Submission to Bioconductor

[iofeidis]

InterTADs R package ISSUES (Bioconductor)

Check the corresponding box when the task is done. Anyone with write access to a repository can edit comments.
Most of the tasks will pop when testing with R CMD check , devtools::check() and BiocCheck::BiocCheck().

Tasks to be completed before submission:

General

• Reform the code into functions that make a pipeline. Nothing should exist outside of a function.

DESCRIPTION

• Add all library() calls into Imports: in DESCRIPTION.

• library(saveImageHigh), library(annotables)

You can find it at https://github.com/nikopech/saveImageHigh and https://github.com/stephenturner/annotables

All packages must be available via Bioconductor or CRAN; the use of Remotes
is not supported hence dependencies only available on e.g. github are not allowed.
Bioconductor Guidelines

Possible solution: Copy code from saveImageHigh and annotables to InterTADs or find similar packages or argue for an exception.

• Import whole tidyverse? It's a collection of packages, so maybe keep only necessary packages (probably only dplyr).

• Libraries karyoploteR and pathview have been commented out. Are they needed?

• Add biocViews

• Maintainer to subscribe to support.bioconductor.org and add "InterTADs" on watched tags.

NAMESPACE

• Import all needed objects either by roxygen import/importFrom tags or by :: operator.

• Keep all roxygen import and importFrom tags in a single .R script, preferably one named "InterTADs_package.R".

• Determine which objects / functions will be exported to user and add the roxygen export tag.

inst/extdata

• Move datasets to inst/extdata

• Edit the corresponding .R scripts where files are used as input (with system.file()).

inst/script

• Add a script in inst/script explaining how you obtained/processed the data in inst/extdata.

R code

• Remove rm(list=ls()) calls as it alters user's environment.

• Remove library(), source() and gc() calls.

• Change cat() to message() if applicable.

• Remove commented-out blocks.

• Indentation: Tabs = 4 spaces

• Line width: 80 characters

vignettes

• Create a minimal first version of the vignette.

• Update vignettes/InterTADs.Rmd

README.md

• Update README.md

CITATION / CITATION.cff

• Add CITATION and/or CITATION.cff if applicable.

• DOI badge at Github

Other

• Potential misspelling in R/events_visualization.R, line 102 (maybe kpBars() missing?)

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Links

Info for submission process is available here
Package guidelines are outlined here