Hub package submission: EPICv2manifest

[timpeters82]

Hi BioC,

Here is a AnnotationHub submission for the Illumina Infinium MethylationEPIC v2.0 kit probe manifest, containing the complete Illumina manifest plus extra columns describing:

• Recommendations, based on real data, for dealing with replicated probes mapping to the same CpG locus
• Flagging of in silico-predicted cross-hybridising probes, and where there is evidence from real data, the positions of their more likely off-targets
• Degree of concordance with matched WGBS samples
• Probe histories from previous array versions

I've been in contact with Lori regarding the deposit of the data.frame in Data Lake; am happy to do so once I receive the token.

Best, Tim

• Repository: https://github.com/timpeters82/EPICv2manifest

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[bioc-issue-bot]

Hi @timpeters82

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: EPICv2manifest
Title: Illumina Infinium MethylationEPIC v2.0 extended manifest from Peters et al. 2024
Version: 0.99.0
Date: 2024-03-02
Authors@R: 
    c(person("Tim", "Peters", , "t.peters@garvan.org.au", role = c("aut", "cre")),
      person("Ruth", "Pidsley", role="ctb"))
Maintainer: Tim Peters <t.peters@garvan.org.au>
Description:  A data.frame containing an extended probe manifest for the Illumina Infinium Methylation v2.0 Kit. Contains the complete manifest from the Illumina-provided EPIC-8v2-0_EA.csv, plus additional probewise information described in Peters et al. (2024).
License: Artistic-2.0
BugReports: https://support.bioconductor.org/t/EPICv2manifest
Depends: R (>= 4.3.0)
Imports: 
    AnnotationHub
Suggests:
    AnnotationHubData, 
    knitr
biocViews: AnnotationData, AnnotationHub, probe, IlluminaChip, Homo_sapiens
Encoding: UTF-8
VignetteBuilder: knitr

[timpeters82]

Cheers for the token. EPICv2manifest.Rda has been uploaded via AzureStor.

Best, Tim

[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.

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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.

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. Or it may mean that there is a problem with the build system itself.

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): EPICv2manifest_0.99.0.tar.gz macOS 12.7.1 Monterey: EPICv2manifest_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 git@git.bioconductor.org:packages/EPICv2manifest 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.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5bfa5aefe6da13418ff698485f337b10d7d8289a

[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.

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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EPICv2manifest_0.99.1.tar.gz macOS 12.7.1 Monterey: EPICv2manifest_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 git@git.bioconductor.org:packages/EPICv2manifest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1ffa276d23452dd0461379c7d23fe85844911a26

[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): EPICv2manifest_0.99.2.tar.gz macOS 12.7.1 Monterey: EPICv2manifest_0.99.2.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 git@git.bioconductor.org:packages/EPICv2manifest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Now that the data is in the AnnotationHub, you should have a sectionto show the AnnotationHub commands for finding and retrieving the data in the vignette.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d50f4451b246be20a218fcf3d3238707689c9999

[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: macOS 12.7.1 Monterey: EPICv2manifest_0.99.3.tar.gz Linux (Ubuntu 22.04.3 LTS): EPICv2manifest_0.99.3.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 git@git.bioconductor.org:packages/EPICv2manifest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

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[lshep]

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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("EPICv2manifest"). The package 'landing page' will be created at

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