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Authors: Brian Schilder, Jack Humphrey, Towfique Raj


Vignette updated: Mar-16-2026

Source: vignettes/echoverseTemplate.Rmd
echoverseTemplate.Rmd

Introduction

echoverseTemplate is a skeleton R package that serves as a starting point for creating new modules within the echoverse suite of genomic fine-mapping tools.

It provides:

  • A ready-made package structure following Bioconductor conventions.
  • Internal utility functions (messager, stopper, message_parallel) for consistent messaging across echoverse modules.
  • Pre-configured CI/CD via rworkflows.

Usage

To create a new echoverse module from this template:

  1. Copy or fork the repository.
  2. Rename the package (update DESCRIPTION, NAMESPACE, vignettes, etc.).
  3. Add your exported functions under R/.
  4. Document with roxygen2 and rebuild the NAMESPACE.

Internal utilities

The package includes three internal helpers shared across echoverse modules:

  • messager() – Conditionally print messages, with support for parallel contexts.
  • stopper() – Conditionally raise stop errors.
  • message_parallel() – Send messages to the console from within parallel processes.

Session Info 

utils::sessionInfo()
## R Under development (unstable) (2026-03-12 r89607)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.39.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.39       desc_1.4.3          R6_2.6.1           
##  [4] bookdown_0.46       fastmap_1.2.0       xfun_0.56          
##  [7] cachem_1.1.0        knitr_1.51          htmltools_0.5.9    
## [10] rmarkdown_2.30      lifecycle_1.0.5     cli_3.6.5          
## [13] sass_0.4.10         pkgdown_2.2.0       textshaping_1.0.5  
## [16] jquerylib_0.1.4     systemfonts_1.3.2   compiler_4.6.0     
## [19] tools_4.6.0         ragg_1.5.1          bslib_0.10.0       
## [22] evaluate_1.0.5      yaml_2.3.12         BiocManager_1.30.27
## [25] otel_0.2.0          jsonlite_2.0.0      rlang_1.1.7        
## [28] fs_1.6.7            htmlwidgets_1.6.4