(inactive) VSOLassoBag

[chywang17]

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

• Repository: https://github.com/likelet/VSOLassoBag

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[bioc-issue-bot]

Hi @chywang17

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: VSOLassoBag
Type: Package
Title: A variable-selection oriented LASSO bagging algorithm for biomarker 
        discovery in omic-based translational research
Version: 0.99.0
Date: 2022-10-05
biocViews: Software, StatisticalMethod, FeatureExtraction
Authors@R: c(
  person('Qi', 'Zhao',  email = 'zhaoqi@sysucc.org.cn', role = c('aut','cre'), comment = c(ORCID = '0000-0002-8683-6145')),
  person('Jiaqi', 'Liang',  email = 'liangjq27@mail2.sysu.edu.cn', role = c('aut')),
  person('Chaoye', 'Wang',  email = 'wangcy1@sysucc.org.cn', role = c('aut'))
  )
Description: VSOLassoBag is a wrapped LASSO approach by integrating an ensemble learning strategy to help select efficient, stable, and high confidential variables from omics-based data. Using a bagging strategy in combination of a parametric method or inflection point search method for cut-off threshold determination, VSOLassoBag can integrate and vote variables generated from multiple LASSO models to determine the optimal candidates.
License: GPL-3
Encoding: UTF-8
Depends:
    R (>= 3.5.0)
Imports: 
    glmnet,
    survival,
    ggplot2,
    POT,
    utils
Enhances: parallel
RoxygenNote: 7.2.0
Suggests: 
    rmarkdown,
    knitr,
    rmdformats,
    qpdf
VignetteBuilder: knitr

[vjcitn]

Thanks for this submission. This package will need some revision in order to enter the review process.

• The simulated_example data is a list with a number of components; it is not documented per se, although test.df is documented
• the x component of test.df is described as having samples in rows and variates in columns ... the layout for Bioconductor data structures is typically genes or features as rows and samples as columns
• Bioconductor data structures like SummarizedExperiment should be used so that metadata and numerical data are tightly coupled
• There is no discussion of genomic application of the methodology. Should this package be distributed via CRAN instead?
• This trace-type information

  > res<-VSOLassoBag(mat=test.df$x,out.mat=test.df$label,bootN=100,a.family="binomial",bagFreq.sigMethod="PST")
  Tue Oct 11 05:58:28 2022 -- INIT process completed, start analyzing  
  Tue Oct 11 05:58:28 2022 -- start calculating observed frequency  
  2022-10-11 05:58:28--One boostrap done. 
  2022-10-11 05:58:29--One boostrap done. 
  2022-10-11 05:58:29--One boostrap done. 
  2022-10-11 05:58:29--One boostrap done. 
  2022-10-11 05:58:30--One boostrap done. 
  2022-10-11 05:58:30--One boostrap done. 

  should probably be presented using a progressBar (see ?txtProgressBar in utils)

Thanks again for your submission. Please describe all changes made in response to these comments, and I will check again.

[chywang17]

Hi @vjcitn, I appreciate the suggestions you provided for our R package. We have already made some modifications to the VSOLassoBag as follows:

① We have revised the data input format of the VSOLassoBag. We now use the SummarizedExperiment format as input, thus ensuring the coupling of the sample information with the expression matrix. In addition, the new input data format requires rows as features, columns as samples, to ensure that the data is in a format commonly used in the R language.

② We recreated the example dataset (ExpressionData) required for the VSOLassoBag and illustrated the contents of it.

③ We use progress Bar to illustrate the running of the program.

④ VSOLassoBag is a variable-selection oriented Lasso bagging algorithm for biomarker development in omics-based translational research. It is particularly suitable for filtering variables in high-dimensional data, which is one of the unique properties of biological data, so we think it is appropriate to cast it on Bioconductor.

The above changes have been re-uploaded to https://github.com/likelet/VSOLassoBag, please check it.

Finally, thank you for your suggestions sincerely!

[chywang17]

Hi @vjcitn , I have updated VSOLassoBag for 22 days ago, please let us know if our package passed pre-check. I'm looking forward to your reply soon.

[vjcitn]

Sorry for the delay on this. I do pre-check and then

stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/JAN9$ dbic VSOLassoBag
1/12 packages newly attached/loaded, see sessionInfo() for details.
ℹ Updating VSOLassoBag documentation
ℹ Loading VSOLassoBag
Warning: [LessPermutation.R:1] @title must be a single paragraph
Warning: [LessPermutation.R:21] Block must have a @name
ℹ Either document an existing object or manually specify with @name
Warning: [lassoBagAddGPD.R:91] Block must have a @name
ℹ Either document an existing object or manually specify with @name
Warning: [simpleEstimation.R:19] Block must have a @name
ℹ Either document an existing object or manually specify with @name
1/11 packages newly attached/loaded, see sessionInfo() for details.
* checking for file 'VSOLassoBag/DESCRIPTION' ... OK
* preparing 'VSOLassoBag':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘VSOLassoBag.Rmd’ using rmarkdown
Quitting from lines 155-160 (VSOLassoBag.Rmd) 
Error: processing vignette 'VSOLassoBag.Rmd' failed with diagnostics:
could not find function "VSOLassoBag"
--- failed re-building ‘VSOLassoBag.Rmd’

Did you run R CMD check on your package on a clean system?

[bioc-issue-bot]

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

[PeteHaitch]

Thank you for submitting VSOLassoBag to Bioconductor, @chywang17. Please address any errors and warnings in the latest build report and I will then schedule time to begin my review. The error should be pretty simple to fix:

* Checking for bioc-devel mailing list subscription...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

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