ADAPT (Analysis of Microbiome Differential Abundance by Pooling Tobit Models)

[mkbwang]

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• Repository: https://github.com/mkbwang/ADAPT

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[bioc-issue-bot]

Hi @mkbwang

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: ADAPT
Title: Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Version: 0.99.0
Authors@R: 
    c(person(given="Mukai", family="Wang", email="[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-1413-1904")),
      person(given="Simon", family="Fontaine", email="[email protected]", role = "ctb"),
      person(given="Hui", family="Jiang", email="[email protected]", role="ctb"),
      person(given="Gen", family="Li", email="[email protected]", role=c("aut", "ctb")))
Description: ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format.
  It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios.
  The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to 
  find the differentially abundant ones.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Imports:
    Rcpp (>= 1.0.8),
    RcppArmadillo (>= 0.10.8),
    RcppParallel (>= 5.1.5),
    phyloseq (>= 1.39.0),
    methods,
    stats,
    ggplot2 (>= 3.4.1),
    ggrepel (>= 0.9.1)
Suggests: 
    rmarkdown (>= 2.11),
    knitr (>= 1.37),
    testthat (>= 3.0.0)
Config/testthat/edition: 3
LinkingTo:
    Rcpp,
    RcppArmadillo,
    RcppParallel
biocViews: 
    DifferentialExpression, 
    Microbiome, 
    Normalization, 
    Sequencing, 
    Metagenomics,
    Software,
    MultipleComparison
Depends: 
    R (>= 4.1.0)
LazyData: false
VignetteBuilder: knitr

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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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 the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): ADAPT_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/ADAPT to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[ococrook]

Hi there,

This looks great! I think there a only a couple of way to improve the code:

• [] The package versions aren't aligned across Description file and NEWS
• [] Add the various bioconductor install instruction to the vignette and readme.
• [] You check for phyloseq objects well but not other parameters - sometimes you get cryptic errors if you doing something wrong

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5eb19743d79fa91735fad41266b3a636fbf9d7e5

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): ADAPT_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/ADAPT to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[mkbwang]

@ococrook Thank you for your encouraging comments!

1. I have updated the version number of both the DESCRIPTION and the NEWS to be 0.99.1 in this commit.
2. I have added Bioconductor installation instructions to both the vignette and readme file in the same commit
3. I have added value check for input arguments censor, prev.filter, depth.filter and alpha in the same commit
4. My collaborators and I noticed some other technical loopholes in the program and improved the package in another earlier commit.

I notice that the bioconductor installation command BiocManager::install("ADAPT", version="devel") does not work as indicated in the message package ‘ADAPT’ is not available for Bioconductor version '3.20'. Is it normal?

Thanks again and look forward for your followup!

[ococrook]

This is all good - the package wont be available on devel until we add it so at the moment that command won't work. Usually, you would set the code chunk to 'eval = FALSE' to get around this.

In any casing moving to accept the package - thank you1

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[mkbwang]

Thank you for your reviewing efforts! I am closing this issue unless there are anything else needed from my side.

[lshep]

Please do not close the issue until we have ingested it into the Bioconductor system

[bioc-issue-bot]

Dear @mkbwang ,

We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[lshep]

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/mkbwang.keys is not empty), then no further steps are required. Otherwise, do the following:

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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("ADAPT"). The package 'landing page' will be created at

https://bioconductor.org/packages/ADAPT

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.