Merge pull request #6 from Big-Life-Lab/cran-prep-fixes

CRAN prep: Add renv, update package metadata, and debug vignettes

Author: rafdoodle

.Rbuildignore

@@ -16,3 +16,11 @@
 ^Meta$
 ^.quarto
 ^_freeze
+^\.claude$
+.*\.log$
+^renv$
+^renv\.lock$
+^test_vignettes\.R$
+^test_vignettes_with_timeout\.sh$
+^vignette_.*\.txt$
+^vignette_.*\.log$

.Rprofile

@@ -0,0 +1,18 @@
+# Activate renv for reproducible package management
+source("renv/activate.R")
+
+# Use binary packages (no compiler needed)
+# Posit Package Manager provides binaries for faster installation
+options(
+  pkgType = "binary",
+  repos = c(CRAN = "https://packagemanager.posit.co/cran/latest")
+)
+
+# Warn if R version is below the package floor
+if (getRversion() < "4.0") {
+  warning(
+    "chmsflow requires R >= 4.0.0. ",
+    "You are using R ", getRversion(), ". ",
+    "Some features may not work correctly."
+  )
+}

.gitignore

@@ -64,9 +64,12 @@ src/*.o
 src/*.so
 src/*.dll
 
-# If you use renv for package dependency management, ignore these files
-renv.lock
-renv/
+# renv for package dependency management
+# Keep renv.lock and renv/activate.R in git for reproducibility
+# Ignore the local library and cache
+renv/library/
+renv/local/
+renv/staging/
 
 # If you use packrat for package dependency management, ignore these files
 packrat/

DESCRIPTION

@@ -2,20 +2,18 @@ Package: chmsflow
 Type: Package
 Title: Transforming and Harmonizing CHMS Variables
 Version: 0.1.0
-Author: Rafidul Islam [aut, cre], Douglas Manuel [aut], Therese Chan [aut]
-Maintainer: Rafidul Islam <raislam@ohri.ca>
 Authors@R: c(
     person("Rafidul", "Islam", email = "raislam@ohri.ca", role = c("aut", "cre")),
-    person("Douglas", "Manuel", email = "dmanuel@ohri.ca", role = c("aut"), comment = c(ORCID = "0000-0003-0912-0845")),    
+    person("Douglas", "Manuel", email = "dmanuel@ohri.ca", role = c("aut"), comment = c(ORCID = "0000-0003-0912-0845")),
     person("Therese", "Chan", email = "TChan@bruyere.org", role = c("aut")))
 Description: Supporting the use of the Canadian Health Measures Survey (CHMS)
     by transforming variables from each cycle into harmonized, consistent 
     versions that span survey cycles 1-6. This package uses rec_with_table(), 
     which was developed from 'sjmisc' rec(). Ludecke D (2018). "sjmisc: Data 
     and Variable Transformation Functions". Journal of Open Source Software, 
     3(26), 754. <doi:10.21105/joss.00754>.
-Depends: 
-    R (>= 3.5)
+Depends:
+    R (>= 4.0)
 Imports: dplyr, haven, logger
 License: MIT + file LICENSE
 URL: https://github.com/Big-Life-Lab/chmsflow, https://big-life-lab.github.io/chmsflow/
@@ -25,4 +23,5 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Suggests: DT, kableExtra, knitr, quarto, readr, recodeflow, testthat (>= 3.0.0)
 VignetteBuilder: quarto
+Config/build/clean-inst-doc: FALSE
 LazyData: true

R/medications.R

@@ -64,6 +64,20 @@ To use `chmsflow` at a Research Data Centre (RDC), you'll need to load the packa
 library(chmsflow)
 ```
 
+## Development setup
+
+This package uses renv for dependency management. After cloning the repository:
+
+```r
+# Restore package dependencies
+renv::restore()
+
+# Install the package locally
+devtools::install()
+```
+
+The project requires R >= 4.0.0. When you load the project, `.Rprofile` will warn if your R version is below this floor.
+
 ## What's Included?
 
 The `chmsflow` package comes with several useful resources: