protGear

[Keniajin]

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

• Repository: https://github.com/Keniajin/protGear

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• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

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[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 79c00667252888c06194e3363e6490620151f99a

[bioc-issue-bot]

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: "WARNINGS, 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/protGear 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: 68f55e7a4a273c5be024aeba93cdbd4a9062dcdc

[bioc-issue-bot]

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

[Kayla-Morrell]

@Keniajin,

Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

• [ ] REQUIRED: There seem to be a few files/directories present in your package that aren't normally included in Bioconductor packages. Please justify their use or remove:
  • docs/
  • help.csv
  • intro_test.html
  • www/

DESCRIPTION

• [ ] REQUIRED: There are far too many packages listed as depends. This field is intended for packages that provide essential functionality for the package. There shouldn't be more than 3 packages listed her. If the packages provide functions, methods, or classes that are used inside your package name space they should be listed under Imports.
• [ ] REQUIRED: The package rlang is listed under both Depends and Imports. This is not allowed. Please pick one or the other.
• [ ] REQUIRED: The package factoextra is listed twice under Imports. Please remove one so it is only listed once.
• [ ] REQUIRED: There are package listed in Depends that are not imported from in the NAMESPACE file. These packages should be imported from in the NAMESPACE file: Biobase, gridExtra, knitr, magrittr, vsn
• [ ] REQUIRED: Update R version from 4.1 to 4.2.
• [ ] REQUIRED: There is a call to scales in the vignette but this package is not listed under depends/imports/suggests. If this is something used only in the vignette example code then I would list it under Suggests.
• [ ] SUGGESTION: There are many suggested biocViews listed in the BiocCheck results of the build report. Please look them over and add any that seem applicable to your package.

NAMESPACE

• [ ] SUGGESTION: Generally importFrom() is encouraged over importing the entire package. However, if there are many functions from a single package, this is when the use of import() is acceptable. Also there are some packages that are imported and then you import individual functions from the package using importFrom. These should be simplified if possible.

NEWS

• [ ] REQUIRED: Including a NEWS file is great, but it seems that yours is not formatted properly. Please see our documentation here to see the correct way to format this file.

Package data

• [ ] REQUIRED: We require documentation for data in the inst/extdata/ directory to be present in the inst/scripts/ directory. The scripts in this directory can vary. They should very clearly state how the data was generated. It should include source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. The idea is users should be able to download the data and roughly reproduce the file or object that is present as data.

Vignette

• [ ] REQUIRED: For reproducability you should not be hiding the libraries being loaded. Also, you should not install a bunch at the beginning but only load the libraries where needed in your code. This will help prevent unneeded libraries from being loaded.
• [ ] REQUIRED: Line 375, when running through your vignette I got an error 'could not find function "kable_styling"' because I didn't load the libraries you loaded because they were hidden. Please add the proper library call to this code chunk so that the code can be executed.
• [ ] REQUIRED: Line 620, when trying to run the shiny app I got the error that there is no package called 'shinythemes', 'shinyjs', 'shinyWidgets', 'shinycssloaders', 'shinyFeedback', 'shinyalert', or 'shinyFiles'.
• [ ] SUGGESTION: We strongly encourage the use of BiocStyle for formatting.
• [ ] REQUIRED: The Installation section should demonstrate to the user how to install the package from Bioconductor, not github.
• [ ] REQUIRED: The final section of the vignette should be Session Info and should include sessionInfo().
• [ ] REQUIRED: Only source vignette files (.Rnw or .Rmd) and any necessary static images should be present in the vignette directory. Please remove the .csv and .R files.

Man pages

• [ ] SUGGESTION: There is a man page for error_replicates but this does not seem to be exported. If this is an internal function I would suggest adding the @keywords internal tag to the documentation.
• [ ] SUGGESTION: We suggest having a package man page with an overview of the package and links to the main functions.
• [ ] REQUIRED: Runnable examples should be added to the following man pages which document exported functions:
  • launch_protGear_interactive
  • launch_select
  • remove_batch_effect
  • rlm_normalise_matrix
  • rlm_normalise
• [ ] REQUIRED: There should not be a figures subdirectory in the man directory. Only man page files should be present here. If the figures are needed they should go in an inst/figures directory and be referenced from that location.

Unit tests

• [ ] SUGGESTION: We strongly encourage the use of unit tests.

R code

• [ ] SUGGESTION: There are many undefined global functions or variables. I would suggest defining as many of these as possible.
• [ ] REQUIRED: Avoid 1:...; instead use seq_len() or seq_along() were possible.
• [ ] REQUIRED: cat and print should not be used outside of show methods. Use message, warning, or stop instead. Found print in files: R/cv_estimation_tag_function.R, line 68 R/global_functions.R, line 165 R/normalisation_functions.R, line 152 R/read_files_functions.R, lines 128 and 603
• [ ] REQUIRED: Avoid the use of paste in condition signals. Found in files: R/cv_estimation_tag_functions.R, lines 41 and 66 R/global_functions.R, line 128 R/read_files_functions.R, lines 57, 112, and 590
• [ ] SUGGESTION: For formating reasons, consider shorter lines. There are 411 lines that are > 80 characters long.
• [ ] SUGGESTION: For formating reasons, consider 4 spaces instead of tabs. There are 4 lines that contain tabs.
• [ ] SUGGESTION: For formating reasons, consider multiples of 4 spaces for line indents. There are 862 lines that are not.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 42492baa9f28d98506e3fe4a431029e20f59b7b6

[bioc-issue-bot]

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/protGear 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: 345e0947f16c8f08c21ff68442db669b07c512ac

[Keniajin]

General package development

• Removed the files/directories aren't normally included in Bioconductor package

DESCRIPTION

• Removed the many packages listed on depends
• Removed rlang in depends
• Removed one of the factoextra files
• Updated the required packages in the NAMESPACE
• Updated the R version to 4.2
• Added Suggests in Description
• Added some of the suggested biocViews

NEWS

• Updated the NEWS format

Package data

• Added a data.R file under inst/scripts/ for data documentation

Vignette

• Packages shown at the top of vignette
• Added the Bioconductor installation
• Removed .csv and .R files. in vignette directory

Man pages

• Runnable examples were added to
  • launch_protGear_interactive
  • launch_select
  • remove_batch_effect
  • rlm_normalise_matrix
  • rlm_normalise
• The figures subdirectory in the man directory removed

R code

• Avoided using 1:....; where possible however I could not avoid it in 1:n()
• Removed cat and print outside of show methods
• Avoided the use of paste in condition signals

Regards, Ken Mwai

[bioc-issue-bot]

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/protGear 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: b5b6d58f37439228226a5a1a57c2b23695d13923

[bioc-issue-bot]

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

[Keniajin]

@Kayla-Morrell the package is ready for re-review

[bioc-issue-bot]

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

[Kayla-Morrell]

@Keniajin - Thank you for making the necessary changes. You mentioned that you removed the R and csv file from the vignette directory but I find them still present. Please be sure these files are removed. Once this is done I'll be able to accept the package.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: bc24ed94d9ece45f2625c41832a7c7933c88c76e

[bioc-issue-bot]

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, skipped". 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/protGear 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: 33249dad8edaabe7d1015720a1c43f87de377325

[Keniajin]

@Keniajin - Thank you for making the necessary changes. You mentioned that you removed the R and csv file from the vignette directory but I find them still present. Please be sure these files are removed. Once this is done I'll be able to accept the package.

Best, Kayla

@Kayla-Morrell thanks for the update. I have confirmed the files are removed now.

[bioc-issue-bot]

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

[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.

[lshep]

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/Keniajin.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("protGear"). The package 'landing page' will be created at

https://bioconductor.org/packages/protGear

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.