Initial commit

.Rbuildignore

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+^changchang\.Rproj$
+^\.Rproj\.user$
+^dev$

.gitignore

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+.Rproj.user
+*.Rproj
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store
+.quarto

DESCRIPTION

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+Package: changchang
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
+    license
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+

dev/01_create_pkg.R

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+## ********************
+## Create the R package
+## ********************
+
+## To get started, install R from https://cran.r-project.org/
+## and RStudio Desktop https://rstudio.com/products/rstudio/download/#download
+## You can install both of them for free.
+
+## Next, open RStudio as the code that will run benefits from running inside
+## RStudio for interactivity purposes.
+
+## Next, you might need to install several R packages that you can install with
+## the following code:
+if (!requireNamespace("remotes", quietly = TRUE)) {
+    install.packages("remotes")
+}
+remotes::install_cran(
+    c(
+        "available",
+        "BiocManager",
+        "biocthis",
+        "devtools",
+        "knitr",
+        "pkgdown",
+        "RefManageR",
+        "rmarkdown",
+        "rstudioapi",
+        "sessioninfo",
+        "styler",
+        "usethis"
+    )
+)
+if (!requireNamespace("BiocStyle", quietly = TRUE)) {
+    BiocManager::install("BiocStyle")
+}
+## In case you want the development version of biocthis from GitHub
+# BiocManager::install("lcolladotor/biocthis")
+
+## Here's a very quick summary of why these packages are useful:
+## * available: to check the name of your package
+## * BiocManager: to install Bioconductor packages
+## * BiocStyle: for styling your vignette and linking to other packages
+## * devtools: to develop R packages
+## * knitr: for making your vignette
+## * pkgdown: for creating beautiful documentation websites
+## * RefManageR: for citing utilities in your package vignette
+## * rmarkdown: for making the README.md and processing your vignette
+## * remotes: for installing R packages from several locations
+## * rstudioapi: for navigating across files in RStudio
+## * sessioninfo: for detailed R session information useful to you and your users
+## * usethis: for creating templates that will jump start your R package work
+
+
+## Package names have some properties. You can also use:
+available::available("changchang")
+## to check that your package name is not taken and that it doesn't have
+## a meaning that you might not be aware of.
+
+usethis::create_package("changchang")
+## This opens a new window in RStudio
+
+## Note: If you create packages frequently, check the help file for
+## usethis::use_description() for more information on how to set some R author
+## defaults.
+
+## Add package development files from biocthis
+biocthis::use_bioc_pkg_templates()
+
+## Move to the next step: setting up Git and GitHub for your package
+rstudioapi::navigateToFile(usethis::proj_path("dev", "02_git_github_setup.R"))
+
+## This template was made using https://lcolladotor.github.io/biocthis/

dev/02_git_github_setup.R

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+## Did you miss the previous step? The one about creating your package
+rstudioapi::navigateToFile(usethis::proj_path("dev", "01_create_pkg.R"))
+
+## ********************
+## Setup Git and GitHub
+## ********************
+
+## Note that Bioconductor doesn't allow *.Rproj files
+## So we have to ignore it before anything else
+usethis::use_git_ignore("*.Rproj")
+usethis::use_git() ## Choose the option to make the commit, then to restart RStudio
+## If you don't have git installed, you will likely benefit from reading
+## "Happy Git and GitHub for the useR" at https://happygitwithr.com/.
+
+## After the restart, we next need to change the default Git branch to "devel"
+## as this is the new standard at Bioconductor. You can choose to ignore
+## this step, but will have to deal with more complicated commands later down
+## the road. So we highly recommend that you use the "devel" Git branch!
+usethis::git_default_branch_rename(to = "devel")
+
+## Next we continue by connecting your local git repository to
+## GitHub. You might want to use the `organisation` and `private` arguments
+args(usethis::use_github)
+
+## If this is your first time running use_github(), you might have to also run:
+usethis::gh_token_help()
+## The above command will suggest that you read more at
+## https://usethis.r-lib.org/articles/articles/git-credentials.html
+## which contains the latest recommendations by the usethis authors for
+## configuring your R to GitHub connection.
+usethis::create_github_token()
+gitcreds::gitcreds_set()
+## Type your GitHub token, not your password! Otherwise you might run into this
+## problem: /~https://github.com/r-lib/usethis/issues/1347
+
+## In some situations, gitcreds::gitcreds_set() might not work. For example,
+## gitcreds::gitcreds_set() is not supported on Linux as discussed at
+## /~https://github.com/r-lib/gitcreds/issues/29. In these situations,
+## you have to rely on the old workflow of editing your
+## .Renviron file with contents like (note the empty line at the end!):
+# GITHUB_PAT=YOUR_40_CHARACTERS_TOKEN
+#
+usethis::edit_r_environ()
+## Then re-start your R session.
+rstudioapi::restartSession()
+## Editing the .Renviron is strongly discouraged now since it stores as
+## simple text your GitHub personal access token (PAT) instead of the
+## more secure approach provided by gitcreds.
+
+## Now run use_github()
+usethis::use_github()
+## Follow any prompts, such as running on the terminal:
+## git push --set-upstream origin devel
+
+## Move to the next step: setting up your package core files
+rstudioapi::navigateToFile(usethis::proj_path("dev", "03_core_files.R"))
+
+## This template was made using https://lcolladotor.github.io/biocthis/

dev/03_core_files.R

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+## Did you miss the previous step? The one about setting up Git and GitHub
+rstudioapi::navigateToFile(usethis::proj_path("dev", "02_git_github_setup.R"))
+
+## ***********************************************************
+## Setup the core files for your Bioconductor-friendly package
+## ***********************************************************
+
+## Edit your package DESCRIPTION file
+## Check http://r-pkgs.had.co.nz/description.html for details
+## as well as http://contributions.bioconductor.org/description.html
+
+## Check /~https://github.com/lcolladotor/biocthis/blob/devel/DESCRIPTION
+## for an example.
+
+## You'll at least want to edit the version to 0.99.0 (or lower) since that's
+## the version number you will need to use with Bioconductor.
+
+## You will also want to add the biocViews field, for example:
+## biocViews: Software
+
+## Many Bioconductor packages use the following license:
+## license: Artistic-2.0
+
+## You might want to add the Date field as well, which is used when creating
+## the package citation information. Use the YYYY-MM-DD format. For example:
+## Date: 2020-04-29
+
+## This function sets all these defaults for you
+biocthis::use_bioc_description()
+## However, you still need to edit parts of it manually
+rstudioapi::navigateToFile(usethis::proj_path("DESCRIPTION"))
+
+## Create your README.Rmd file
+biocthis::use_bioc_readme_rmd()
+devtools::build_readme()
+
+## Edit accordingly. You might want to install your package also using
+## devtools::build() or the RStudio keyboard shortcut:
+## macoS: command + shift + B
+## Windows: control + shift + B
+
+## Click on the `knit` button on your README.Rmd file to create the README.md
+## file.
+
+## Add a NEWS.md file
+## See http://bioconductor.org/developers/package-guidelines/#news for more
+## details about Bioconductor news files.
+biocthis::use_bioc_news_md()
+
+## Add information for users and contributors
+biocthis::use_bioc_coc()
+usethis::use_tidy_contributing()
+biocthis::use_bioc_support()
+biocthis::use_bioc_issue_template()
+biocthis::use_bioc_feature_request_template()
+biocthis::use_bioc_citation()
+
+## Add badges to the README.Rmd file
+usethis::use_lifecycle_badge("Experimental")
+biocthis::use_bioc_badges()
+## NOTE: If your Bioconductor package is an experiment, annotation or workflow
+## package, you will need to edit the resulting badge!
+usethis::use_github_actions_badge("check-bioc.yml")
+
+## Enable using tests
+usethis::use_testthat()
+usethis::use_test("example_test") ## You need at least one test to run covr
+usethis::use_coverage()
+
+## Re-knit your README.Rmd file to update your README.md file
+devtools::build_readme()
+
+## Add a vignette template
+pkg <- basename(usethis::proj_get())
+biocthis::use_bioc_vignette(pkg, paste("Introduction to", pkg))
+
+## Add a Bioconductor-friendly GitHub actions workflow to check your package
+biocthis::use_bioc_github_action()
+## You will need to go to /~https://github.com//settings/actions
+## to and enable:
+## > Workflow permissions > Read and write permissions
+## Then click save before you can continue with the instructions in this script.
+
+## While biocthis::use_bioc_github_action() has arguments for all these options,
+## if you missed them, and:
+## * your package doesn't have testthat tests, use: has_testthat = 'false'
+## * you don't want to run the covr step, use: run_covr = 'false'
+## * you don't want to use pkgdown, use: run_pkgdown = 'false'
+## * you don't want to build a docker image, use: run_docker = 'false'
+rstudioapi::navigateToFile(usethis::proj_path(".github", "workflows", "check-bioc.yml"))
+
+## Setup up your global git config
+usethis::edit_git_config()
+## Use the information that matches your GitHub account
+## Example contents (4 space indentation):
+# [user]
+#     name = Your Full Name
+#     email = your.email@somewhere.com
+#
+
+## Setup your pkgdown css file
+biocthis::use_bioc_pkgdown_css()
+
+## Install your package locally before building the documentation website
+devtools::install()
+
+## ************************* WARNING START *********************************
+## WARNING: git commit before running this next function!
+## Otherwise you can lose your work!!!
+## ************************* WARNING END ***********************************
+##
+## Deploy with pkgdown at least once locally such that the automatic updates
+## from GitHub actions will work. This creates the gh-pages branch in your
+## GitHub repository in such a way that pkgdown will recognize it and be
+## able to use it later.
+pkgdown::deploy_to_branch() ## Check the WARNING above before running this!
+
+## For more details about package development, check:
+## * http://contributions.bioconductor.org/
+## * https://r-pkgs.org/
+
+## Move to the next step: updating your package code before a "git commit"
+rstudioapi::navigateToFile(usethis::proj_path("dev", "04_update.R"))
+
+## This template was made using https://lcolladotor.github.io/biocthis/

dev/04_update.R

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+## Did you miss the previous step? The one about setting up the R package core
+## files.
+rstudioapi::navigateToFile(usethis::proj_path("dev", "03_core_files.R"))
+
+## ********************************************
+## Update your package code before a git commit
+## ********************************************
+
+## Automatically re-style the code in your package to a Bioconductor-friendly
+## format
+## Note that you can pair this function with the RStudio "Reformat code"
+## button on the magic wand drop down menu. The keyboard shortcut is
+## macOS: shift + command + A
+## Windows: shift + control + A
+styler::style_pkg(transformers = biocthis::bioc_style())
+styler::style_dir(usethis::proj_path("dev"), transformers = biocthis::bioc_style())
+styler::style_dir(
+    usethis::proj_path("vignettes"),
+    transformers = biocthis::bioc_style(),
+    filetype = "Rmd"
+)
+styler::style_file(usethis::proj_path("README.Rmd"), transformers = biocthis::bioc_style())
+
+## Re-make the documentation files
+devtools::document()
+
+## You might also need to update the README.md by re-rendering the README.Rmd
+## file.
+devtools::build_readme()
+
+## This template was made using https://lcolladotor.github.io/biocthis/