updated revdep issues

revdep/examples/README.md

@@ -1,53 +1,81 @@
 # Reverse Dependency Problem Examples
 
-This directory contains minimal reproducible examples for packages that have newly broken checks compared to the most recent CRAN version of igraph.
+This directory contains minimal reproducible examples for packages flagged as newly broken in the latest `revdepcheck` run against the development version of igraph. See [`../problems-analysis.md`](../problems-analysis.md) for the corresponding analysis and recommended fixes.
 
 ## Files
 
 Each issue has two files:
-- `*.R` - Runnable R script with the minimal example
-- `*.md` - Markdown documentation with example output (reprex-style)
+- `*.R` — runnable R script with the minimal reproduction
+- `*.md` — markdown documentation with reprex-style output
 
 ### Issues
 
-1. **cascade-circulant-issue** - Namespace collision between `igraph::circulant` and `magic::circulant`
-2. **diagrammer-neighbors-issue** - `neighbors()` now requires exactly one vertex
-3. **jewel-integer-issue** - Strict integer validation in `rewire_impl()`
-4. **manynet-scalar-issue** - Scalar integer validation in `sample_last_cit()`
-5. **rspectral-modularity-issue** - Automatic weight usage in modularity calculations
-6. **sfnetworks-from-issue** - `from` parameter must specify exactly one vertex
+#### Group A — `bfs/dfs(father = )` argument defunct (igraph 2.2.0)
+1. **tidygraph-bfs-father-issue** — `bfs(father = )` defunct (root of the dci/ggraph/scistreer cascade)
+2. **nat-dfs-father-issue** — `dfs(father = )` defunct (direct caller)
+
+#### Group B — Defunct top-level functions
+3. **comato-layout-spring-issue** — `layout.spring()` defunct
+4. **ecol-hub-score-issue** — `hub.score()` defunct
+5. **vkr-get-edge-missing-issue** — `igraph::get.edge` removed
+
+#### Group C — Defunct argument values / behaviors on retained functions
+6. **cranly-eigen-centrality-scale-issue** — `eigen_centrality(scale = FALSE)` defunct
+7. **qgraph-sample-degseq-method-issue** — `sample_degseq(method = "simple.no.multiple")` defunct
+8. **goodfitsbm-get-edge-ids-issue** — `get_edge_ids(vp = <2xn matrix>)` orientation defunct
+
+#### Group D — Deprecation warnings surfacing as NOTE/WARNING
+9. **frf2-deprecation-warnings-issue** — multiple deprecation warnings → NOTE
+10. **r6causal-attribute-deprecations-issue** — install-time attribute getter/setter warnings
+11. **migraph-create-ring-width-issue** — `create_ring(width = )` deprecation warning → test failure
+
+#### Group E — Indirect path through a defunct fallback
+12. **degreenet-reedmolloy-issue** — defunct `sample_degseq(method = "simple.no.multiple")` fallback inside `reedmolloy()`'s retry loop
+
+Three packages from the failure set (dci, ggraph, scistreer) are pure cascades through tidygraph and have no separate reproducer — see `tidygraph-bfs-father-issue` for the root cause.
 
 ## Running the Examples
 
 Each R script can be run with:
 
 ```r
-source("revdep/examples/cascade-circulant-issue.R")
+source("revdep/examples/tidygraph-bfs-father-issue.R")
 ```
 
 Or from the command line:
 
 ```bash
-Rscript revdep/examples/cascade-circulant-issue.R
+Rscript revdep/examples/tidygraph-bfs-father-issue.R
 ```
 
+The scripts are designed to be run against the **development version** of igraph (the version produced by `R CMD INSTALL .` from the repo root). Against the CRAN release of igraph many of them will not yet hard-error — they will only emit deprecation warnings.
+
 ## Format
 
 The examples follow a simplified format:
-- No `cat()` statements for output (comments instead)
-- No `tryCatch()` blocks (commented out error cases)
+- No `cat()` statements for output (use comments instead)
+- No `tryCatch()` blocks (commented-out error cases)
 - Clean, runnable code that can be used with `reprex::reprex()`
 - Corresponding `.md` files show the expected output
 
 ## Summary of Issues
 
 | Package | Issue | Severity | Type |
-|---------|-------|----------|------|
-| Cascade | Namespace collision warning | Low | Inadvertent behavior change |
-| DiagrammeR | `neighbors()` requires single vertex | High | API tightening |
-| jewel | Integer validation error | High | Uncovered downstream bug |
-| manynet | Scalar integer validation | High | API tightening |
-| rSpectral | Modularity test failures | Medium | Behavior change with workaround |
-| sfnetworks | `from` requires single vertex | High | API tightening |
-
-See `../problems-analysis.md` for detailed analysis and recommendations.
+|---|---|---|---|
+| tidygraph | `bfs(father=)` defunct | High | API rename (root of cascade) |
+| nat | `dfs(father=)` defunct | High | API rename |
+| dci | Cascades through tidygraph | High | Cascading |
+| ggraph | Cascades through tidygraph | High | Cascading |
+| scistreer | Cascades through tidygraph | High | Cascading |
+| comato | `layout.spring()` defunct | High | Defunct function |
+| ECoL | `hub.score()` defunct | High | Defunct function |
+| vkR | `get.edge` removed | Medium | Removed function |
+| cranly | `eigen_centrality(scale=)` defunct | High | Defunct argument value |
+| qgraph | `sample_degseq(method=)` value defunct | High | Defunct argument value |
+| GoodFitSBM | `get_edge_ids()` matrix orientation defunct | High | Defunct call form |
+| FrF2 | Deprecation warnings → NOTE | Low | Pre-emptive rename needed |
+| R6causal | Install-time deprecation warnings | Medium | Pre-emptive rename needed |
+| migraph | `create_ring(width=)` warning → test failure | Low | Deprecated argument |
+| degreenet | Defunct fallback `sample_degseq(method=)` value | High | Defunct argument value (indirect) |
+
+See [`../problems-analysis.md`](../problems-analysis.md) for detailed analysis and recommendations.

revdep/examples/comato-layout-spring-issue.R

@@ -0,0 +1,31 @@
+# comato layout.spring() defunct
+# Issue: comato:::plot.conceptmaps() passes layout = "spring", which dispatches
+# to igraph::layout.spring() -- defunct since igraph 2.1.0.
+
+library(igraph)
+
+g <- make_ring(10)
+
+# Old call -- now defunct in igraph 2.1.0
+# layout.spring(g)
+# Error:
+# ! `layout.spring()` was deprecated in igraph 2.1.0 and is now defunct.
+# i Please use `layout_with_fr()` instead.
+
+# Working replacement
+coords <- layout_with_fr(g)
+dim(coords)
+
+# Root cause:
+# - layout.spring(), layout.svd(), and layout.fruchterman.reingold.grid()
+#   all advanced from deprecated to defunct in #2634
+# - comato hardcodes layout = "spring" in plot.conceptmaps()
+
+# Assessment:
+# - Bug in comato -- references a layout function deprecated since 2.1.0
+
+# Recommendation:
+# - For comato: switch layout = "spring" to the Fruchterman-Reingold layout,
+#   either by passing layout = layout_with_fr or by computing coordinates
+#   beforehand. Also rename graph.union() -> union() to silence the
+#   remaining deprecation warning.

revdep/examples/comato-layout-spring-issue.md

@@ -0,0 +1,30 @@
+# comato layout.spring() defunct
+
+## Issue
+`comato:::plot.conceptmaps()` passes `layout = "spring"`, which dispatches to `igraph::layout.spring()` — defunct since igraph 2.1.0. The package also still calls `graph.union()` (currently deprecated but slated to become defunct).
+
+## Reproducible Example
+
+```r
+library(igraph)
+
+g <- make_ring(10)
+
+# Old call -- now defunct
+layout.spring(g)
+#> Error:
+#> ! `layout.spring()` was deprecated in igraph 2.1.0 and is now defunct.
+#> i Please use `layout_with_fr()` instead.
+
+# Working replacement
+coords <- layout_with_fr(g)
+```
+
+## Root Cause
+`layout.spring()`, `layout.svd()`, and `layout.fruchterman.reingold.grid()` all advanced from deprecated to defunct in [#2634](https://github.com/igraph/rigraph/pull/2634). comato hardcodes `layout = "spring"`.
+
+## Assessment
+Bug in comato — references a layout function deprecated since igraph 2.1.0.
+
+## Recommendation
+**For comato**: switch `layout = "spring"` to a Fruchterman–Reingold layout (e.g. `layout = layout_with_fr` or precompute coordinates). Also rename `graph.union()` → `union()` to silence the remaining deprecation warning.

revdep/examples/cranly-eigen-centrality-scale-issue.R

@@ -0,0 +1,33 @@
+# cranly eigen_centrality(scale = ) defunct
+# Issue: cranly:::summary.cranly_network() calls
+# igraph::eigen_centrality(cranly_graph, scale = FALSE), defunct since 2.1.1.
+
+library(igraph)
+
+g <- sample_gnp(20, 0.3)
+
+# Old call -- now defunct in igraph 2.1.1
+# eigen_centrality(g, scale = FALSE)
+# Error:
+# ! The `scale` argument of `eigen_centrality()` always as if TRUE as of
+#   igraph 2.1.1.
+# i Normalization is always performed
+
+# Working replacement
+res <- eigen_centrality(g)
+str(res$vector)
+
+# If raw (un-normalized) values are needed, rescale manually after the call
+# (e.g. multiply by some reference value)
+
+# Root cause:
+# - eigen_centrality(scale = ) was deprecated in 2.1.1 (#1543); normalization
+#   is now mandatory
+# - Advanced from deprecate_warn to deprecate_stop in #2634
+
+# Assessment:
+# - Bug in cranly -- relies on an argument whose effect has been removed
+
+# Recommendation:
+# - For cranly: drop the `scale = FALSE` argument. If un-normalized values
+#   are genuinely needed downstream, scale them manually afterwards.

revdep/examples/cranly-eigen-centrality-scale-issue.md

@@ -0,0 +1,31 @@
+# cranly eigen_centrality(scale = ) defunct
+
+## Issue
+`cranly:::summary.cranly_network()` calls `igraph::eigen_centrality(cranly_graph, scale = FALSE)`. Defunct since igraph 2.1.1. Breaks the `cranly.Rmd` vignette re-build.
+
+## Reproducible Example
+
+```r
+library(igraph)
+
+g <- sample_gnp(20, 0.3)
+
+eigen_centrality(g, scale = FALSE)
+#> Error:
+#> ! The `scale` argument of `eigen_centrality()` always as if TRUE as of
+#>   igraph 2.1.1.
+#> i Normalization is always performed
+
+# Working replacement
+res <- eigen_centrality(g)
+res$vector
+```
+
+## Root Cause
+`eigen_centrality(scale = )` was deprecated in igraph 2.1.1 ([#1543](https://github.com/igraph/rigraph/pull/1543)); normalization is now mandatory. Advanced from `deprecate_warn` to `deprecate_stop` in [#2634](https://github.com/igraph/rigraph/pull/2634).
+
+## Assessment
+Bug in cranly — relies on an argument whose effect has been removed.
+
+## Recommendation
+**For cranly**: drop the `scale = FALSE` argument. If un-normalized values are needed downstream, rescale manually afterwards.

revdep/examples/degreenet-reedmolloy-issue.R

@@ -0,0 +1,49 @@
+# degreenet reedmolloy() fails through a defunct fallback method
+# Issue: reedmolloy() retries via igraph::degree.sequence.game(method =
+# "simple.no.multiple") whenever its first attempt with method = "vl" fails.
+# That fallback value is defunct in dev igraph, so the retry loop never
+# succeeds and reedmolloy reports its own error.
+
+library(degreenet)
+library(igraph)
+
+set.seed(2)
+s4 <- simpln(n = 100, v = c(-1, 1))
+table(s4)
+#>  1  2  3  4  5  6
+#> 65 18  7  4  4  2
+
+# Step 1: confirm the VL call deterministically fails on this sequence (this
+# is NOT a regression -- VL only produces connected graphs, and s4's 65
+# degree-1 vertices preclude a connected configuration in practice).
+# Verified against CRAN igraph 2.3.1: 50/50 VL attempts errored.
+res_vl <- try(sample_degseq(s4, method = "vl"), silent = TRUE)
+cat("VL succeeded:", !inherits(res_vl, "try-error"), "\n")
+
+# Step 2: the fallback path -- works on CRAN 2.3.1 (with a deprecation
+# warning), but hard-errors on dev igraph.
+# sample_degseq(s4, method = "simple.no.multiple")
+# Error on dev:
+# ! The `method` argument of `sample_degseq()` must be fast.heur.simple
+#   instead of simple.no.multiple as of igraph 2.1.0.
+
+# Step 3: proper replacement -- works on every igraph 2.x version.
+g_new <- sample_degseq(s4, method = "fast.heur.simple")
+vcount(g_new); ecount(g_new)
+
+# Putting it together: reedmolloy(s4) succeeds on CRAN 2.3.1 because the
+# fallback path produces a (warned) graph; it fails on dev igraph because
+# the fallback is now defunct and .catchToList() converts the error into a
+# retry, exhausting maxit and triggering reedmolloy's own error message.
+
+# Root cause:
+# - The lifecycle promotion of sample_degseq(method = "simple.no.multiple")
+#   from deprecate_warn to deprecate_stop in #2634.
+
+# Assessment:
+# - Bug in degreenet -- depends on the obsolete fallback method name.
+
+# Recommendation:
+# - For degreenet: replace the fallback method with "fast.heur.simple".
+#   Also rename degree.sequence.game() -> sample_degseq() and
+#   get.edgelist() -> as_edgelist().