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XAItest #3519

Open GhislainFievet opened 2 months ago

GhislainFievet commented 2 months 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 2 months ago

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", , "ghislain.fievet@gmail.com", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-0337-7327")),
    person("Sébastien", "HERGALANT", role = "aut",
    email="sebastien.hergalant@inserm.fr", 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] (<adresse_email@exemple.com>)
Maintainer: Prénom Nom <adresse_email@exemple.com>
lshep commented 2 months ago

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

lshep commented 2 months ago

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

GhislainFievet commented 1 month ago

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

GhislainFievet commented 1 month ago

Hi lshep,

I modified what you mentionned:

Thank you :-)

Ghislain

bioc-issue-bot commented 1 month 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.

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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.

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

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

bioc-issue-bot commented 1 month ago

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

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.

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 git@git.bioconductor.org:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 month ago

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

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.

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 git@git.bioconductor.org:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 month ago

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

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.

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 git@git.bioconductor.org:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 month ago

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

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.

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 git@git.bioconductor.org:packages/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 month ago

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

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.

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_0.99.5.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_0.99.5.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/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 month ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c681fc974ad68ac14b9bba12f7c6b1207b6bc8e0

bioc-issue-bot commented 1 month ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0d76526ca49200d52cb2af95c27dd25d01c89ed1

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): XAItest_0.99.6.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_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/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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): XAItest_0.99.7.tar.gz Linux (Ubuntu 24.04.1 LTS): XAItest_0.99.7.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/XAItest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 month ago

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

LiNk-NY commented 2 weeks ago

Hi @GhislainFievet

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

Best regards, Marcel


XAItest #3519

DESCRIPTION

NAMESPACE

vignettes

R

tests

GhislainFievet commented 2 weeks ago

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