MicrobiomeBenchmarkData

[sdgamboa]

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

• Repository: https://github.com/waldronlab/MicrobiomeBenchmarkData

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[bioc-issue-bot]

Hi @sdgamboa

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: MicrobiomeBenchmarkData
Title: Datasets for benchmarking in microbiome research
Version: 0.99.0
Description: The MicrobiomeBenchmarkData package provides functionality to 
    access microbiome datasets suitable for benchmarking. These datasets
    have some biological truth, which allows to have expected results for
    comparison. The datasets come from various published sources and
    are provided as TreeSummarizedExperiment objects. Currently, 
    only datasets suitable for benchmarking differential abundance
    methods are available.
Authors@R: 
    c(
        person(
  given = "Samuel", family = "Gamboa", 
  role = c("aut", "cre"),
  email = "[email protected]",
  comment = c(ORCID = "0000-0002-6863-7943")
        ),
        person(
  given = "Levi", family = "Waldron",
  role = c("aut")
        ),
        person("Marcel", "Ramos", role = "ctb")
    )
License: Artistic-2.0
LazyData: true 
Depends: 
    R (>= 4.2),
    SummarizedExperiment,
    TreeSummarizedExperiment
Imports:
    BiocFileCache,
    tools,
    S4Vectors,
    ape,
    utils
Suggests: 
    rmarkdown,
    knitr,
    BiocStyle,
    testthat (>= 3.0.0),
    mia,
    ggplot2,
    tidyr,
    dplyr,
    magrittr,
    tibble,
    purrr
biocViews:
    ExperimentData,
    MicrobiomeData,
    ReproducibleResearch
BugReports: https://github.com/waldronlab/MicrobiomeBenchmarkData/issues
URL: https://github.com/waldronlab/MicrobiomeBenchmarkData,
    http://waldronlab.io/MicrobiomeBenchmarkData/
BiocType: ExperimentData
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
VignetteBuilder: knitr
Config/testthat/edition: 3

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

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.

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 [email protected]:packages/MicrobiomeBenchmarkData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Kayla-Morrell]

@sdgamboa - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

• [ ] REQUIRED: For packages that include data, we recommend not including LazyData: TRUE. In our experience it only slows down the loading of packages with large data. If necessary, please provide reasoning.
• [ ] SUGGESTION: Consider adding automatically suggested biocViews: SequencingData.

Data

• [ ] REQUIRED: To accompany the 'inst/extdata/' directory there needs to be an 'inst/script/' directory that contains the documentation. The script present in 'inst/script/' must clearly document how the data was generated and contain source information. It should include source URLS and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data in 'inst/extdata/'.
• [ ] SUGGESTION: The 'data-raw/' directory seems like it might do better in the 'inst/script/' directory. If not please explain what these scripts are used for since we normally don't allow this type of directory in our packages.

R code

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 6 lines that are > 80 characters long.
• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 6 lines that are not.

Best, Kayla

[sdgamboa]

@Kayla-Morrell, thank you! I've made the requested updates to the package. Please see below:

Updates:

• LazyData was set to false in the DESCRIPTION file. This required the addition of a helper function

• Added sequencingData to BiocViews in the DESCRIPTION file.

• Added inst/scripts for inst/extdata.

• data-raw directory has been removed.

• Lines are all below 80 characters long.

• All indents are multiples of four now.

[Kayla-Morrell]

@sdgamboa - Please push a version bump to the git version of the package to trigger a new build report. See here on how this can be done.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: df9ba8daaf7735976ea7cd5ee33de1f754efd317

[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. 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 [email protected]:packages/MicrobiomeBenchmarkData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Kayla-Morrell]

@sdgamboa - Thank you for making those changes. I've looked them over and everything looks good. I am more than happy to accept the package.

Best, Kayla

[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.

[sdgamboa]

@Kayla-Morrell, thank you!

[lshep]

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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

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

https://bioconductor.org/packages/MicrobiomeBenchmarkData

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.