ROCpAI

[juanpegarcia]

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

• Repository: https://github.com/juanpegarcia/ROCpAI

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[bioc-issue-bot]

Hi @juanpegarcia

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: ROCpAI
Type: Package
Title: ROC Partial Area Indexes for evaluating classifiers
Version:  0.99.0
Author: c(
    person("Manuel", "Franco", email = "mfranco@um.es", role = "aut"),
    person("Juana-María", "Vivo", email = "jmvivomo@um.es", role = "aut"),
    person("Juan-Pedro", "García", email = "juanpedro.garcia4@um.es", role = "aut")
    )
BugReports: https://github.com/juanpegarcia/ROCpAI/tree/master/issues
Maintainer: Juan Pedro García Ortiz <juanpedro.garcia4@um.es>
Description: The package analyzes the Curve ROC, identificates it among different types of Curve ROC and calculates the area under de curve through the method that is most accuracy. More about what it does (maybe more than one line)
License: GPL-3
Encoding: UTF-8
LazyData: FALSE
Depends: boot, SummarizedExperiment, bibtex, fission
import: boot, SummarizedExperiment, bibtex, fission
biocViews: Software, StatisticalMethod, Classification
RoxygenNote: 7.0.0
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown

[mtmorgan]

This looks like a very general purpose package that might be better suited to CRAN?

[mtmorgan]

@juanpegarcia will you submit this to CRAN instead? If so please close this issue.

[juanpegarcia]

Sorry for the late answer. But we think that is better suited for Bioconductor. We development this package after seeing that, when working with data gene expression arrays, there were cases we couldn't analysed. These cases are frequent when working with biologic data. So this package is interesting for investigators and bioinformaticians. Moreover, high-throughput data generation techniques have led to the flood of gene expression arrays, protein mass spectrometry and so on, which have become an important challenge for lifescience researchers. This package allows one to simultaneously evaluate and compare thousands of potential biomarkers. This is what that plays an important role in biomarker discovery, ranking classifiers to identifying informative genes or proteins based on differential expression. It's due to this that we development the package with Bioconductor's type data like "SummarizedExperiment". It maybe could be used in other fields but we are sure that it will be used in life science investigations. Finally I wanted to add that I am a bioinformatics and this is part of my master thesis in bioinformatics.

[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.

[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.

[mtmorgan]

NOTE: comments are made about specific lines of code, but code should be updated throughout the pacakge.

DESCRIPTION

• Please avoid abbreviatinos in the Title.
• Please update the Description: field to avoid boiler plate and to clearly indicate how your package provides functionality different from other packages.
• bibtex is not a likely package for 'Depends or even Imports: (NB: the field names is Imports:, not "import"); if it is used in your vignette then it belongs in the Suggests: field.
• Use Authors@R: with the format you provide, instead of Authors:, add role = c("cre", "aut")) to your name, and remove the Maintainer: field.

vignettes

• The directory name is vignettes; it is important to match on for platforms where case is important.
• Remove .Rhistory from your git checkin.
• Remove the build products, e.g., my-Vignette.html, from the git checkin. This is produced from the .Rmd file when the package is built (R CMD build ROCpAI).
• consider carefully wehter ieee.csl is required; unneccesarily complicated vignette formatting often leads to problems for long-term maintenance.
• I do not understand why the vignette has many functions define but hidden from the user. At least some of these are 'internal' functions and it should not be necessary to define them here.
• In this code

  strain <- fission@colData@listData$strain

  one should ALWAYS use the 'accessors' defined on the object, thus colData(fission)$strain. But I don't really understand the purpose of constructing genes here; the idea of a SummarizedExperiment is to coordinate manipulation of complicated data, but this code undoes this benefit. For instance one might

  points_curve(colData(fission)$strain, assay(fission)["SPNCRNA.1080",])

• Again the defintion of complicated functions in the vignette, points_curve() and McpAUC() seems not helpful -- if these functions are already in the package, they do not need to be re-defined here. If they are not yet in the package, then perhaps they should be added to the package?
• please adopt a standard function naming convention; the Bioconductor recommendation is lowerCamelCase() so pointsCurve() and mcpAUC() might be possible names.
• use citation("ROCpAI") for standard package citation format.

R

• make sure that the @examples code lines do not exceed 80 characters wide, otherwise the format poorly on some help displays.
• when documenting parameters, adopt a convention where the type of the argument is given clearly and unambiguously, e.g., MCpAUCboot.R

  #' @param seed Seed

  might become

  #' @param seed integer(1) random number seed.

  HOWEVER, there is no reason for your function to manipulate the random number seed, and this is strongly discouraged. If the user wishes for reproducibility, they may simply set.seed(123) in their own script before calling your function.

• please consider using the formatR package or similar to arrive at a more standard representation of your code -- you adopt conventions that make the code difficult to read.
• as a general rule, start each user-facing function with checks on the arguments; provide default values if appropriate, e.g., for MCpAUCboot

  stopifnot(
    is.data.frame(dataset) || is(dataset, "SummarizedExperiment"),
    is.numeric(low.value), length(low.value) == 1, 
    low.value > 0 && low.value < 1,
    ...
  )

  by asserting these values first, the user is informed immediately of incorrect arguments, your own code can then focus on implementing the algorithm rather than repeatedly checking for validity, and your code is more robust.

• It is usually better to write simple sequential code rather than 'nesting' for compactness, thus

  McpNA <-assay(McpAUC(dataset, low.value=low.value, up.value = up.value ))$St_pAUC

  might be better written (more readable, easier to debug) as

  value <- McpAUC(dataset, low.value=low.value, up.value = up.value)
  McpNA <-assay(value)$St_pAUC

• avoid use of 1:XXX, e.g., for (i in 1:dim(result_boot$t)[2]) which results in surprises when XXX is 0. Use seq_len() or seq_along() instead, e.g., for (i in seq_len(ncol(result_boot$t)))
• do not use if (class(dataset)=="RangedSummarizedExperiment") { but instead is(dataset, "RangedSummarizedExperiment"). Using class(X) == fails when class() returns a vector of length greater than 1. Here the requirement is not RangedSummarizedExperiment but simply SummarizedExperiment.

[mtmorgan]

Please post a comment here indicating when you hope to have a response available.

[juanpegarcia]

Thanks for waiting. I think that the February 23th everything should be fixed. However I'll try to do it sooner

[juanpegarcia]

The package is ready

[lshep]

Please make sure your webhook is initialized and do a version bump in your package DESCRIPTION to receive a new build report that reflects your changes.

[bioc-issue-bot]

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

29f7acd Update DESCRIPTION

[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.

[bioc-issue-bot]

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

043109a Update DESCRIPTION

[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:

26892a1 Update DESCRIPTION

[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, 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]

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

72cb559 Update DESCRIPTION

[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.

[mtmorgan]

Please remove the files .RData and .Rpoj.user from your git repository. Please rename the folder Vignettes to 'vignettes' (lower-case). Please remove Vignettes/vignettes.html.

Please briefly summarize the changes you made to your package in response to the earlier comments.

[bioc-issue-bot]

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

7c0d58f 0.99.5 Changes in the description files to make e...

[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.

[juanpegarcia]

@mtmorgan I have done the solicited changes

[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]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/juanpegarcia.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("ROCpAI"). The package 'landing page' will be created at

https://bioconductor.org/packages/ROCpAI

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.