SynExtend

[npcooley]

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• Repository: https://github.com/npcooley/SynExtend

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[lshep]

Looking at it now.

[lshep]

A few more minor comments that should be doable:

NEWS

• [ ] not formatted properly. See ?news in R and/or Bioc news linke

README

• [ ] Don't include version in BiocManager::install() This will change will given Bioconductor releases and BiocManager should pick up the necessary (and correct) version automatically

Vignette okay

Other

• [x] we still would recommend using the rtracklayer::import but your ranges are imported with Bioconductor standards so we will let this go. In the future if you develop more packages reuse existing imports and class structures wherever possible.

man

NucleotideOverlap

• [ ] Again I would put in the man page that the object of class 'Synteny' is from DECIPHER.

PairSummaries

• [ ] Since it seems like correction can only be none or jukes-cantor it probably should be explicitly stated so a user doesnt have to then go to the DistanceMatrix help page to find what it can be.

Other

• [ ] Since you reference them as output formats and input formats, you should have a help page describing the strucutre of the LinkedPairs object. What does it contain? And then link this help page in the other pages that take as input or output.

R code

• [ ] Remove paste from messsage/warning/error code. It pastes automatically.

Cheers,

[bioc-issue-bot]

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

6eec396 vignette and man file clarity

[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:

79cf763 value section

[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.

[npcooley]

Hi,

I've attempted to address all issues, please let me know if further changes are required.

Cheers, Nick

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

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

https://bioconductor.org/packages/SynExtend

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.