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Repository: https://github.com/GhislainFievet/XAItest

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Aug 20 '24 04:08 GhislainFievet

Hi @GhislainFievet

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: XAItest 
Title: XAItest: Enhancing Feature Discovery with eXplainable AI
Version: 0.99.0
Authors@R: c(
    person("Ghislain", "FIEVET", , "[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-0337-7327")),
    person("Sébastien", "HERGALANT", role = "aut",
    email="[email protected]", comment=c(ORCID = "0000-0001-8456-7992")))
Description:
    XAItest is an R Package that identifies features using explainable AI
    methods such as SHAP or LIME. This package allows users to compare
    these methods with traditional statistical tests like t-tests, empirical
    Bayes, and Fisher's test. Additionally, it includes a system that enables
    the comparison of feature importance with p-values by incorporating
    calibrated simulated data.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: Software, StatisticalMethod, FeatureExtraction, Classification, Regression
Suggests: knitr, ggplot2, ggforce, shapr
Imports: limma, randomForest, kernelshap, caret, lime, DT, methods
VignetteBuilder: knitr
Author: Prénom Nom [aut, cre] (<[email protected]>)
Maintainer: Prénom Nom <[email protected]>

Aug 20 '24 04:08 bioc-issue-bot

When I try to build your vignette I get an ERROR

R CMD build XAItest 
* checking for file 'XAItest/DESCRIPTION' ... OK
* preparing 'XAItest':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘doc.Rmd’ using knitr

Quitting from lines 120-122 [unnamed-chunk-4] (doc.Rmd)
Error: processing vignette 'doc.Rmd' failed with diagnostics:
Predictions must be numeric!
--- failed re-building ‘doc.Rmd’

SUMMARY: processing the following file failed:
  ‘doc.Rmd’

Error: Vignette re-building failed.
Execution halted

This package doesn't currently integrate with any existing Bioconductor classes. Could you show an example in the vignette, possibly with already existing data from another package and how your functions can be integrated into a Bioconductor ecosystem. See https://contributions.bioconductor.org/important-bioconductor-package-development-features.html#commonclass

Sep 03 '24 18:09 lshep

Also please consider renaming the vignette file to something more informative than doc.Rmd; we recommend the name of the package

Sep 03 '24 18:09 lshep

Thank you for the review :-) I'll work on it.

Sep 04 '24 04:09 GhislainFievet

Hi lshep,

I modified what you mentionned:

I fixed the Error problem, now the devtools::install_github("GhislainFievet/XAItest", build_vignettes = TRUE, force=TRUE) runs fine.
I added the possibility to take as input a SummarizedExperiment object for the main function XAI.test, I also added some example of it in the man documentation, and added as a first example in the vignette the dataset airway from the bioconductor airway package.
I renamed the vignette as XAItest.Rmd.

Thank you :-)

Ghislain

Sep 14 '24 05:09 GhislainFievet

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.

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Sep 17 '24 17:09 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): XAItest_0.99.0.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_0.99.0.tar.gz

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sep 17 '24 17:09 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 8c94d6c04147daa1ba43a418011e5cc50a5a2386

Sep 19 '24 04:09 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 24.04.1 LTS): XAItest_0.99.1.tar.gz Linux (Ubuntu 22.04.3 LTS): XAItest_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 [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: e92555f395a8edf9c29ebb54528fe00fd55f8a93

Sep 19 '24 04:09 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): XAItest_0.99.2.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_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 [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: d0fe83e715ca1ba6f4aee039eec37b18d528bf9c

Sep 19 '24 05:09 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 24.04.1 LTS): XAItest_0.99.3.tar.gz Linux (Ubuntu 22.04.3 LTS): XAItest_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 [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: 595c94194ceb35d66f73dbaae30e0e34bd3342bc

Sep 19 '24 06:09 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: "WARNINGS". 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): XAItest_0.99.4.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_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 [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: a3d726a2cd42be0102a6bf85a4782cff0135d2d5

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Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): XAItest_0.99.5.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_0.99.5.tar.gz

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): XAItest_0.99.6.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_0.99.6.tar.gz

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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): XAItest_0.99.7.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_0.99.7.tar.gz

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

Sep 23 '24 14:09 bioc-issue-bot

Hi @GhislainFievet

Sorry for the delay. Thank you for your submission. Please see the review below.

Best regards, Marcel

XAItest #3519

Please make a stronger case for submission to Bioconductor. The main data representation in the package is data.frame and many of the functions and classes use either a data.frame or a list. The use of S4 should be reconsidered given the type of classes that your class inherits from.

DESCRIPTION

Add BugReports and URL fields.
Add xgboost, shapr to the Suggests field in the DESCRIPTION

NAMESPACE

Looks good.

vignettes

Consider wrapping text within the 80 character width.
Use the citation feature of RMarkdown with following in the YAML front matter:

bibliography: ../inst/REFERENCES.bib

Remove the reference to the devel version from the vignette. After acceptance, the vignette will be published to the release version.
Remove any commented code from the vignette.
It is strongly discouraged to use static images. Please run the function and show any graphical outputs for mapPvalImportance(objXAI).
Consider moving the custom function creation to a different vignette.

R

S4 classes have the convention of starting with a capital letter.
The class constructor should usually be .objXAI rather than contXAI
Reconsider using S4 for your composed class. It seems to be more fitting as an S3.
Use cat for the show method.
Wrap text in the documentation and code to a limit of 80 character width.
Set the defaults refPvalColumn and featImpColumns to be the ones you are grepping for i.e., adjpval and let the user change it if the column names are different (e.g., refPvalColumn = "adjpval").
Avoid the use of sapply and use either lapply or vapply.
Create class accessors and avoid using objXAI@metricsTable or use S3.
Avoid using print and use message instead for verbose outputs.
Check that ggplot2 is installed if you will keep it in Suggests e.g., with BiocBaseUtils::checkInstalled. Otherwise move it to the Imports field.
Rename df input of your main function XAI.test to be more descriptive as it also accepts SummarizedExperiment.

tests

Coverage looks good. Consider increasing the coverage for plotModel.R:

> covr::package_coverage(type = "all")
XAItest Coverage: 86.50%
R/plotModel.R: 66.67%
R/getFeatImpThresholds.R: 82.35%
R/mapPvalImportance.R: 88.89%
R/XAI.test.R: 89.01%
R/modelsOverview.R: 93.75%
R/allClasses.R: 100.00%

Oct 17 '24 17:10 LiNk-NY

Thank you for the review :-) I will make those changes and get back to you.

Oct 18 '24 05:10 GhislainFievet

Received a valid push on git.bioconductor.org; starting a build for commit id: 71f86283e3114e723574d3d0c646fdfaa9942c91

Dec 09 '24 05:12 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: "WARNINGS". 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 24.04.1 LTS): XAItest_0.99.8.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 [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 09 '24 05:12 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 24615ea3b9e76ab15a2a195d9cb8ede786249542

Dec 09 '24 06:12 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 24.04.1 LTS): XAItest_0.99.9.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 [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 09 '24 06:12 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 9f358b2be69f7a139d5a192b6bac025265aa85d7

Dec 09 '24 06:12 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: "WARNINGS". 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 24.04.1 LTS): XAItest_0.99.10.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 [email protected]:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 09 '24 06:12 bioc-issue-bot

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XAItest

XAItest #3519

DESCRIPTION

NAMESPACE

vignettes

R

tests

Contributions
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