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R CMD BUILD
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* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* preparing ‘adverSCarial’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vign01_adverSCarial.Rmd’ using knitr
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<h1 id="introduction">Introduction</h1>
<p><strong>adverSCarial is a package for generating and evaluating vulnerability to adversarial attacks on single-cell RNA sequencing classifiers.</strong>
Single cell analysis are on the way to be used in clinical routine. As a critical use, algorithms must address the challenge of ensuring reliability, one concern being the susceptibility to adversarial attacks.</p>
<p>Zhang, J., Wang, W., Huang, J., Wang, X., & Zeng, Y. (2020). How far is single-cell sequencing from clinical application?. Clinical and translational medicine, 10(3), e117. <a href="https://doi.org/10.1002/ctm2.117">https://doi.org/10.1002/ctm2.117</a></p>
<p>de Hond, A.A.H., Leeuwenberg, A.M., Hooft, L. et al. Guidelines and quality criteria for artificial intelligence-based prediction models in healthcare: a scoping review. npj Digit. Med. 5, 2 (2022). <a href="https://doi.org/10.1038/s41746-021-00549-7">https://doi.org/10.10 [... truncated]
--- finished re-building ‘vign01_adverSCarial.Rmd’
--- re-building ‘vign02_overView_analysis.Rmd’ using knitr
Warning in file.info(x, extra_cols = FALSE) :
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<p>title: “adverSCarial, generate and analyze the vulnerability of scRNA-seq
classifiers to adversarial attacks”
shorttitle: “adverSCarial”
author: Ghislain FIEVET <a href="mailto:ghislain.fievet@gmail.com">ghislain.fievet@gmail.com</a>
package: adverSCarial
abstract: >
adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq
classifiers to adversarial attacks. The package is versatile and provides a format for integrating
any type of classifier. It offers functions for studying and generating two types of attacks,
min change attack and max change attack. The min change attack involves making a small modification
to the input to alter the classification. The max change attack involves making a large modification
to the input without changing its classification.
The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers
against adversarial attacks [... truncated]
--- finished re-building ‘vign02_overView_analysis.Rmd’
--- re-building ‘vign03_adapt_classifier.Rmd’ using knitr
Warning in file.info(x, extra_cols = FALSE) :
expanded path length 12185 would be too long for
<p>title: “adverSCarial, generate and analyze the vulnerability of scRNA-seq
classifiers to adversarial attacks”
shorttitle: “adverSCarial”
author: Ghislain FIEVET <a href="mailto:ghislain.fievet@gmail.com">ghislain.fievet@gmail.com</a>
package: adverSCarial
abstract: >
adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq
classifiers to adversarial attacks. The package is versatile and provides a format for integrating
any type of classifier. It offers functions for studying and generating two types of attacks,
min change attack and max change attack. The min change attack involves making a small modification
to the input to alter the classification. The max change attack involves making a large modification
to the input without changing its classification.
The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers
against adversarial attack [... truncated]
--- finished re-building ‘vign03_adapt_classifier.Rmd’
--- re-building ‘vign04_advRandWalkMinChange.Rmd’ using knitr
Quitting from lines 29-50 (vign04_advRandWalkMinChange.Rmd)
Error: processing vignette 'vign04_advRandWalkMinChange.Rmd' failed with diagnostics:
attempt to use zero-length variable name
--- failed re-building ‘vign04_advRandWalkMinChange.Rmd’
SUMMARY: processing the following file failed:
‘vign04_advRandWalkMinChange.Rmd’
Error: Vignette re-building failed.
Execution halted
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R CMD BUILD
===============================
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* preparing ‘adverSCarial’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vign01_adverSCarial.Rmd’ using knitr
Warning in file.info(x, extra_cols = FALSE) :
expanded path length 10719 would be too long for
<h1 id="introduction">Introduction</h1>
<p><strong>adverSCarial is a package for generating and evaluating vulnerability to adversarial attacks on single-cell RNA sequencing classifiers.</strong>
Single cell analysis are on the way to be used in clinical routine. As a critical use, algorithms must address the challenge of ensuring reliability, one concern being the susceptibility to adversarial attacks.</p>
<p>Zhang, J., Wang, W., Huang, J., Wang, X., & Zeng, Y. (2020). How far is single-cell sequencing from clinical application?. Clinical and translational medicine, 10(3), e117. <a href="https://doi.org/10.1002/ctm2.117">https://doi.org/10.1002/ctm2.117</a></p>
<p>de Hond, A.A.H., Leeuwenberg, A.M., Hooft, L. et al. Guidelines and quality criteria for artificial intelligence-based prediction models in healthcare: a scoping review. npj Digit. Med. 5, 2 (2022). <a href="https://doi.org/10.1038/s41746-021-00549-7">https://doi.org/10.10 [... truncated]
--- finished re-building ‘vign01_adverSCarial.Rmd’
--- re-building ‘vign02_overView_analysis.Rmd’ using knitr
Warning in file.info(x, extra_cols = FALSE) :
expanded path length 8932 would be too long for
<p>title: “adverSCarial, generate and analyze the vulnerability of scRNA-seq
classifiers to adversarial attacks”
shorttitle: “adverSCarial”
author: Ghislain FIEVET <a href="mailto:ghislain.fievet@gmail.com">ghislain.fievet@gmail.com</a>
package: adverSCarial
abstract: >
adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq
classifiers to adversarial attacks. The package is versatile and provides a format for integrating
any type of classifier. It offers functions for studying and generating two types of attacks,
min change attack and max change attack. The min change attack involves making a small modification
to the input to alter the classification. The max change attack involves making a large modification
to the input without changing its classification.
The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers
against adversarial attacks [... truncated]
--- finished re-building ‘vign02_overView_analysis.Rmd’
--- re-building ‘vign03_adapt_classifier.Rmd’ using knitr
Warning in file.info(x, extra_cols = FALSE) :
expanded path length 12185 would be too long for
<p>title: “adverSCarial, generate and analyze the vulnerability of scRNA-seq
classifiers to adversarial attacks”
shorttitle: “adverSCarial”
author: Ghislain FIEVET <a href="mailto:ghislain.fievet@gmail.com">ghislain.fievet@gmail.com</a>
package: adverSCarial
abstract: >
adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq
classifiers to adversarial attacks. The package is versatile and provides a format for integrating
any type of classifier. It offers functions for studying and generating two types of attacks,
min change attack and max change attack. The min change attack involves making a small modification
to the input to alter the classification. The max change attack involves making a large modification
to the input without changing its classification.
The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers
against adversarial attack [... truncated]
--- finished re-building ‘vign03_adapt_classifier.Rmd’
--- re-building ‘vign04_advRandWalkMinChange.Rmd’ using knitr
Quitting from lines 29-50 (vign04_advRandWalkMinChange.Rmd)
Error: processing vignette 'vign04_advRandWalkMinChange.Rmd' failed with diagnostics:
attempt to use zero-length variable name
--- failed re-building ‘vign04_advRandWalkMinChange.Rmd’
SUMMARY: processing the following file failed:
‘vign04_advRandWalkMinChange.Rmd’
Error: Vignette re-building failed.
Execution halted