SpliceWiz R package submission

[alexchwong]

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• Repository: https://github.com/alexchwong/SpliceWiz

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[bioc-issue-bot]

Hi @alexchwong

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: SpliceWiz
Title: Efficient and precise alternative splicing analysis in R
Version: 0.99.0
Date: 2022-06-02
Authors@R: c(person("Alex Chit Hei", "Wong", email="a.wong@centenary.org.au", 
		role=c("aut", "cre", "cph")),
	person("Ulf", "Schmitz", role=c("ctb")),
	person("William", "Ritchie", role=c("cph")))
Description: Reads and fragments aligned to splice junctions can be used to
    quantify alternative splicing events (ASE). However, overlapping ASEs can
	confound their quantification. SpliceWiz quantifies ASEs, calculating
	percent-spliced-in (PSI) using junction reads, and intron retention using
	IRFinder-based quantitation. Novel filters identify ASEs that are relatively
	less confounded by overlapping events, whereby PSIs can be calculated with
	higher confidence. SpliceWiz is ultra-fast, using multi-threaded processing
	of BAM files. It can be run using a graphical user or command line 
	interfaces. GUI-based interactive visualization of differential ASEs,
	including novel group-based RNA-seq coverage visualization, simplifies
	short-read RNA-seq analysis in R.
License: MIT + file LICENSE
Depends: NxtIRFdata
Imports:
    ompBAM,
	methods, stats, utils, tools, parallel,
	magrittr,
	Rcpp (>= 1.0.5),
	data.table,
	fst,
	ggplot2,
	AnnotationHub, 
	BiocFileCache,
	BiocGenerics,
	BiocParallel,
	Biostrings, 
	BSgenome,
	DelayedArray,
	DelayedMatrixStats,
	genefilter,
	GenomeInfoDb,
	GenomicRanges,
	HDF5Array,
	IRanges,
	progress,
	plotly,
	R.utils,
	rhdf5,
	rtracklayer,
	SummarizedExperiment, 
	S4Vectors,
	shiny,
	shinyFiles,
	shinyWidgets,
	shinydashboard,
	rhandsontable,
	DT,
	grDevices,
	heatmaply, pheatmap,
	matrixStats,
	RColorBrewer,
	XML
Suggests: 
    knitr, rmarkdown, openssl, crayon, egg,
    DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0)
LinkingTo: 
    ompBAM,
    Rcpp,
    zlibbioc, 
	RcppProgress
SystemRequirements: C++11
Collate: AllImports.R
	RcppExports.R
	zzz.R
	AllClasses.R
	AllGenerics.R
	ASEFilter-methods.R
	NxtSE-methods.R
	globals.R
	ggplot_themes.R
	example_data.R
	wrappers.R
	make_plot_data.R
	Coverage.R
	utils.R
	File_finders.R
	BuildRef.R
	STAR_utils.R
	Mappability.R
	ProcessBAM.R
	CollateData.R
	MakeSE.R
	Filters.R
	ASE-methods.R
	dash_filterModules.R
	dash_globals.R
	dash_settings.R
	dash_ref_new_ui.R
	dash_ref_new_server.R
	dash_expr_ui.R
	dash_expr_server.R
	dash_QC.R
	dash_filters.R
	dash_DE_ui.R
	dash_DE_server.R
	dash_vis_ui.R
	dash_vis_server.R
	dash_cov_ui.R
	dash_cov_server.R
	dash_ui.R
	dash_server.R
	dash.R
	SpliceWiz-package.R
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
VignetteBuilder: knitr
biocViews: Software, Transcriptomics, RNASeq, AlternativeSplicing, Coverage, 
  DifferentialSplicing, DifferentialExpression, GUI, Sequencing
URL: https://github.com/alexchwong/SpliceWiz
BugReports: https://support.bioconductor.org/
Config/testthat/edition: 3

[alexchwong]

Dear Reviewers,

Please be aware that SpliceWiz is intended to replace the NxtIRFcore R package already in Bioconductor (and should be reviewed in this context). It includes some performance improvements as well as the introduction of a shiny-based GUI. SpliceWiz is submitted as a separate package to facilitate the package name change.

[bioc-issue-bot]

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

[alexchwong]

@Kayla-Morrell CHECK is timing out at ~15 min for MacOS but runs fine at 4.5 min on Linux.

Seems like Bioconductor's MacOS is much slower than Linux. Running R cmd check on GitHub action, I am getting 8min 41sec for MacOS. Also the longest example "NxtSE-class" is taking 65 sec on Bioconductor's MacOS, whereas it takes 28 sec on GitHub action's MacOS.

Is there something going on with the MacOS server on Bioconductor's end that is slowing it down?

[Kayla-Morrell]

@alexchwong - I can confirm that on my personal Mac it only took about 7 minutes to run R CMD check. I'm not sure what might be happening on the Bioc Mac but I can review in the meantime and perhaps the issue will work itself out. If there needs to be further investigation we can do that while the review is taking place. I should have the initial review posted by the beginning of next week.

Best,
Kayla

[Kayla-Morrell]

@alexchwong - Thank you for submitting to Bioconductor. Please see the initial review of
the package below. The required changes must be made while the suggested
changes do not have to be (though we strongly encourage them). Comment back
here with updates that have been made and when the package is ready for a
re-review.

General package development

• REQUIRED: In the README file, the installation instructions should also
  include how to install the package from Bioconductor.

DESCRIPTION

• SUGGESTION: Consider adding these automatically suggested biocViews:
  ATACSeq, DNASeq, RIPSeq, Microarray, mRNAMicroarray, CRISPR

Data

• REQUIRED: The inst/extdata/ files need to have documentation in the
  inst/script/ directory. There needs to be documentation on how the data was
  generated and source information. It should include source URLs and any key
  information regarding filtering or processing. It can be executable code, sudo
  code, or a text description. Users should be able to download and roughly
  reproduce the file or object that is present as data.

Vignettes

• REQUIRED: Most of the code chunks in the SW_Cookbook.Rmd file contain
  eval = FALSE. We don't allow for static vignettes and executable code is a
  must.
• SUGGESTION: We encourage the use of BiocStyle for formatting.
• REQUIRED: I couldn't find reference to img/MenuBar.jpg or
  img/Settings.jpg in the vignettes. If these images aren't needed they should
  be removed.

SW_QuickStart.Rmd

• REQUIRED: The 'Introduction' section needs more detail about the package
  itself. It should serve as an abstract to introduce the objective, models,
  unique functions, key points, etc. that distinguish the package from other
  packages in the same area. This should also include a short motivation for the
  package in general as well as motivation for inclusion in Bioconductor.
• SUGGESTION: I would suggest not hiding results so if a user is running
  through the vignette code they will be able to compare their results to yours
  to be sure they are getting the correct output.

Man pages

• REQUIRED: Usage of dontrun{} / donttest{} tags found in man page
  examples. This is acceptable if the functions are run elsewhere, such as in
  the vignette(s) or tests. I could not find where calculateMappability(),
  STAR_buildRef(), STAR_alignReads(), STAR_alignExperiment(), or
  findFASTQ() were run. Please make sure these functions are being run in code
  somewhere (i.e., man page examples, vignette executable code, or runnable unit
  tests).
• REQUIRED: For those functions that are being run else where but you don't
  want to have run in the man page examples use donttest{} over dontrun{},
  since donttest{} requires valid R code.

R code

• REQUIRED: Avoid cat and print outside of show methods.
• SUGGESTION: For formatting reasons, consider shorter lines. There are 146
  lines that are > 80 characters long.
• SUGGESTION: For formatting reasons, consider multiples of 4 spaces for
  line indents. There are 229 lines that are not.

Best,
Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 3c27fe3b26a0335cf3343cd88b00a1b32f504e59

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

[alexchwong]

Thanks @Kayla-Morrell for the initial review / feedback. I have addressed all REQUIRED
sections in the comments below:

General package development

* [ ]  REQUIRED: In the README file, the installation instructions should also
  include how to install the package from Bioconductor.

Added instructions for installation from Bioconductor (for devel / 3.16)

DESCRIPTION

* [ ]  SUGGESTION: Consider adding these automatically suggested biocViews:
  ATACSeq, DNASeq, RIPSeq, Microarray, mRNAMicroarray, CRISPR

Data

* [ ]  REQUIRED: The `inst/extdata/` files need to have documentation in the
  `inst/script/` directory.  There needs to be documentation on how the data was
  generated and source information. It should include source URLs and any key
  information regarding filtering or processing. It can be executable code, sudo
  code, or a text description. Users should be able to download and roughly
  reproduce the file or object that is present as data.

The data in inst/extdata/ can be reproduced by calling the make_example_NxtSE
function found within inst/scripts/make-data.R file. I have updated the documentation
as comments above this function in make-data.R

Vignettes

* [ ]  REQUIRED: Most of the code chunks in the `SW_Cookbook.Rmd` file contain
  `eval = FALSE`. We don't allow for static vignettes and executable code is a
  must.

I have removed SW_Cookbook.Rmd

* [ ]  SUGGESTION: We encourage the use of `BiocStyle` for formatting.

* [ ]  REQUIRED: I couldn't find reference to `img/MenuBar.jpg` or
  `img/Settings.jpg` in the vignettes. If these images aren't needed they should
  be removed.

I have added an extra section that utilises img/MenuBar.jpg. img/Settings.jpg is now removed

SW_QuickStart.Rmd

* [ ]  REQUIRED: The 'Introduction' section needs more detail about the package
  itself. It should serve as an abstract to introduce the objective, models,
  unique functions, key points, etc. that distinguish the package from other
  packages in the same area. This should also include a short motivation for the
  package in general as well as motivation for inclusion in Bioconductor.

I have updated the vignette to briefly explain SpliceWiz.

* [ ]  SUGGESTION: I would suggest not hiding results so if a user is running
  through the vignette code they will be able to compare their results to yours
  to be sure they are getting the correct output.

Thanks Kayla. I have run all the code in the non-hidden cells and found that the
output reproduces what is displayed in the non-hidden cells in the vignette.

Man pages

* [ ]  REQUIRED: Usage of `dontrun{}` / `donttest{}` tags found in man page
  examples. This is acceptable if the functions are run elsewhere, such as in
  the vignette(s) or tests. I could not find where `calculateMappability()`,
  `STAR_buildRef()`, `STAR_alignReads()`, `STAR_alignExperiment()`, or
  `findFASTQ()` were run. Please make sure these functions are being run in code
  somewhere (i.e., man page examples, vignette executable code, or runnable unit
  tests).

I have removed all dontrun{} segments except the one for Mappability-methods.
calculateMappability() is now tested via unit tests (tests\testthat\test-Mappa.R)

The STAR methods have now been removed, as well as findFASTQ. They were wrapper
functions for the STAR RNA-seq aligner, that would only work on linux systems with
STAR installed.

* [ ]  REQUIRED: For those functions that are being run else where but you don't
  want to have run in the man page examples use `donttest{}` over `dontrun{}`,
  since `donttest{}` requires valid R code.

I have tried using donttest{} for Mappability-methods segment but this throws a
warning in R CMD CHECK. This is because the example calls Rsubread::buildindex
which would only work if the current directory is the reference directory. Calling
setwd throws the warning. This is otherwise a working example that is essentially
replicated in tests\testthat\test-Mappa.R, and I ask that you consider this an exceptional
circumstance and allow this instance of dontrun{}.

R code

* [ ]  REQUIRED: Avoid `cat` and `print` outside of `show` methods.

All cat calls occur in the context of the show method of the ASEFilter S4 object.

All print calls occur in the context of renderPlotly() segments of the SpliceWiz GUI.
They are essential to correctly display the plotly interactive plots in the GUI. I ask
that you consider renderPlotly(print(x)) as equivalent to show in context
of the shiny-based GUI, otherwise there is no way to render plots via the shiny app.

I'd be grateful if you could re-review SpliceWiz. On a side note, it seems that the MacOS
issues has resolved itself. Thanks!

[Kayla-Morrell]

@alexchwong - Thank you for the thorough comments and making the necessary changes. I have looked everything over and I'd be more than happy to accept the package.

Best,
Kayla

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

[lshep]

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See further instructions at

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

https://bioconductor.org/packages/SpliceWiz

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.