(inactive) DMEA

[BelindaBGarana]

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

• Repository: https://github.com/BelindaBGarana/DMEA

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[bioc-issue-bot]

Hi @BelindaBGarana

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: DMEA
Type: Package
Title: Drug Mechanism Enrichment Analysis
Version: 0.99.0
Authors@R: c(
    person(given = c("Belinda", "B."),
         family = "Garana", 
         role = c("aut", "cre"),
         email = "garana.belinda@gmail.com",
         comment = c(ORCID = "0000-0001-8906-5270")),
    person(given = c("James", "H."),
         family = "Joly", 
         role = "ctb",
         comment = c(ORCID = "0000-0003-3780-9412")))
Description: Though there are many algorithms for drug repurposing, most only evaluate individual drugs which can be prone to off-target effects. In contrast, our approach is to evaluate drug mechanisms-of-action by aggregating results across many drugs. With our tool Drug Mechanism Enrichment Analysis (DMEA), users can query any dataset of interest using either an input gene signature or drug rank list to identify enriched mechanisms-of-action for drug repurposing efforts.
License: CC0
URL: https://belindabgarana.github.io/DMEA, https://github.com/BelindaBGarana/DMEA
BugReports: https://github.com/BelindaBGarana/DMEA/issues
Encoding: UTF-8
biocViews:
    BiomedicalInformatics, GeneExpression, GeneSetEnrichment,
    GeneTarget, GraphAndNetwork, NetworkEnrichment, 
    Pharmacogenetics, Pharmacogenomics, Proteomics, 
    Regression, SystemsBiology, Transcriptomics
Imports:
    aplot, cowplot, dplyr, foreach, 
    ggrepel, gridExtra, ggplot2, 
    patchwork, qvalue, reshape2,
    stats, testthat, tidyselect, utils
Enhances:
    parallel, snow, doSNOW
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown
Collate:
    'as_gmt.R'
    'rank_corr.R'
    'WV.R'
    'drugSEA.R'
    'DMEA.R'

[bioc-issue-bot]

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IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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

[PeteHaitch]

Hi @BelindaBGarana,

Would you please push a version bump to git.bioconductor.org to trigger a new build. It would be good to get a clean build of the package before I begin my review.

Thanks, Pete

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 430f5d49248ce3a9be84a332141ccc8602121ede

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

[PeteHaitch]

Hi @BelindaBGarana,

Thank you for submitting DMEA to Bioconductor.

The package needs some work before it can be considered for a full review.

The most pressing issue is how parallelisation is implemented in DMEA because there is no way to control or disable parallelisation in DMEA::drugSEA():

• Internally, this function calls cores <- parallel::detectCores() and doSNOW::registerDoSNOW().
  • You code should not automatically use all cores (or all cores - 1). It must use a minimal number of cores (1 or 2) by default (https://contributions.bioconductor.org/r-code.html?q=paralle#parallel-recommendations). This is the cause of the build error on the Linux Single Package Builder (nebbiolo2) where your code tries to use 71 out of nebbiolo2's 72 logical CPUs and effectively crashes the system (see https://bioconductor.org/spb_reports/DMEA_buildreport_20230530085127.html#nebbiolo2_buildsrc_anchor).
  • More generally and importantly, Bioconductor strongly recommended parallelisation be implemented using BiocParallel (https://contributions.bioconductor.org/r-code.html?q=paralle#parallel-recommendations).

In summary, DMEA needs to use BiocParallel for parallelisation or you need to provide strong reasons for why you cannot do so. Regardless of the parallelisation implementation, it must allow the user to control how many cores on their system DMEA uses and must only use 1-2 cores by default.

I won't do a complete review until this is addressed, but some other things I noted in looking over the package that would come up in any subsequent review for inclusion in Biocondcutor are given below:

• DMEA::drugSEA() is a monolothic and very long function. I recommend splitting it up into component functions. In fact, there are already internal functions, but they don't need to (and probably shouldn't) be defined within the function body. Instead, make them stand-alone functions and don't export them (unless you the user to be able to call them directly). This will make it easier to read the code and review it.

• Don't use testthat within package code. It's intended and designed for use within unit tests. Instead, just use base R functionality (e.g., is.data.frame(x) or is(x, "data.frame") along with stopifnot() instead of testthat::expect_is(x, "data.frame")). Alternatively, you might consider the assertthat package (https://cran.r-project.org/web/packages/assertthat/index.html).

• parallel, snow, doSNOW should not be under Enhances in the DESCRIPTION. These packages should instead be listed under Suggests in the DESCRIPTION (see https://cran.r-project.org/doc/manuals/R-exts.html for where Enhances is appropriate, but it's not often used).

• The vignette needs improvement. It mostly just repeats a subset of the information that's already available in the package man pages (e.g., the information and example in ?drugSEA). A vignette should demonstrates how to accomplish non-trivial tasks embodying the core functionality of your package. In the current vignette, it's not clear what the user would do with the outputs or how to interpret them. A good vignette will demonstrate more than just how to run some functions from the package. For example, a good vignette will help the user understand when this package might be useful in their work and how to interpret the outputs. Think of a new user who might want/need to use your package and the information they would find helpful. I see you have a paper that describes the method - think of what information you could take from it to help a new user of your package.

• Other vignette comments

  • Please check the formatting of the vignette is as you want. For example, I can see you are trying to create a list of dot points (*) but these aren't being rendered properly (I think you need a newline before the start of the list, but you may need to check the markdown/Rmarkdown documentation).
  • The vignette links to https://raw.github.com/BelindaBGarana/DMEA/shiny-app/Inputs/MOA_gmt_file_n6_no_special_chars.gmt. If this file is important and relevant to DMEA then it should be included in the package itself. Please see https://contributions.bioconductor.org/data.html for how to include package data.

For now I am going to tag this submission as 'pending pre-review changes'. We can re-open the issue as needed, please just let me know if you like to proceed and then address the requested changes.

Thanks, Pete

[lshep]

@BelindaBGarana is there any updates concerning @PeteHaitch comments? We like to see responses in a 2-3 week time frame to move packages through the review process and make available in Bioconductor as soon as possible.

[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.

Thank you for your interest in Bioconductor.