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ExpHunterSuite #1835

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jimrperkins opened this issue Dec 26, 2020 · 35 comments
Closed
9 tasks done

ExpHunterSuite #1835

jimrperkins opened this issue Dec 26, 2020 · 35 comments
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@jimrperkins
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@jimrperkins jimrperkins commented Dec 26, 2020

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

Confirm the following by editing each check box to '[x]'

  • I understand that by submitting my package to Bioconductor,
    the package source and all review commentary are visible to the
    general public.

  • I have read the Bioconductor Package Submission
    instructions. My package is consistent with the Bioconductor
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  • I understand that a minimum requirement for package acceptance
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    Passing these checks does not result in automatic acceptance. The
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  • My package addresses statistical or bioinformatic issues related
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@bioc-issue-bot bioc-issue-bot commented Dec 26, 2020

Hi @jimrperkins

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: ExpHunterSuite
Title: Package For The Comprehensive Analysis Of Transcriptomic Data
Version: 0.99.0
Authors@R: 
    c(person(given = "James",
 family = "Perkins",
 role = c("aut", "cre"),
 email = "jimrperkins@gmail.com",
 comment = c(ORCID = "0000-0003-4108-096X")),
    person(given = "Pedro",
 family = "Seoane Zonjic",
 role = c("aut"),
 email = "seoanezonjic@uma.es",
 comment = c(ORCID = "0000-0002-3020-1415")),
    person(given = "Fernando",
 family = "Moreno Jabato",
 role = c("aut"),
 email = "fmjabato@gmail.com",
 comment = c(ORCID = "0000-0001-7498-1962")),     
    person(given = "José",
 family = "Córdoba Caballero",
 role = c("aut"),
 email = "josecordoba1995@gmail.com",
 comment = c(ORCID = "0000-0002-1821-5742")),      
    person(given = "Elena",
 family = "Rojano Rivera",
 role = c("aut"),
 email = "elenarojano@outlook.com",
 comment = c(ORCID = "0000-0002-2678-710X")),
    person(given = "Rocio",
 family = "Bautista Moreno",
 role = c("aut"),
 email = "rociobm@uma.es",
 comment = c(ORCID = "0000-0003-1685-8119")),
    person(given = "M. Gonzalo",
 family = "Claros",
 role = c("aut"),
 email = "claros@uma.es",
 comment = c(ORCID = "0000-0002-0112-3550")),          
    person(given = "Isabel",
 family = "Gonzalez Gayte",
 role = c("aut"),
 email = "isabel.ggayte@gmail.com"),         
    person(given = "Juan Antonio",
 family = "García Ranea",
 role = c("aut"),
 email = "ranea@uma.es",
 comment = c(ORCID = "0000-0003-0327-1837"))
    )
Description: The ExpHunterSuite implements a comprehensive protocol for the analysis of transcriptional data using established *R* packages and combining their results. It covers all key steps in DEG detection, CEG detection and functional analysis for RNA-seq data. It has been implemented as an R package containing functions that can be run interactively. In addition, it also contains scripts that wrap the functions and can be run directly from the command line.
Depends: R (>= 4.0.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
biocViews: GeneExpressionWorkflow
Suggests: optparse
VignetteBuilder: knitr
Imports: 
    ReactomePA,
    limma,
    edgeR,
    NOISeq,
    biomaRt,
    topGO,
    clusterProfiler,
    diffcoexp,
    DT,
    ggplot2,
    stringr,
    reshape2,
    WGCNA,
    dplyr,
    AnnotationDbi,
    BiocGenerics,
    enrichplot,
    rmarkdown,
    stats,
    Biobase,
    DESeq2,
    ROCR,
    data.table,
    knitr,
    magrittr,
    SummarizedExperiment,
    miRBaseConverter,
    pbapply,
    grDevices,
    graphics,
    utils,
    BiocParallel,
    MKinfer

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@bioc-issue-bot bioc-issue-bot added OK and removed WARNINGS labels Feb 2, 2021
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@nturaga nturaga commented Feb 12, 2021

ExpHunterSuite review

General

  • Please fix NOTEs related to coding practice in your
    package. Especially the ones for using vapply and seq_len(). I'm
    particualr about these practices.

  • It's a good idea to keep your build report as clean as possible.

  • I will do a second review of the package once you fix the issues highlighted below. Some issues occur in more than one place. Please fix all occurrences.

DESCRIPTION

ok

NAMESPACE

ok

NEWS

  • It's always good to add a NEWS file, it'll be included in the
    release documentation of every Bioconductor release.

R

  • IMP Indent your code according to coding style,
    http://bioconductor.org/developers/how-to/coding-style/. This is
    very important for code readability. 80 chars per line.

  • Please fix the 1:len issue for your loops.

  • ‘Pre-allocate and fill’ if iterations are
    necessary. http://bioconductor.org/developers/how-to/efficient-code/

    You seem to be making a lot of empty lists and vectors in
    perform_expression_analysis() and filling them. This is bad coding
    practice. Especially when you know the size of your lists / vectors.

  • Instead of nesting multiple "if" statements, use logical operators
    like & between conditions. This is done in check_results().

  • Follow good documentation rules, follow the devtools documentation
    principles. Remove commented out code where it's not needed.

    eg:translate_id().

  • In functions like scaled_data_matrix you can easily avoid the
    apply function. Vectorize your code when you
    can. http://bioconductor.org/developers/how-to/efficient-code/

man

  • Some functions have very limited man pages and need to be more
    detailed.

  • No runnable examples in man pages.

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@bioc-issue-bot bioc-issue-bot commented Mar 9, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 539d24d075b5834a9e242b3ab02ec37138bbbed6

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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
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@bioc-issue-bot bioc-issue-bot added ERROR and removed OK labels Mar 9, 2021
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Received a valid push on git.bioconductor.org; starting a build for commit id: e73a8be9f980c64dfe0ff7ed42785499c2828b9e

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@bioc-issue-bot bioc-issue-bot commented Mar 9, 2021

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

@bioc-issue-bot bioc-issue-bot added OK and removed ERROR labels Mar 9, 2021
@jimrperkins
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@jimrperkins jimrperkins commented Mar 9, 2021

ExpHunterSuite review

General

  • Please fix NOTEs related to coding practice in your
    package. Especially the ones for using vapply and seq_len(). I'm
    particualr about these practices.

All notes fixed with the exception of i) the use of <<- which we used in some situations in which the side effect of the function was more important than the return value, ii) Some functions are > 50 lines - this is unavoidable given the way the program is structured such that it can be run from the command line. iii) Unit tests - most of the functions are highly complex and it is not trivial to design unit tests to cover the multiple possible ways of running the package. In any case, the package is largely concerned with calling existing Bioc packages/functions which should themselves have their own testing implemented. iv) Multiples of 4 spaces for line indents - this is not always met in order to align functions on different lines in a clearer manner. i.e. in line with parentheses.

  • It's a good idea to keep your build report as clean as possible.

This is now MUCH cleaner. There are still a number of notes related to the code in the Rmd files - this appears to be unavoidable, as this is called using render from a different file - as such it appears as though some variables are not declared in the Rmd files (i.e. in tests for running chunks).

  • I will do a second review of the package once you fix the issues highlighted below. Some issues occur in more than one place. Please fix all occurrences.

DESCRIPTION

ok

NAMESPACE

ok

NEWS

  • It's always good to add a NEWS file, it'll be included in the
    release documentation of every Bioconductor release.

Added

R

This has been done, with the exception of that in some cases non-multiples of 4 spaces have been used to make things line up properly when functions are broken over several lines.

  • Please fix the 1:len issue for your loops.

Fixed

  • ‘Pre-allocate and fill’ if iterations are
    necessary. http://bioconductor.org/developers/how-to/efficient-code/
    You seem to be making a lot of empty lists and vectors in
    perform_expression_analysis() and filling them. This is bad coding
    practice. Especially when you know the size of your lists / vectors.

In this function we concatenate the results of other functions into vectors/lists because, later on, these results will be used to generate plots/reports by applying the same operations to each list member.
We had two possible options here:

  1. Create a list with all possible containers and fill which will be executed and stay empty which will not be executed. After this, check one by one if each method had been executed and apply operations over those that are not empty only.

  2. Create an empty list and use it as a linked list where each execution is performed and, after, apply operations over the full list (because list only contains executed results).We decided to code the second strategy in order to avoid empty containers. For this second strategy, we do know the maximum potential size (which corresponds to the maximum available modules in our code) but, if we create those lists with fixed size, we will be implementing the strategy 1 with potential empty spaces.,This will also break our ability to include new modules easily.

  • Instead of nesting multiple "if" statements, use logical operators
    like & between conditions. This is done in check_results().

We have rewritten this function and reduced some nested "ifs", but there are some others which cannot be simplified using logical operators. For example, we have the following code:

if(is.data.frame(df)){  
  if(nrow(df) <= 0){    
    return(FALSE)
  }
}

In this case, we must perform it independently because it now only works for matrix and dat.aframes but df can be a list, in case of execute nrow() it will return a logical(0) which is not treated as a TRUE/FALSE element.

Same problem occurs at:

if("pvalueCutoff" %in% slotNames(df)){    
  if(nrow(df@result[which(df@result$p.adjust <= df@pvalueCutoff),]) < 1){      
    return(FALSE)    
  }  
}else if(length(get_categories(df)) < 1){    
  return(FALSE)  
}

In this case we are checking and external object which can have two formats, one containing pvalue threshold used into slot pvalueCutoff or storing it into a parental slot called params. For that reason, we must first check the slots architecture in order to correctly access the slot value.

  • Follow good documentation rules, follow the devtools documentation
    principles. Remove commented out code where it's not needed.
    eg:translate_id().

We have followed the devtools documentation as much as possible and commented out all unnecessary code 

We have changed this function so it does not use apply - the functions are performed on the whole matrix instead using rowSums style functions.

man

  • Some functions have very limited man pages and need to be more
    detailed.

We have improved documentation.

  • No runnable examples in man pages.

All man pages should now have runnable examples.

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@nturaga nturaga commented Mar 16, 2021

Hi @jimrperkins i'm happy with the changes you made.

Although looking at the build report, it seems like there are issues with the variables which cannot be found in scope. Please fix these although they might be minor. I'm happy to accept your package after.

@jimrperkins
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@jimrperkins jimrperkins commented Mar 16, 2021

Hi @nturaga - great, thank you for your dedication and comments which have improved the package greatly.

The issues re: the variables out of scope in the build report - I assume you mean in the bioccheck report, not CMD build? Things like Error in eval(x, envir = envir) : object 'executed' not found ?

These are due to the Rmd templates in the inst/templates folder, not code within the R folder - these Rmd templates are called via the rmarkdown::render function, which passes the variables. As such, the variables appear to not have been initialised, but in reality this doesn't cause an issue when running the package.

I can't think of any way of solving this problem, short of deleting the templates which obviously I don't want to do as the output reports are an integral part of the package functionality.

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@bioc-issue-bot bioc-issue-bot commented Mar 18, 2021

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

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@vjcitn vjcitn commented Mar 19, 2021

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/jimrperkins.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("ExpHunterSuite"). The package 'landing page' will be created at

https://bioconductor.org/packages/ExpHunterSuite

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.

@vjcitn vjcitn closed this as completed Mar 19, 2021
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