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methylscaper #1921

Closed rhondabacher closed 3 years ago

rhondabacher commented 3 years ago

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

Confirm the following by editing each check box to '[x]'

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For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 3 years ago

Hi @rhondabacher

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: methylscaper
Type: Package
Title: Visualization of Methylation Data
Description: A shiny app for visualizing methylation data.
Version: 0.99.0
Authors@R: c(person("Bacher", "Rhonda", email = "rbacher@ufl.edu", role = c("aut", "cre")), person("Parker", "Knight", email = "pknight24@ufl.edu", role = c("aut")))
Depends: R (>= 4.0.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports:
  shiny,
  seriation,
  BiocParallel,
  seqinr,
  Biostrings,
  Rfast,
  svglite,
  grDevices, 
  graphics, 
  stats, 
  utils,
  shinyFiles,
  data.table
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, devtools
VignetteBuilder: knitr
biocViews: 
    DNAMethylation,
    Epigenetics,
    PrincipalComponent,
    Visualization,
    SingleCell
bioc-issue-bot commented 3 years ago

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.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 3 years ago

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: "skipped, ERROR, 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/methylscaper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6e39d56fd23f439256bdb7ee38a58ca7f5d96e40

bioc-issue-bot commented 3 years ago

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: "skipped, WARNINGS, 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. 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/methylscaper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b8edd74951f949f302e1bd79bf851ee66460771d

bioc-issue-bot commented 3 years ago

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: "skipped, WARNINGS, 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. 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/methylscaper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d6e5c48968b9f136b91cadd239f42da16a273b05

bioc-issue-bot commented 3 years ago

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

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8bbeb18e0e5fd50a61521b9507cb978a51770c59

bioc-issue-bot commented 3 years ago

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: "skipped, 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. 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/methylscaper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fb7e0152f70202456aa9c2bd98feddaacf37465c

bioc-issue-bot commented 3 years ago

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: "skipped, ERROR, 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/methylscaper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 522ab5745f7640e46810181afe3670625ee8a4ea

bioc-issue-bot commented 3 years ago

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: "skipped, 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. 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/methylscaper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a6ac4bcce2247eeb39ba186c5044a8ce02358f92

bioc-issue-bot commented 3 years ago

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

lshep commented 3 years ago

Thank you for your submission to Bioconductor. Please see comments below:

README

NEWS.md

DESCRIPTION

inst

vignette

R code/man pages

Please address the above issues. When ready please do a version bump to trigger a new build report and comment back here with how the package was updated and that it is ready for a re-review.

Cheers

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2c98c9f666afcaf4c69c3c1b248c1f88fb615272

bioc-issue-bot commented 3 years ago

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

rhondabacher commented 3 years ago

Hi,

We've pushed a successful build incorporating all the comments below and are ready for a re-review. Thank you for your time and consideration.

Two things I'd like to note for the re-review:

  1. For SingleCellExperiment, there are no existing packages that I found that use this structure for single cell methylation (yet). We have included a function that could accept and reformat an SCE and which can also be updated as needed at any time in the future.
  2. For GenomicRanges, this was an excellent point to include this and I began rewriting as indicated. However, after testing we found it was significantly slower than data.table for our purposes. I've included the code comparison as an attachment bioc_submission_example.txt

In summary we compared a simple range subset using subsetByOverlaps() which takes just under 2 seconds, however the same operation using data.table completes in less than 0.1 seconds. On the practical side, since users can make many positional adjustments that need to appear in the plot as fast as possible the speed difference is quite significant. We hope that you understand and it is OK to use data.table. We are not doing any extensive or complicated range calculations where I expect that GenomicRanges is the much better performer.

Thank you for your submission to Bioconductor. Please see comments below:

README

  • [X] Include Bioconductor installation instrcutions

NEWS.md

  • [X] Formatted incorrectly. See news? and Bioc news

DESCRIPTION

  • [X] Remove LazyData: true. This rarely proves useful and can actually slow installation

inst

  • [X] You will also need an inst/script directory that contains files explaining how the files in inst/extdata were generated. This should include source information and any processing. In can be code, sudo-code, or text.

vignette

  • [X] Please include Bioconductor installation instructions

R code/man pages

  • [X] Bioconductor likes to see interoperability with existing classes. The SingleCellExperiment is widely used for Single cell data in Bioconductor. Can you adapt to also be able to accept a SingleCellExperiment object as input or do a wrapper around the standard Bioconductor object?
  • [X] Similarly Genomic positions should be GenomicRanges not data.frames.
  • [X] You should be able to filter also by GenomicRanges in additional to start and end position.

Please address the above issues. When ready please do a version bump to trigger a new build report and comment back here with how the package was updated and that it is ready for a re-review.

Cheers

lshep commented 3 years ago

Thank you for making the changes. Given the leg work and example you provided it is fine to keep as you have implemented. Cheers.

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

rhondabacher commented 3 years ago

Thank you!!

vjcitn commented 3 years ago

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/rhondabacher.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("methylscaper"). The package 'landing page' will be created at

https://bioconductor.org/packages/methylscaper

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.