bioc-issue-bot]

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
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version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org
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[bioc-issue-bot]

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]

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

[danymukesha]

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

[lshep]

Please see previous post #3315 (comment) You will need to push your changes to git.bioconductor.org to trigger a new build

[danymukesha]

I already committed the modification to bioconductor

[lshep]

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

[bioc-issue-bot]

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

[bioc-issue-bot]

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]

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

[bioc-issue-bot]

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]

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

[jianhong]

Could you please fix the error first? Thank you.

[bioc-issue-bot]

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

[bioc-issue-bot]

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]

Could you please fix the error first? Thank you.

@jianhong , I fixed the error

[jianhong]

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

• Important: Depends field is not found in DESCRIPTION.
• Important: R version is not clear in DESCRIPTION.
• Important: If you are not using the namespace in the R code, please move biocViews and sessioninfo into Suggests

The NAMESPACE file

• Important: Selective imports using importFrom instead of import all with import.
  • in line 12 import(SummarizedExperiment)
  • in line 13 import(animation)
  • in line 14 import(biocViews)
  • in line 15 import(ggplot2)
  • in line 16 import(graphics)
  • in line 18 import(sessioninfo)

General package development

• Important: Consider adding more unit tests. Current unit tests only covered 10.435% (less than 30%).

Documentation

• Note: Vignette should use BiocStyle package for formatting.
  • rmd file vignettes/Introduction.Rmd
  • rmd file vignettes/Overview.Rmd
  • rmd file vignettes/Usage.Rmd
• Important: Vignette should have an Introduction section..
  • rmd file vignettes/Overview.Rmd
  • rmd file vignettes/Usage.Rmd
• Important: Vignette should have an Installation section.
  • rmd file vignettes/Introduction.Rmd
  • rmd file vignettes/Overview.Rmd
  • rmd file vignettes/Usage.Rmd
• Important: Please include Bioconductor installation instructions using BiocManager.
  • rmd file vignettes/Introduction.Rmd
  • rmd file vignettes/Overview.Rmd
  • rmd file vignettes/Usage.Rmd

C and Fortran code

• NOTE: Makevars and Makefile not within a package when CPP version is lower than 0.11.0 or not restricted.
• Important: Using R's internal random number generator instead of std::rand
  • file src/crossover.cpp
    - line 30: int parent1_index = rand() % num_parents;
    - line 31: int parent2_index = rand() % num_parents;
  • file src/initialize_population.cpp
    - line 1:#include // Include the header for rand() function
    - line 30: int sample_index = std::rand() % num_samples;
  • file src/replacement.cpp
    - line 34: int index_to_replace = rand() % population_size;
• Note: If you are modifying code from somewhere, the original license should also be included.

[jianhong]

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

[danymukesha]

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

[bioc-issue-bot]

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

[bioc-issue-bot]

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]

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

Could you please check if everything is alright?

[jianhong]

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]

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?

[bioc-issue-bot]

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

[bioc-issue-bot]

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]

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]

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.