SingleMoleculeFootprintingData

[GuidoBarzaghi]

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[GuidoBarzaghi]

@LiNk-NY thanks for the suggestion: I am moving the data package to Suggests.

About the file extension issue, I am keen on implementing a better solution if available.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 38270c2272887165937dc013584f2369caf0a351

[bioc-issue-bot]

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/SingleMoleculeFootprinting to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[grimbough]

Hi Marcel (@LiNk-NY),

As a minor contributor to this package, I just wanted to chime in with my 2 cents on the use of the cached ExperimentHub data. We tried quite a few ways to "trick" QuasR into using the files as they R in the ExperimentHub cache, but things like symlinks were always resolved to the original file and then it would complain about the file extension. Making a copy from the cache to tempdir() seemed like the least-worst strategy. It should be relatively inexpensive as the cached version remains in place between runs, we can guarantee write access, and we aren't polluting anywhere else as the temporary copy will be deleted after the vignette or example has been run.

We did talk to @Kayla-Morrell about whether it would be possible to retain file extensions on entries in the cache, but I think that was something that would have to wait until after this release. We would of course be willing to update the mechanism in the future if a solution like that become available, it would clearly be nicer to use the files in-place.

[lshep]

This is probably okay and the best middle ground for now and we can work on a better solution in the hubs and in collaboration with you over the next release cycle.

[LiNk-NY]

Thanks Lori and Mike for looking into this!

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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

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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.

[vjcitn]

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/GuidoBarzaghi.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("SingleMoleculeFootprinting"). The package 'landing page' will be created at

https://bioconductor.org/packages/SingleMoleculeFootprinting

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.