GARS

[BioinfoMonzino]

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[bioc-issue-bot]

Hi @BioinfoMonzino

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: GARS
Type: Package
Date: 2017-09-25
Title: GARS: a clustering-based Genetic Algorithm for the identification
 of Robust Subsets of variables in high-dimensional and challenging
 datasets
Version: 0.99.0
Author: Mattia Chiesa <mattia.chiesa@hotmail.it>, 
    Luca Piacentini <luca.piacentini@cardiologicomonzino.it>
Maintainer: Mattia Chiesa <mattia.chiesa@hotmail.it>
Description: More about what it does (maybe more than one line)
    Use four spaces when indenting paragraphs within the Description.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
biocViews: Classification, FeatureExtraction
Imports: DaMiRseq, MLSeq, stats, methods
Suggests: BiocStyle, knitr, testthat
Depends: R (>= 3.4), ggplot2, cluster

[bioc-issue-bot]

A reviewer has been assigned to your package Learn What to Expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[mtmorgan]

Looks like the Description: field needs updating.

[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: "skipped, ERROR, 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

2a7f362 update DESCRIPTION file

[BioinfoMonzino]

We have modified and updated the Description file as suggested. We have also bumped the version from 0.99.0 to 0.99.1.

[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: "skipped, 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.

[BioinfoMonzino]

Dear reviewers, GARS is in ERROR status in OS X system. This is due to the dependency "DaMiRseq" that depends on FSelector and, in turn, on RWeka/RWekajars, which is in ERROR in the OS X system (https://cran.r-project.org/web/checks/check_results_RWeka.html). By the way, I have the same problem with "DaMiRseq" package, which is OK in the current version (all systems), OK in Windows and Unix (devel version) and ERROR in OS X (devel version). How could I handle this issue?

[lshep]

For now you can ignore the MAC ERROR, we will look into it on our end. It may be that the binaries are not yet available for MAC which is still an issue with a number of CRAN packages, once those binaries are available this will clear up. I will look if it there is something additional to this.

In the meantime, I will review your package in the next day or two and have an official review for you.

[lshep]

Thank you for your submission to Biocoductor. Please see the comments below:

Build Report

• [ ] Note for global variables see ?globalVariables

Organizational

• [ ] Add ^.*.Rproj$ and ^.Rproj.user$ as you did for the .Rbuildignore to a .gitignore as well.

man For your data object can you please explain in more detail how the objects were created.

vignette

• [ ] The class_vector as you have created it seems subjective - could you please create it off the cervical colnames (assuming why it is N/T 29/29)
• [ ] Would it be worth creating an S4 class for your output and providing accessor methods for the results? Formulating or reusing exisiting class structure is general prefered than a generic list. This would also allow you to create wrappers around the DaMiRseq functions, if you think they would be utilized often.
• [ ] Don't use a '.' in function names. This indicates method dispatch on S3 objects. please use either '_' or camelcase. I understand that this emulated DaMiRseq but it is not recommended and generally

R CODE In general the code looks good and well formatted.

• [ ] GARS.create.rnd.population/GARS.Crossover - when would a user use this function? Is this an internal function?
• [ ] GARS.Elitism/GARS.Mutation what are the point of these only discussed use of GARS.GA in vignette? - are these steps that can be run individually and GARS.GA is the wrapper around all steps? Would a user want to only run one step of the pipeline?
• [ ] GARS.FitFun should be able to take in a SummarizedExperiment as well?

Please address the above issues, when ready ensure that a new build report is created with a version bump and please comment back here with what has been updated or comments to address any concerns.

Cheers, Lori

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

50f3513 GARS version 0.99.2

[BioinfoMonzino]

Dear Lori, thanks for your suggestions, which have been really useful! We addressed most of your issues:

1. We created a S4 object to store the outputs of GARS: we named this S4 object “GarsSelectedFeatures”; then, we implemented four generic functions (MatrixFeatures, AllPop, LastPop, FitScore) to extract the information from the “GarsSelectedFeatures” class object. We also tried to document class and methods, following the roxygen2 specifications. However, we got these warnings, which we are not able to address:

<U+2714>  checking Rd cross-references
W  checking for missing documentation entries
   Undocumented S4 classes:
     'GarsSelectedFeatures'
   Undocumented S4 methods:
     generic 'AllPop' and siglist 'GarsSelectedFeatures'
     generic 'FitScore' and siglist 'GarsSelectedFeatures'
     generic 'LastPop' and siglist 'GarsSelectedFeatures'
     generic 'MatrixFeatures' and siglist 'GarsSelectedFeatures'
   All user-level objects in a package (including S4 classes and methods)
   should have documentation entries.
   See chapter 'Writing R documentation files' in the 'Writing R
   Extensions' manual.

<U+2714>  checking for code/documentation mismatches
W  checking Rd \usage sections
   Objects in \usage without \alias in documentation object 'AllPop methods':
     '\S4method{AllPop}{GarsSelectedFeatures}'
   Objects in \usage without \alias in documentation object 'FitScore methods':
     '\S4method{FitScore}{GarsSelectedFeatures}'
   Objects in \usage without \alias in documentation object 'LastPop methods':
     '\S4method{LastPop}{GarsSelectedFeatures}'
   Objects in \usage without \alias in documentation object 'MatrixFeatures methods':
     '\S4method{MatrixFeatures}{GarsSelectedFeatures}'
   Functions with \usage entries need to have the appropriate \alias
   entries, and all their arguments documented.
   The \usage entries must correspond to syntactically valid R code.
   See chapter 'Writing R documentation files' in the 'Writing R
   Extensions' manual.

Please, do you have any suggestions?

2. We added .gitignore file with ^.*.Rproj$ and ^.Rproj.user$
3. We renamed all the functions, replacing '.' with '_';
4. In the vignette, we used the cervical names to create the ‘class_vector’;
5. Concerning the functions embedded in GARS_GA, the user can exploit them to generate a custom GA: e.g. a user could decide to skip the Elitism step; we added a brief explanatory section in the vignette;
6. Now GARS_GA, GARS_FitFun and GARS_create_rnd_population are able to take a “SummaizedExperiment” object;
7. Concerning the global variables, actually we do not use global variables inside functions; so we did not address this note.

[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: "WARNINGS, skipped, 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.

[lshep]

Thank you for your updates a few minor comments below:

• [ ] I'm still pullilng down the GARS.Rproj when I clone - could you try adding that file explicitly to the .gitignore or just *.Rproj

Build Report

• [ ] You do use variables and functions that are not defined - these are globalVariables and global functions - variables should be remedied see globalVariables and functions should be properly imported in the NAMESPACE with importFrom

  * checking R code for possible problems ... [26s/24s] NOTE
  GARS_FitFun: no visible global function definition for assay
  GARS_GA: no visible global function definition for assay
  GARS_PlotFeaturesUsage: no visible binding for global variable
  Feature
  GARS_PlotFeaturesUsage: no visible binding for global variable Times
  GARS_PlotFitnessEvolution: no visible binding for global variable V1
  GARS_PlotFitnessEvolution: no visible binding for global variable
  fit_list
  GARS_create_rnd_population: no visible global function definition for
  assay
  Undefined global functions or variables:
  Feature Times V1 assay fit_list

• [ ] Are the suggested biocViews of Clustering and Regression also valid? If so please add to DESCRIPTION biocViews

• [ ] documentation warnings: I think The @name needs to be GarsSelectedFeatures-class and I think you might have to @exportClass GarsSelectedFeatures or @export GarsSelectedFeaturesfor it to register the class. Similar for the generics I think you would have to change the tag to @exportMethod MatrixFeatures.

man

• [ ] (optional) I suggest having a GARS package page summarizing and pointing to main functions

Cheers,

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

7aa8317 update version 0.99.3

[BioinfoMonzino]

Dear Lori, thanks for your suggestions! We addressed all your issues except the last one. In particular:

1. we added *.Rproj and GARS.proj to the .gitignore file;
2. we handled globar variables and functions; now, there isn't any NOTES;
3. we added Clustering to biocViews; Regression is not applicable to GARS.
4. we modified the documentation codes of the GarsSelectedFeaturesclass and its methods; the WARNING massages disappeared. Concerning the last point, we do not understand exactly what you mean for " GARS package page". Thanks again!

[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: "skipped, 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.

[lshep]

The last point about a GARS package page in documentation - Would be to create a man packaga for GARS or having an \alias{GARS} so that a users could type ?GARS and be directed to a man page describing the package and the main function or directly to the main function of the package.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

e4dbf35 updates version 0.99.4

[BioinfoMonzino]

Dear @lshep , we added the man package for GARS. You can check it, typing ?GARS Thanks.

[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: "skipped, 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.

[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: "skipped, 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.

[lshep]

One last minor comment: In the vignette: when you run the GARS_GA function - you show two plots in the vignette but only one is produced when running the function in linux - could it be worth saying how you would generate Figure 1: Fitness Evolution plot - Or changing the plotting output to depict both par(mfrow=c(2,1)) ?

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

77215b8 updates 0.99.5

[BioinfoMonzino]

Dear @lshep, following your suggestion we tried par(mfrow=c(2,1)) inside GARS_GA. However, it does not seem to have effect on plots generated by ggplot2. So, we decided to modify the vignette: in the first chunk, we launched GARS_GA with plot = “no”. Then, we added a paragraph and a new chunk, where we explained how to use the functions GARS_PlotFitnessEvolution() and GARS_PlotFeaturesUsage(). Could it be ok, now? Thanks again!

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

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