microbiomeDataSets #1853

FelixErnst · 2021-01-22T09:18:44Z

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

Repository: https://github.com/microbiome/microbiomeDataSets

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bioc-issue-bot · 2021-01-22T09:18:45Z

Hi @FelixErnst

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: microbiomeDataSets
Title: Experiment Hub based microbiome datasets
Version: 0.99.0
Authors@R: 
    c(person(given = "Felix G.M.", family = "Ernst", role = c("aut", "cre"),
   email = "felix.gm.ernst@outlook.com",
   comment = c(ORCID = "0000-0001-5064-0928")),
      person("Leo", "Lahti", role = c("aut"),
   comment = c(ORCID = "0000-0001-5537-637X")),
      person(given = "Sudarshan", "Shetty", role = c("aut"),
   email = "sudarshanshetty9@gmail.com",
   comment = c(ORCID = "0000-0001-7280-9915"))
	     )
Description:
    microbiomeDataSets is a collection of microbiome datasets loaded from 
    Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference
    for workflows and vignettes published adjacent to the microbiome analysis 
    tools on Bioconductor. Additional datasets can be added overtime and 
    additions from authors are welcome.
License: CC0
Encoding: UTF-8
LazyData: false
biocViews:
    ExperimentHub,
    ExperimentData
Depends:
    R (>= 4.0),
    SummarizedExperiment,
    TreeSummarizedExperiment,
    MultiAssayExperiment
Imports:
    methods,
    utils,
    BiocGenerics,
    ExperimentHub,
    Biostrings,
    ape
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle,
    testthat
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
VignetteBuilder: knitr

FelixErnst · 2021-01-22T09:19:32Z

Thanks @lshep for the help!

FelixErnst · 2021-01-22T09:27:32Z

Tagging @antagomir @microsud

bioc-issue-bot · 2021-01-23T17:19:26Z

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bioc-issue-bot · 2021-01-23T17:37:42Z

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.
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Please see the build report for more details. This link will be active
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Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2021-01-23T20:02:40Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 9b8501c1454e35ba2fb86a5a6878867ad5c4a1e2

bioc-issue-bot · 2021-01-23T20:11:30Z

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

bioc-issue-bot · 2021-01-23T20:17:34Z

Received a valid push on git.bioconductor.org; starting a build for commit id: d718683efd48af1e6df4bd71680f2fcbbd5ea1c6

bioc-issue-bot · 2021-01-23T20:39:45Z

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

lshep · 2021-01-26T13:25:51Z

A few very minor comments:

DESCRIPTION

(optional) We recommend removing entry Date: 2021-01-23 as it is often not updated
We recommend removing LazyData: false. We have rarely found it useful and can actually slow installation

NEWS

Please use a valid date

Cheers,

bioc-issue-bot · 2021-01-26T13:53:40Z

Received a valid push on git.bioconductor.org; starting a build for commit id: cf0f4450012a0d460a58ce79e7695cfd56ef97f0

bioc-issue-bot · 2021-01-26T14:19:16Z

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

bioc-issue-bot · 2021-01-26T15:50:40Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 9238c8253f05652201292c78d55a6de4455fcb77

bioc-issue-bot · 2021-01-26T16:09:32Z

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

bioc-issue-bot · 2021-01-28T09:16:15Z

Received a valid push on git.bioconductor.org; starting a build for commit id: dc1f324d7706c32c31c590c2d785f25989b07d96

bioc-issue-bot · 2021-01-28T09:44:43Z

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

bioc-issue-bot · 2021-01-29T13:31:37Z

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

Thank you for contributing to Bioconductor!

FelixErnst · 2021-01-29T14:55:29Z

Thanks!

mtmorgan · 2021-02-03T20:45:38Z

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

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

https://bioconductor.org/packages/microbiomeDataSets

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.

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Jan 22, 2021

bioc-issue-bot added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed 1. awaiting moderation submitted and waiting clearance to access resources labels Jan 23, 2021

bioc-issue-bot assigned mtmorgan Jan 23, 2021

mtmorgan assigned lshep and unassigned mtmorgan Jan 23, 2021

bioc-issue-bot added the ERROR label Jan 23, 2021

bioc-issue-bot added WARNINGS and removed ERROR labels Jan 23, 2021

bioc-issue-bot added OK and removed WARNINGS labels Jan 23, 2021

bioc-issue-bot added WARNINGS and removed OK labels Jan 26, 2021

bioc-issue-bot added OK and removed WARNINGS labels Jan 26, 2021

FelixErnst mentioned this issue Jan 26, 2021

additional datasets + submission? microbiome/microbiomeDataSets#3

Closed

lshep added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Jan 29, 2021

mtmorgan closed this as completed Feb 3, 2021

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microbiomeDataSets #1853

microbiomeDataSets #1853

FelixErnst commented Jan 22, 2021 •

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microbiomeDataSets #1853

microbiomeDataSets #1853

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