Submitting MMUPHin to Bioconductor

[syma-research]

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

• Repository: https://github.com/biobakery/MMUPHin

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

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

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @sma-hsph

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: MMUPHin
Type: Package
Title: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in 
    Microbiome Studies
Version: 0.99.0
Author: Siyuan Ma
Maintainer: Siyuan MA <siyuanma@g.harvard.edu>
Description: MMUPHin is an R package for meta-analysis tasks of microbiome 
    cohorts. It has function interfaces for:
    a) covariate-controlled batch- and cohort effect adjustment, 
    b) meta-analysis differential abundance testing, 
    c) meta-analysis unsupervised discrete structure (clustering) discovery, and 
    d) meta-analysis unsupervised continuous structure discovery.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Depends: R (>= 3.6)
Imports:
    Maaslin2,
    metafor,
    fpc,
    igraph,
    ggplot2,
    dplyr,
    tidyr,
    cowplot,
    utils,
    stats,
    grDevices
Suggests: 
    testthat,
    BiocStyle, 
    knitr, 
    rmarkdown,
    magrittr,
    vegan,
    phyloseq,
    curatedMetagenomicData,
    genefilter
biocViews: Metagenomics, Microbiome, BatchEffect

Add SSH keys to your GitHub account. SSH keys will are used to control access to accepted Bioconductor packages. See these instructions to add SSH keys to your GitHub account.

[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: "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:

c6dcd8f fix Rd references

[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.

[dvantwisk]

Here is a review of your package. It looks expertly written and I only have one issue that needs to be addressed. Please make the following change by October 23rd to have this package accepted and included in the Bioconductor 3.10 release.

R/helpers_lm_meta.R

• [ ] [REQUIRED] L107, 233: We generally don't want to see output directories write to the user's current directory as it tends to clutter it up without the user even knowing it. We ask that you change the default value of output to tempdir().

[bioc-issue-bot]

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

20c5fe0 change default output to tempdir()

[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". 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:

ab2805f change Rd accordingly

[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.

[syma-research]

Hi @dvantwisk , thanks for the quick review and the suggestion! I have changed the default output dir and the automated build did not have any errors or warnings. Please let me know if you need anything else from me to proceed with our package submission.

Thanks! Siyuan

[dvantwisk]

The changes look good! I'm going to accept the package now.

[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/sma-hsph.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("MMUPHin"). The package 'landing page' will be created at

https://bioconductor.org/packages/MMUPHin

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.