## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", eval = FALSE)

## -----------------------------------------------------------------------------
# install.packages("courieR")

## -----------------------------------------------------------------------------
# install.packages(c("shiny", "bslib", "bsicons", "DT"))

## -----------------------------------------------------------------------------
# library(courieR)
# 
# routes <- find_routes()
# routes
# #>   version                                          rscript_path is_current
# #> 1   4.4.2        C:/Program Files/R/R-4.4.2/bin/x64/Rscript.exe       TRUE
# #> 2   4.3.1  C:/Users/you/AppData/Local/Programs/R/R-4.3.1/bin/...      FALSE
# #> 3   4.1.3            C:/Users/you/Documents/R/R-4.1.3/bin/...      FALSE

## -----------------------------------------------------------------------------
# routes <- find_routes(search_paths = "/opt/custom-r/bin/Rscript")

## -----------------------------------------------------------------------------
# # scan the first (newest) R
# src_pkgs <- manifest(rscript_path = routes$rscript_path[1])
# head(src_pkgs[, c("package", "version", "source")])
# #>     package version source
# #> 1     broom   1.0.7   CRAN
# #> 2    callr   3.7.6   CRAN
# #> 3   courieR   0.2.0 GitHub
# #> 4   ggplot2   3.5.1   CRAN
# #> 5      glue   1.8.0   CRAN
# #> 6   stringr   1.5.1   CRAN

## -----------------------------------------------------------------------------
# my_pkgs <- manifest()
# nrow(my_pkgs)
# #> [1] 312

## -----------------------------------------------------------------------------
# user_pkgs <- src_pkgs[is.na(src_pkgs$priority) | !(src_pkgs$priority %in% c("base", "recommended")), ]

## -----------------------------------------------------------------------------
# src_pkgs <- manifest(rscript_path = routes$rscript_path[2])  # old R
# tgt_pkgs <- manifest(rscript_path = routes$rscript_path[1])  # new R
# 
# comp <- inventory(src_pkgs, tgt_pkgs)

## -----------------------------------------------------------------------------
# # packages in source but missing from target
# nrow(comp$missing)
# #> [1] 47
# 
# # packages where source has a newer version
# nrow(comp$outdated)
# #> [1] 12
# 
# # packages at the same version in both
# nrow(comp$same)
# #> [1] 201

## -----------------------------------------------------------------------------
# comp$missing[, c("package", "version", "source")]
# #>       package version  source
# #>  1:    bookdown   0.39    CRAN
# #>  2:  brms   2.21.0    CRAN
# #>  3:   officer   0.6.6    CRAN
# #>  ...
# 
# comp$outdated[, c("package", "version_src", "version_tgt", "source")]
# #>    package version_src version_tgt source
# #> 1:  ggplot2       3.5.1       3.4.4   CRAN
# #> 2:   tibble       3.2.1       3.2.0   CRAN

## -----------------------------------------------------------------------------
# result <- ship(
#   source_path = routes$rscript_path[2],   # old R — package source
#   target_path = routes$rscript_path[1]    # new R — install destination
# )

## -----------------------------------------------------------------------------
# result <- ship(
#   source_path = routes$rscript_path[2],
#   target_path = routes$rscript_path[1],
#   dry_run = TRUE
# )
# 
# # review the plan before anything is installed
# print(result$plan)
# #>         package action  pak_spec
# #>  1:    bookdown install bookdown
# #>  2:        brms install     brms
# #>  3:     ggplot2 upgrade  ggplot2
# #>  ...

## -----------------------------------------------------------------------------
# result <- ship(
#   source_path = routes$rscript_path[2],
#   target_path = routes$rscript_path[1],
#   upgrade = TRUE
# )

## -----------------------------------------------------------------------------
# # summary counts
# result$summary
# #> $installed   47
# #> $upgraded    12
# #> $failed       1
# #> $skipped      0
# 
# # per-package results
# result$results[result$results$status == "error", c("package", "message")]
# #>    package                         message
# #> 1:    rJava  installation of rJava failed...

## -----------------------------------------------------------------------------
# # mixed-source example — all handled automatically
# result$plan[, c("package", "source", "pak_spec")]
# #>    package   source        pak_spec
# #> 1:  ggplot2     CRAN         ggplot2
# #> 2:  courieR   GitHub  lennon-li/courieR
# #> 3:    DESeq2  Bioconductor  bioc::DESeq2

## -----------------------------------------------------------------------------
# library(courieR)
# 
# routes  <- find_routes()
# old_r   <- routes$rscript_path[!routes$is_current][1]
# new_r   <- routes$rscript_path[routes$is_current]
# 
# # dry run
# ship(source_path = old_r, target_path = new_r, dry_run = TRUE, upgrade = TRUE)
# 
# # for real
# result <- ship(source_path = old_r, target_path = new_r, upgrade = TRUE)
# result$summary

## -----------------------------------------------------------------------------
# r_a <- routes$rscript_path[1]
# r_b <- routes$rscript_path[2]
# 
# # push everything A has to B
# ship(source_path = r_a, target_path = r_b, upgrade = TRUE)
# 
# # push everything B has to A
# ship(source_path = r_b, target_path = r_a, upgrade = TRUE)

## -----------------------------------------------------------------------------
# src  <- manifest(rscript_path = old_r)
# tgt  <- manifest(rscript_path = new_r)
# comp <- inventory(src, tgt)
# 
# # only migrate CRAN packages — skip GitHub/unknown sources
# cran_missing <- comp$missing[comp$missing$source == "CRAN", ]
# cat(nrow(cran_missing), "CRAN packages to install\n")

## -----------------------------------------------------------------------------
# pkgs <- manifest(rscript_path = routes$rscript_path[1])
# write.csv(pkgs[, c("package", "version", "source")], "my_packages.csv", row.names = FALSE)

## -----------------------------------------------------------------------------
# saved <- read.csv("my_packages.csv", stringsAsFactors = FALSE)
# # pak installs from a character vector of package names
# pak::pkg_install(saved$package)

## -----------------------------------------------------------------------------
# install.packages(c("shiny", "bslib", "bsicons", "DT"))
# open_hub()