336 cran warning futilelogger set to be archived

.Rbuildignore

@@ -16,6 +16,7 @@
 ^CODEOWNERS
 ^vignettes.*
 ^release_testing*
+^CLAUDE.md$
 
 # History files
 ^\.Rhistory*

.github/workflows/smoke-tests.yaml

@@ -39,7 +39,6 @@ jobs:
           - fontawesome
           - formatR
           - fs
-          - futile.logger
           - futile.options
           - glue
           - highr

CLAUDE.md

@@ -0,0 +1,190 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+pkgnet is an R package for analyzing R packages using graph theory. It builds network representations of packages to:
+- Analyze function interdependencies within a package
+- Map recursive package dependencies
+- Trace class inheritance structures (S4, R5/Reference Classes, R6)
+- Prioritize functions for unit testing based on centrality metrics
+
+The core functionality is `CreatePackageReport()` which generates HTML reports analyzing package structure.
+
+## Architecture
+
+### Reporter System (R6-based)
+
+The package uses an object-oriented architecture built on R6 classes with a hierarchical reporter system:
+
+**Base Classes:**
+- `AbstractPackageReporter` (R/AbstractPackageReporter.R): Base class for all reporters. Handles package setup via `set_package()` method.
+- `AbstractGraphReporter` (R/AbstractGraphReporter.R): Extends AbstractPackageReporter for network-based reporters. Provides `nodes`, `edges`, `network_measures`, and `pkg_graph` active bindings.
+
+**Concrete Reporters:**
+- `DependencyReporter` (R/DependencyReporter.R): Analyzes recursive package dependencies
+- `FunctionReporter` (R/FunctionReporter.R): Maps function call networks and test coverage
+- `InheritanceReporter` (R/InheritanceReporter.R): Traces S4/R5/R6 class inheritance
+
+**Report Generation:**
+- `PackageReport` (R/CreatePackageReport.R): Aggregates multiple reporters and renders HTML via rmarkdown
+- `CreatePackageReport()`: Convenience function that instantiates PackageReport with default reporters
+
+### Graph Models
+
+`DirectedGraph` class (R/GraphClasses.R) wraps igraph functionality and provides:
+- Node and graph measure calculations
+- Network visualization via visNetwork
+- Integration with reporter system
+
+### Key Patterns
+
+1. **Reporter Lifecycle**: Instantiate → `set_package()` → extract nodes/edges → calculate measures → render
+2. **Active Bindings**: Reporters use R6 active bindings for lazy evaluation of `nodes`, `edges`, and `network_measures`
+3. **Namespacing**: All non-base function calls must use `::` namespace operator (e.g., `data.table::data.table()`)
+4. **data.table convention**: data.table objects named with `DT` suffix (e.g., `nodesDT`)
+
+## Commands
+
+### Testing
+
+Run full test suite (builds tarball and runs R CMD check):
+```bash
+./test.sh
+```
+
+This script:
+- Builds package tarball with `R CMD build`
+- Runs `R CMD check --as-cran` in isolated directory
+- Fails if any WARNINGs found
+- Fails if NOTEs exceed allowed count (currently 0)
+
+Run tests interactively in R:
+```R
+# Set to run NOT_CRAN tests
+Sys.setenv(NOT_CRAN = "true")
+
+# Run all tests
+devtools::test()
+
+# Run specific test file
+devtools::test(filter = "FunctionReporter")
+```
+
+### Test Environment
+
+Tests use a temporary package library (`PKGNET_TEST_LIB`) with fake test packages (baseballstats, sartre, milne). Setup/teardown in:
+- `tests/testthat/setup-setTestEnv.R`
+- `tests/testthat/teardown-setTestEnv.R`
+
+On CRAN, only `test-cran-true.R` runs due to complications with temporary package handling.
+
+### Building
+
+```bash
+# Build tarball
+R CMD build .
+
+# Install locally
+R CMD INSTALL pkgnet_*.tar.gz
+
+# Build documentation
+Rscript -e "devtools::document()"
+```
+
+### Coverage
+
+```R
+covr::package_coverage()
+```
+
+## Code Style
+
+### Naming Conventions
+
+- **R6 classes**: UpperCamelCase (e.g., `FunctionReporter`)
+- **Exported functions**: UpperCamelCase (e.g., `CreatePackageReport`)
+- **Methods/fields**: snake_case (e.g., `set_package`, `pkg_name`)
+- **data.table objects**: camelCase ending in `DT` (e.g., `nodesDT`)
+
+### Dependencies
+
+- Always use `::` namespacing for non-base calls
+- Add `#' @importFrom package function` in roxygen docs
+- Exceptions: operators like `%>%` and `:=` don't need namespacing
+- New package dependencies must be added to DESCRIPTION `Imports`
+
+### Indentation
+
+- Use 4 spaces (never tabs)
+- Comma-first style for multi-line lists:
+```r
+sample_list <- list(
+    norm_sample = rnorm(100)
+    , unif_sample = runif(100)
+    , t_sample = rt(100, df = 100)
+)
+```
+
+### Comments
+
+- All comments above code, never beside
+- Avoid comments where code is self-evident
+
+### Roxygen Documentation
+
+**Functions** require:
+- `#' @title`
+- `#' @name`
+- `#' @description`
+- `#' @param` (for each parameter)
+- `#' @export` (if public API)
+
+**R6 Classes** require sections:
+- `#' @section Class Constructor:`
+- `#' @section Public Methods:`
+- `#' @section Public Members:`
+- Document all public methods and active bindings
+
+## R6 Method Support
+
+**FunctionReporter** treats R6 methods as functions with naming convention:
+- Format: `<classname>$<methodtype>$<methodname>`
+- Example: `FunctionReporter$private$extract_nodes`
+- Uses **generator object name** from namespace, not `classname` attribute
+
+**InheritanceReporter** naming:
+- **Reference Classes**: Uses `Class` arg from `setRefClass()`
+- **R6 Classes**: Uses generator object name in namespace (not `classname` arg)
+
+## Known Limitations
+
+1. **FunctionReporter**:
+   - Non-standard evaluation can cause false positives when column names match function names
+   - Functions stored in lists (not namespace) are invisible
+   - Instantiated R6/reference object method calls not recognized
+   - Reference class methods not yet supported
+
+2. **InheritanceReporter**:
+   - S3 classes not supported (no formal class definitions)
+
+## Package Versioning
+
+Follows semantic versioning (MAJOR.MINOR.PATCH):
+- Development versions append `.9999` (e.g., `0.5.0.9999`)
+- Release versions remove `.9999` for CRAN submission
+
+## CI/CD
+
+GitHub Actions workflows:
+- `.github/workflows/ci.yml`: Tests on Ubuntu/macOS with R release
+- `.github/workflows/release.yml`: Tests on R-devel for CRAN submission
+- `.github/workflows/smoke-tests.yaml`: Runs `CreatePackageReport()` on many packages
+- `.github/workflows/website.yaml`: Builds pkgdown site
+
+## Rendering Reports
+
+Reports use rmarkdown templates from `inst/package_report/`:
+- Work done in temp directory to avoid writing to package repo
+- See `PackageReport$render_report()` in R/CreatePackageReport.R:67-98

DESCRIPTION

@@ -18,9 +18,8 @@ Imports:
     covr,
     data.table,
     DT,
-    futile.logger,
     glue,
-    igraph(>= 1.3),
+    igraph,
     knitr,
     magrittr,
     methods,
@@ -38,4 +37,4 @@ Suggests:
 License: BSD_3_clause + file LICENSE
 URL: https://github.com/uptake/pkgnet, https://uptake.github.io/pkgnet/
 BugReports: https://github.com/uptake/pkgnet/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3

NAMESPACE

@@ -26,27 +26,20 @@ importFrom(data.table,copy)
 importFrom(data.table,data.table)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setkeyv)
-importFrom(futile.logger,INFO)
-importFrom(futile.logger,flog.fatal)
-importFrom(futile.logger,flog.info)
-importFrom(futile.logger,flog.threshold)
-importFrom(futile.logger,flog.warn)
-importFrom(futile.logger,logger.options)
 importFrom(glue,glue)
 importFrom(grDevices,colorRamp)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,rgb)
 importFrom(igraph,V)
-importFrom(igraph,authority_score)
 importFrom(igraph,betweenness)
 importFrom(igraph,centr_betw_tmax)
 importFrom(igraph,centr_clo_tmax)
 importFrom(igraph,centr_degree_tmax)
 importFrom(igraph,centralize)
 importFrom(igraph,closeness)
 importFrom(igraph,degree)
-importFrom(igraph,graph.edgelist)
-importFrom(igraph,hub_score)
+importFrom(igraph,graph_from_edgelist)
+importFrom(igraph,hits_scores)
 importFrom(igraph,make_empty_graph)
 importFrom(igraph,neighborhood.size)
 importFrom(igraph,page_rank)

NEWS.md

@@ -5,6 +5,7 @@
 
 ## BUGFIXES
 * Moved `rmarkdown::render` interium files to occur within a temp directory, not the installed package directory (#329 Thanks @jcarbaut!) 
+* Removed `futile.logger` dependency (#338)
 
 # pkgnet 0.5.0
 ## NEW FEATURES

R/AbstractGraphReporter.R

@@ -72,9 +72,9 @@ AbstractGraphReporter <- R6::R6Class(
         #' column acts the identifier. Read-only.
         nodes = function(){
             if (is.null(private$cache$nodes)){
-                private$extract_nodes()
+                invisible(private$extract_nodes())
             }
-            return(private$cache$nodes)
+            invisible(private$cache$nodes)
         },
 
         #' @field edges A data.table, containing information about
@@ -83,9 +83,9 @@ AbstractGraphReporter <- R6::R6Class(
         #' specify the node identifiers. Read-only.
         edges = function(){
             if (is.null(private$cache$edges)) {
-                private$extract_edges()
+                invisible(private$extract_edges())
             }
-            return(private$cache$edges)
+            invisible(private$cache$edges)
         },
 
         #' @field network_measures A list, containing any measures 

R/FunctionReporter.R

@@ -260,7 +260,7 @@ FunctionReporter <- R6::R6Class(
 
             private$cache$nodes <- nodes
 
-            log_info(sprintf('... done extracting functions as nodes.'
+            log_info(sprintf('%s ... done extracting functions as nodes.'
                              , self$pkg_name))
 
             return(invisible(nodes))

R/GraphClasses.R

@@ -13,7 +13,7 @@
 #' @concept Graph Classes
 #' @keywords internal
 #' @importFrom R6 R6Class
-#' @importFrom igraph graph.edgelist make_empty_graph vertex
+#' @importFrom igraph graph_from_edgelist make_empty_graph vertex
 #' @importFrom data.table data.table
 #' @importFrom assertthat assert_that
 AbstractGraph <- R6::R6Class(
@@ -172,7 +172,7 @@ AbstractGraph <- R6::R6Class(
             # Connected graph
             if (nrow(self$edges) > 0) {
                 # A graph with edges
-                connectedGraph <- igraph::graph.edgelist(
+                connectedGraph <- igraph::graph_from_edgelist(
                     as.matrix(self$edges[,list(SOURCE,TARGET)])
                     , directed = directed
                 )
@@ -227,8 +227,8 @@ AbstractGraph <- R6::R6Class(
 #' @concept Graph Classes
 #' @importFrom R6 R6Class
 #' @importFrom igraph degree closeness betweenness
-#' @importFrom igraph page_rank hub_score authority_score
-#' @importFrom igraph neighborhood.size vcount V
+#' @importFrom igraph page_rank hits_scores
+#' @importFrom igraph ego_size vcount V
 #' @importFrom igraph centralize centr_degree_tmax
 #' @importFrom igraph centr_clo_tmax centr_betw_tmax
 #' @seealso DirectedGraphMeasures
@@ -324,7 +324,7 @@ DirectedGraph <- R6::R6Class(
             , numRecursiveDeps = function(self){
                 # Calculate using out-neighborhood size with order of longest
                 # possible path
-                result <- igraph::neighborhood.size(
+                result <- igraph::ego_size(
                     graph = self$igraph
                     , order = igraph::vcount(self$igraph)
                     , mode = "out"
@@ -340,7 +340,7 @@ DirectedGraph <- R6::R6Class(
             , numRecursiveRevDeps = function(self){
                 # Calculate using in-neighborhood size with order of longest
                 # possible path
-                result <- igraph::neighborhood.size(
+                result <- igraph::ego_size(
                     graph = self$igraph
                     , order = igraph::vcount(self$igraph)
                     , mode = "in"
@@ -370,18 +370,18 @@ DirectedGraph <- R6::R6Class(
 
             # Hub Score
             , hubScore = function(self){
-                igraph::hub_score(
+                igraph::hits_scores(
                     graph = self$igraph
                     , scale = TRUE
-                )$vector
+                )$hub
             }
 
             # Authority Score
             , authorityScore = function(self){
-                igraph::authority_score(
+                igraph::hits_scores(
                     graph = self$igraph
                     , scale = TRUE
-                )$vector
+                )$authority
             }
 
         ) #/node_measure_functions
@@ -477,11 +477,11 @@ DirectedGraph <- R6::R6Class(
 #'     [\href{https://en.wikipedia.org/wiki/Closeness_centrality}{Wikipedia}]}
 #'     \item{\bold{\code{numRecursiveDeps}}}{number recursive dependencies, i.e., count of all nodes reachable by following edges
 #'     out from this node.
-#'     Calculated by \code{\link[igraph:neighborhood.size]{igraph::neighborhood.size}}.
+#'     Calculated by \code{\link[igraph:ego_size]{igraph::ego_size}}.
 #'     [\href{https://en.wikipedia.org/wiki/Rooted_graph}{Wikipedia}]}
 #'     \item{\bold{\code{numRecursiveRevDeps}}}{number of recursive reverse dependencies (dependents), i.e., count all nodes reachable by following edges
 #'     into this node in reverse direction.
-#'     Calculated by \code{\link[igraph:neighborhood.size]{igraph::neighborhood.size}}.
+#'     Calculated by \code{\link[igraph:ego_size]{igraph::ego_size}}.
 #'     [\href{https://en.wikipedia.org/wiki/Rooted_graph}{Wikipedia}]}
 #'     \item{\bold{\code{betweenness}}}{betweenness centrality, a measure of
 #'     the number of shortest paths in graph passing through this node