Closed rhondabacher closed 3 years ago
Hi @rhondabacher
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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
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This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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Thank you for your submission to Bioconductor. Please see comments below:
README
NEWS.md
news?
and Bioc newsDESCRIPTION
LazyData: true
. This rarely proves useful and can actually slow installationinst
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
R code/man pages
[ ] 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?
[ ] Similarly Genomic positions should be GenomicRanges not data.frames.
[ ] 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
Received a valid push on git.bioconductor.org; starting a build for commit id: 2c98c9f666afcaf4c69c3c1b248c1f88fb615272
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
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to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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:
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 newsDESCRIPTION
- [X] Remove
LazyData: true
. This rarely proves useful and can actually slow installationinst
- [X] You will also need an
inst/script
directory that contains files explaining how the files ininst/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
Thank you for making the changes. Given the leg work and example you provided it is fine to keep as you have implemented. Cheers.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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