Open GhislainFievet opened 3 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>
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
Also please consider renaming the vignette file to something more informative than doc.Rmd; we recommend the name of the package
Thank you for the review :-) I'll work on it.
Hi lshep,
I modified what you mentionned:
devtools::install_github("GhislainFievet/XAItest", build_vignettes = TRUE, force=TRUE)
runs fine.Thank you :-)
Ghislain
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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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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 8c94d6c04147daa1ba43a418011e5cc50a5a2386
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: e92555f395a8edf9c29ebb54528fe00fd55f8a93
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: d0fe83e715ca1ba6f4aee039eec37b18d528bf9c
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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 595c94194ceb35d66f73dbaae30e0e34bd3342bc
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: a3d726a2cd42be0102a6bf85a4782cff0135d2d5
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: c681fc974ad68ac14b9bba12f7c6b1207b6bc8e0
Received a valid push on git.bioconductor.org; starting a build for commit id: 0d76526ca49200d52cb2af95c27dd25d01c89ed1
Dear Package contributor,
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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.
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.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Hi @GhislainFievet
Sorry for the delay. Thank you for your submission. Please see the review below.
Best regards, Marcel
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.BugReports
and URL
fields.xgboost
, shapr
to the Suggests
field in the DESCRIPTION
bibliography: ../inst/REFERENCES.bib
devel
version from the vignette. After
acceptance, the vignette will be published to the release version.mapPvalImportance(objXAI)
..objXAI
rather than contXAI
cat
for the show
method.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"
).sapply
and use either lapply
or vapply
.objXAI@metricsTable
or use S3.print
and use message
instead for verbose
outputs.ggplot2
is installed if you will keep it in Suggests
e.g.,
with BiocBaseUtils::checkInstalled
. Otherwise move it to the Imports
field.df
input of your main function XAI.test
to be more descriptive as
it also accepts SummarizedExperiment
.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%
Thank you for the review :-) I will make those changes and get back to you.
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