Initial commit

.Rbuildignore

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+.*\.Rproj$
+^\.Rproj\.user$
+^README.Rmd
+^\.github$
+^doc$
+^Meta$
+^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+Dockerfile
+^LICENSE\.md$
+
+node_modules$
+package-lock\.json$
+package\.json$

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+## 1. Bug description
+
+(A clear and concise description of what the bug is.)
+
+### Expected behaviour   
+
+(A clear and concise description of what you expected to happen.)
+
+
+## 2. Reproducible example   
+
+### Code 
+
+(Please add the steps to reproduce the bug here. See [here](https://www.r-bloggers.com/2020/10/how-to-make-a-reprex/) for an intro to making a reproducible example (i.e. reprex) and why they're important! __This will help us to help you much faster.__)
+
+```R
+# Paste example here
+
+```
+
+### Console output 
+
+```
+# Paste console output here (e.g. from R/python/command line)
+
+```
+
+### Data
+
+(If possible, upload a small sample of your data so that we can reproduce the bug on our end. If that's not possible, please at least include a screenshot of your data and other relevant details.)
+
+
+## 3. Session info
+
+(Add output of the R function `utils::sessionInfo()` below. This helps us assess version/OS conflicts which could be causing bugs.)
+
+<details>
+
+```
+# Paste utils::sessionInfo() output 
+
+```
+</details>

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/rworkflows.yml

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+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions:
+      contents: write
+      packages: write
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1

.gitignore

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+# R project files
+*.Rproj
+.Rproj.user
+.Ruserdata 
+# History files
+.Rhistory
+.Rapp.history
+# Session Data files
+.RData
+# User-specific files
+.Ruserdata
+# .DS_Store
+# find . -name .DS_Store -print0 | xargs -0 git rm -f --ignore-unmatch
+.DS_Store
+./.DS_Store
+./**/.DS_Store
+./**/**/.DS_Store
+./**/**/**/.DS_Store
+./**/**/**/**/.DS_Store
+./**/**/**/**/**/.DS_Store
+./**/**/**/**/**/**/.DS_Store
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+vignettes/*.R
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+# R Environment Variables
+.Renviron 

DESCRIPTION

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+Package: echoverseTemplate
+Type: Package
+Title: echoverse module: echoversePackageTitle
+Version: 0.99.0
+Authors@R: 
+    c(person(given = "Brian",
+           family = "Schilder",
+           role = c("aut","cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-5949-2191")),
+    person(given = "Jack",
+           family = "Humphrey",
+           role = c("aut"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-6274-6620")),
+    person(given = "Towfique",
+           family = "Raj",
+           role = c("aut"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-9355-5704"))
+           ) 
+Description: echoverse module: echoversePackageDescription.
+URL: https://github.com/RajLabMSSM/echoverseTemplate
+BugReports: https://github.com/RajLabMSSM/echoverseTemplate/issues
+Encoding: UTF-8
+Depends: R (>= 4.1)
+biocViews:
+    Software, Genetics, FunctionalGenomics, SystemsBiology
+Imports:
+Suggests:
+    rworkflows,
+    markdown,
+    rmarkdown,
+    remotes,
+    knitr,
+    BiocStyle,
+    covr,
+    testthat (>= 3.0.0),
+    utils,
+    rlang,
+    methods
+RoxygenNote: 7.2.3
+VignetteBuilder: knitr
+License: GPL-3
+Config/testthat/edition: 3

NAMESPACE

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

NEWS.md

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+# echoverseTemplate 0.99.0
+
+* Added a `NEWS.md` file to track changes to the package.

R/message_parallel.r

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+#' Message parallel
+#' 
+#' Send messages to console even from within parallel processes
+#' @return Null
+#' @keywords internal
+message_parallel <- function(...) {
+    system(sprintf('echo "%s"', paste0(..., collapse = "")))
+}

R/messager.R

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+#' Print messages 
+#' 
+#' Conditionally print messages.
+#'  Allows developers to easily control verbosity of functions, 
+#'  and meet Bioconductor requirements that dictate the message 
+#'  must first be stored to a variable before passing to \link[base]{message}. 
+#'  
+#' 
+#' @param v Whether to print messages or not.
+#' @param parallel Whether to enable message print when wrapped 
+#' in parallelised functions.
+#' 
+#' @return Null 
+#' @keywords internal 
+messager <- function(..., v = TRUE, parallel = FALSE) {
+    if(parallel){
+        if(v) try({message_parallel(...)})
+    } else {
+        msg <- paste(...)
+        if (v) try({message(msg)})
+    }
+}

R/stopper.R

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+#' Stop messages
+#' 
+#' Conditionally print stop messages.
+#' Allows developers to easily control verbosity of functions, 
+#'  and meet Bioconductor requirements that dictate the stop message 
+#'  must first be stored to a variable before passing to \link[base]{stop}. 
+#' @param v Whether to print messages or not.
+#' 
+#' @return Null 
+#' @keywords internal 
+stopper <- function(..., v = TRUE) {
+    msg <- paste(...)
+    if (v) {
+        stop(msg)
+    } else {
+        stop()
+    }
+}

README.Rmd

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+---
+title: ""  
+author: "`r rworkflows::use_badges(add_doi = '10.1093/bioinformatics/btab658')`"
+output:
+  github_document
+---
+
+```{r, echo=FALSE, include=FALSE}
+pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
+description <- read.dcf("DESCRIPTION", fields = "Description")[1] |> 
+    gsub(pattern="\n", replacement=" ")
+```
+
+## ``r pkg``: `r gsub("echoverse module: ","", description)`
+
+This R package is part of the *echoverse* suite that supports
+[`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
+an automated genomic fine-mapping pipeline. 
+
+If you use ``r pkg``, please cite: 
+
+> `r citation(pkg)$textVersion`
+
+## Installation 
+
+```R
+if(!require("remotes")) install.packages("remotes")
+
+remotes::install_github("RajLabMSSM/`r pkg`")
+library(`r pkg`)
+```
+## Documentation 
+
+### [Website](https://rajlabmssm.github.io/`r pkg`) 
+### [Get started](https://rajlabmssm.github.io/`r pkg`/articles/`r pkg`) 
+
+<hr>
+
+## Contact
+
+<a href="https://bschilder.github.io/BMSchilder/" target="_blank">Brian
+M. Schilder, Bioinformatician II</a>  
+<a href="https://rajlab.org" target="_blank">Raj Lab</a>  
+<a href="https://icahn.mssm.edu/about/departments/neuroscience" target="_blank">Department
+of Neuroscience, Icahn School of Medicine at Mount Sinai</a>  

README.md

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+<img src='https://github.com/RajLabMSSM/echoverseTemplate/raw/master/inst/hex/hex.png' title='Hex sticker for echoverseTemplate' height='300'><br>
+[![License:
+GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
+[![](https://img.shields.io/badge/doi-10.1093/bioinformatics/btab658-blue.svg)](https://doi.org/10.1093/bioinformatics/btab658)
+[![](https://img.shields.io/badge/devel%20version-0.99.0-black.svg)](https://github.com/RajLabMSSM/echoverseTemplate)
+[![](https://img.shields.io/github/languages/code-size/RajLabMSSM/echoverseTemplate.svg)](https://github.com/RajLabMSSM/echoverseTemplate)
+[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoverseTemplate.svg)](https://github.com/RajLabMSSM/echoverseTemplate/commits/master)
+<br> [![R build
+status](https://github.com/RajLabMSSM/echoverseTemplate/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoverseTemplate/actions)
+[![](https://codecov.io/gh/RajLabMSSM/echoverseTemplate/branch/master/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoverseTemplate)
+<br>
+<a href='https://app.codecov.io/gh/RajLabMSSM/echoverseTemplate/tree/master' target='_blank'><img src='https://codecov.io/gh/RajLabMSSM/echoverseTemplate/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
+<h4>  
+Authors: <i>Brian Schilder, Jack Humphrey, Towfique Raj</i>  
+</h4>
+
+## `echoverseTemplate`: echoversePackageDescription.
+
+This R package is part of the *echoverse* suite that supports
+[`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR): an automated
+genomic fine-mapping pipeline.
+
+If you use `echoverseTemplate`, please cite:
+
+> Brian M Schilder, Jack Humphrey, Towfique Raj (2021) echolocatoR: an
+> automated end-to-end statistical and functional genomic fine-mapping
+> pipeline, *Bioinformatics*; btab658,
+> <https://doi.org/10.1093/bioinformatics/btab658>
+
+## Installation
+
+``` r
+if(!require("remotes")) install.packages("remotes")
+
+remotes::install_github("RajLabMSSM/echoverseTemplate")
+library(echoverseTemplate)
+```
+
+## Documentation
+
+### [Website](https://rajlabmssm.github.io/echoverseTemplate)
+
+### [Get started](https://rajlabmssm.github.io/echoverseTemplate/articles/echoverseTemplate)
+
+<hr>
+
+## Contact
+
+<a href="https://bschilder.github.io/BMSchilder/" target="_blank">Brian
+M. Schilder, Bioinformatician II</a>  
+<a href="https://rajlab.org" target="_blank">Raj Lab</a>  
+<a href="https://icahn.mssm.edu/about/departments/neuroscience" target="_blank">Department
+of Neuroscience, Icahn School of Medicine at Mount Sinai</a>