docs(revdep): Add reprexes for bootcluster, checked, htna and SEMdeep

revdep/examples/README.md

@@ -35,6 +35,18 @@ Each issue has two files:
 #### Group F — `tkplot()` defunct (igraph 3.0.0)
 13. **tkplot-defunct-issue** — shared reproducer for Boptbd, c3net, ggm, optbdmaeAT, optrcdmaeAT (all direct callers of `igraph::tkplot()`)
 
+#### Group C (continued) — new in the `revdep2` run 31048405399
+14. **bootcluster-sample-degseq-method-issue** — `sample_degseq(method = "simple.no.multiple")` defunct, same as qgraph/degreenet
+
+#### Group G — Optional arguments passed positionally (deprecated for 3.0.0)
+15. **checked-neighbors-positional-issue** — `neighbors(g, v, "out")` warns; snapshot tests turn 315 warnings into a failure
+
+#### Group H — igraph regressions from the ellipsis move
+16. **htna-tna-empty-argument-issue** — a trailing comma reached the migration handler and errored; **fixed**, kept as the regression reproducer (htna cascades through tna)
+
+#### Group I — Silent result changes, not yet traced
+17. **semdeep-semrun-subscript-issue** — `SEMml(algo = "sem")` → subscript out of bounds inside `SEMgraph::SEMrun()`; unreduced, and the only example here without rendered output (SEMgraph needs Bioconductor packages)
+
 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

revdep/examples/bootcluster-sample-degseq-method-issue.R

@@ -0,0 +1,35 @@
+# bootcluster sample_degseq(method = "simple.no.multiple") defunct
+# Issue: bootcluster:::scheme2.exp() calls
+# igraph::sample_degseq(out.deg = degree.seq, method = "simple.no.multiple"),
+# which now hard-errors because the "simple.no.multiple" method value is
+# defunct. Surfaces as an ERROR in the network.stability() example.
+
+library(igraph)
+
+deg <- rep(2, 10) # any graphical degree sequence
+
+# Old call -- defunct since igraph 2.1.0
+sample_degseq(out.deg = deg, method = "simple.no.multiple")
+
+# Working replacement -- new method name, same sampler
+g <- sample_degseq(out.deg = deg, method = "fast.heur.simple")
+vcount(g)
+ecount(g)
+
+# Root cause:
+# - sample_degseq() had three legacy method values renamed in 2.1.0:
+#   "simple"                     -> "configuration"
+#   "simple.no.multiple"         -> "fast.heur.simple"
+#   "simple.no.multiple.uniform" -> "configuration.simple"
+# - All three advanced from deprecate_warn to deprecate_stop in #2634
+
+# Assessment:
+# - Bug in bootcluster -- pinned to an obsolete method name.
+# - Same root cause as qgraph and degreenet; see
+#   qgraph-sample-degseq-method-issue and degreenet-reedmolloy-issue.
+
+# Recommendation:
+# - For bootcluster: switch to method = "fast.heur.simple" in scheme2.exp().
+#   While there, the same example emits deprecation warnings for clusters(),
+#   induced.subgraph() and fastgreedy.community(); their replacements are
+#   components(), induced_subgraph() and cluster_fast_greedy().

revdep/examples/bootcluster-sample-degseq-method-issue.md

@@ -0,0 +1,54 @@
+# bootcluster `sample_degseq(method = "simple.no.multiple")` defunct
+
+## Issue
+`bootcluster:::scheme2.exp()` calls
+`igraph::sample_degseq(out.deg = degree.seq, method = "simple.no.multiple")`,
+which hard-errors because the `"simple.no.multiple"` method value is defunct as
+of igraph 2.1.0. It surfaces as an ERROR in the `network.stability()` example.
+
+## Reproducible Example
+
+``` r
+library(igraph)
+
+deg <- rep(2, 10) # any graphical degree sequence
+
+# Old call -- defunct since igraph 2.1.0
+sample_degseq(out.deg = deg, method = "simple.no.multiple")
+#> Error:
+#> ! The `method` argument of `sample_degseq()` must be fast.heur.simple
+#>   instead of simple.no.multiple as of igraph 2.1.0.
+
+# Working replacement -- new method name, same sampler
+g <- sample_degseq(out.deg = deg, method = "fast.heur.simple")
+vcount(g)
+#> [1] 10
+ecount(g)
+#> [1] 10
+```
+
+## Root Cause
+`sample_degseq()` had three legacy method values renamed in 2.1.0:
+
+| Old value | New value |
+|---|---|
+| `"simple"` | `"configuration"` |
+| `"simple.no.multiple"` | `"fast.heur.simple"` |
+| `"simple.no.multiple.uniform"` | `"configuration.simple"` |
+
+All three advanced from `deprecate_warn` to `deprecate_stop` in [#2634](https://github.com/igraph/rigraph/pull/2634).
+
+## Assessment
+Bug in bootcluster — pinned to an obsolete method name. Same root cause as
+qgraph and degreenet; see `qgraph-sample-degseq-method-issue` and
+`degreenet-reedmolloy-issue`.
+
+## Recommendation
+**For bootcluster**: switch to `method = "fast.heur.simple"` in
+`scheme2.exp()`. The same example also emits deprecation warnings for
+`clusters()`, `induced.subgraph()` and `fastgreedy.community()`; their
+replacements are `components()`, `induced_subgraph()` and
+`cluster_fast_greedy()`.
+
+CRAN has no URL or BugReports field for bootcluster, so this one goes to the
+maintainer by email: Tianmou Liu &lt;tianmouliu@outlook.com&gt;.

revdep/examples/checked-neighbors-positional-issue.R

@@ -0,0 +1,33 @@
+# checked neighbors(graph, v, mode) positional deprecation
+# Issue: checked:::deduplicate_task_graph() calls
+# igraph::neighbors(g, i, "out"), passing `mode` positionally. Since the
+# optional arguments moved behind `...`, that call is soft-deprecated and
+# warns. checked's tests are snapshot tests, so 315 warnings turn into a
+# test failure -- the package itself still works.
+
+library(igraph)
+
+g <- make_ring(4, directed = TRUE)
+
+# Old call -- soft-deprecated for 3.0.0, warns under testthat
+neighbors(g, 1, "out")
+
+# Working replacement -- name the argument
+neighbors(g, 1, mode = "out")
+
+# Root cause:
+# - neighbors() is now neighbors(graph, v, ..., mode = ...); everything after
+#   `...` has to be named. The generated argument handler recovers the old
+#   positional call and warns through lifecycle::deprecate_soft().
+# - deprecate_soft() is quiet in ordinary use and loud where it matters for a
+#   maintainer: under testthat, and in code run directly at the prompt. That
+#   is why this surfaces as a test failure rather than a user-visible warning.
+
+# Assessment:
+# - Not a bug in checked -- the call is correct today and deprecated for
+#   3.0.0. It is a one-word fix that also silences the warning for their users.
+
+# Recommendation:
+# - For checked: `neighbors(g, i, mode = "out")` in deduplicate_task_graph().
+#   The same rule applies to any other igraph call passing an optional
+#   argument positionally.

revdep/examples/checked-neighbors-positional-issue.md

@@ -0,0 +1,52 @@
+# checked `neighbors(graph, v, mode)` positional deprecation
+
+## Issue
+`checked:::deduplicate_task_graph()` calls `igraph::neighbors(g, i, "out")`,
+passing `mode` positionally. Since the optional arguments moved behind `...`,
+that call is soft-deprecated and warns. checked's tests are snapshot tests, so
+315 warnings turn into `[ FAIL 1 | WARN 315 | SKIP 0 | PASS 171 ]` — the
+package itself still works.
+
+## Reproducible Example
+
+``` r
+library(igraph)
+
+g <- make_ring(4, directed = TRUE)
+
+# Old call -- soft-deprecated for 3.0.0, warns under testthat
+neighbors(g, 1, "out")
+#> Warning: Calling `neighbors()` with positional or abbreviated arguments was deprecated
+#> in igraph 3.0.0.
+#> ℹ Detected call: neighbors(graph, v, mode)
+#> ℹ Use instead: neighbors(graph, v, mode = )
+#> This warning is displayed once per session.
+#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+#> generated.
+#> ── <vertex sequence> 1/4 · from b36f274 ────────────────────────────────────────
+#> [1] 2
+
+# Working replacement -- name the argument
+neighbors(g, 1, mode = "out")
+#> ── <vertex sequence> 1/4 · from b36f274 ────────────────────────────────────────
+#> [1] 2
+```
+
+## Root Cause
+`neighbors()` is now `neighbors(graph, v, ..., mode = ...)`: everything after
+`...` has to be named. The generated argument handler recovers the old
+positional call and warns through `lifecycle::deprecate_soft()`, which is quiet
+in ordinary use and loud exactly where a maintainer will see it — under
+testthat, and at the prompt. That is why this surfaces as a test failure rather
+than as a user-visible warning.
+
+## Assessment
+Not a bug in checked: the call is correct today and deprecated for 3.0.0. It is
+a one-word fix that also silences the warning for their users ahead of time.
+
+## Recommendation
+**For checked**: `neighbors(g, i, mode = "out")` in
+`deduplicate_task_graph()`. The same rule applies to any other igraph call that
+passes an optional argument positionally.
+
+File at <https://github.com/Genentech/checked/issues>.

revdep/examples/htna-tna-empty-argument-issue.R

@@ -0,0 +1,41 @@
+# htna: empty argument in `...` -- igraph regression, already fixed
+# Issue: htna's tests call tna::estimate_cs(), which reaches
+# tna:::as.igraph.matrix() -> igraph::graph_from_adjacency_matrix(). That call
+# ends in a trailing comma, so an empty argument lands in `...`. In the
+# ellipsis-move refactoring that reached migrate_recover_args() and errored
+# with "argument is missing, with no default".
+#
+# This is an igraph bug, not an htna or tna one, and the current development
+# version handles it -- the script below runs clean. It is kept as the
+# regression reproducer.
+
+library(igraph)
+
+m <- matrix(c(0, 1, 1, 0), 2, dimnames = list(c("a", "b"), c("a", "b")))
+
+# tna:::as.igraph.matrix(), reduced -- note the trailing comma
+tna_shape <- function(x, mode = "directed", ...) {
+  igraph::graph_from_adjacency_matrix(
+    adjmatrix = x,
+    mode = mode,
+    weighted = TRUE,
+  )
+}
+tna_shape(m)
+
+# The other form from the same class of failure: a skipped positional slot
+graph_from_data_frame(data.frame(from = "a", to = "b"), , directed = FALSE)
+
+# Root cause:
+# - Moving the optional arguments behind `...` made every call with an empty
+#   argument reach the migration handler, where forcing dots[[k]] errored.
+# - Fixed by skipping missing dots; both forms above now work.
+
+# Assessment:
+# - Ours, not theirs. Same root cause as tna, lagdynamics, modelbpp and
+#   NetSci in #2646, all tagged [IGRAPH BUG].
+
+# Recommendation:
+# - Nothing to send upstream. Re-check htna and tna against the current dev
+#   version to confirm they are green again; a trailing comma is legal R and
+#   igraph has to accept it.

revdep/examples/htna-tna-empty-argument-issue.md

@@ -0,0 +1,67 @@
+# htna — empty argument in `...` (igraph regression, fixed)
+
+## Issue
+htna's tests call `tna::estimate_cs()`, which reaches
+`tna:::as.igraph.matrix()` → `igraph::graph_from_adjacency_matrix()`. That call
+ends in a trailing comma, so an empty argument lands in `...`. During the
+ellipsis-move refactoring it reached `migrate_recover_args()` and errored with
+`argument is missing, with no default`.
+
+**This is an igraph bug, not an htna or tna one, and it is already fixed** —
+the example below runs clean on igraph 2.3.3.9029. It is kept as the regression
+reproducer.
+
+## Reproducible Example
+
+``` r
+library(igraph)
+
+m <- matrix(c(0, 1, 1, 0), 2, dimnames = list(c("a", "b"), c("a", "b")))
+
+# tna:::as.igraph.matrix(), reduced -- note the trailing comma
+tna_shape <- function(x, mode = "directed", ...) {
+  igraph::graph_from_adjacency_matrix(
+    adjmatrix = x,
+    mode = mode,
+    weighted = TRUE,
+  )
+}
+tna_shape(m)
+#> ── <igraph> ───────────────────────────────────────────────────────── cb5ccda ──
+#> ℹ directed · named · weighted
+#> ℹ 2 vertices · 2 edges
+#> 
+#> ── Attributes ──────────────────────────────────────────────────────────────────
+#> → vertex: name <chr>
+#> → edge:   weight <dbl>
+#> 
+#> ── Edges (vertex names) ────────────────────────────────────────────────────────
+#> [1] a → b  b → a
+
+# The other form from the same class of failure: a skipped positional slot
+graph_from_data_frame(data.frame(from = "a", to = "b"), , directed = FALSE)
+#> ── <igraph> ───────────────────────────────────────────────────────── d5e4d69 ──
+#> ℹ undirected · named
+#> ℹ 2 vertices · 1 edges
+#> 
+#> ── Attributes ──────────────────────────────────────────────────────────────────
+#> → vertex: name <chr>
+#> 
+#> ── Edges (vertex names) ────────────────────────────────────────────────────────
+#> [1] a ─ b
+```
+
+## Root Cause
+Moving the optional arguments behind `...` made every call carrying an empty
+argument reach the migration handler, where forcing `dots[[k]]` errored. The
+handler now skips missing dots, and both forms above work again.
+
+## Assessment
+Ours, not theirs. Same root cause as tna, lagdynamics, modelbpp and NetSci in
+[#2646](https://github.com/igraph/rigraph/issues/2646), all tagged
+`[IGRAPH BUG]`.
+
+## Recommendation
+Nothing to send upstream. Re-check htna and tna against the current development
+version to confirm they are green again — a trailing comma is legal R and
+igraph has to accept it.

revdep/examples/semdeep-semrun-subscript-issue.R

@@ -0,0 +1,54 @@
+# SEMdeep SEMml(algo = "sem") -- subscript out of bounds [NEEDS TRIAGE]
+# Issue: the SEMml() example fails at the algo = "sem" step with
+#   Error in x[, ii] : subscript out of bounds
+#   Calls: SEMml ... model.frame.default -> na.omit -> na.omit.data.frame
+# The failing call is SEMgraph::SEMrun(dag, data, algo = "cggm"); no igraph
+# function is on the backtrace, so this is a silent change in what igraph
+# returns rather than a lifecycle error.
+#
+# Unlike the other examples here this one is NOT reduced to an igraph call
+# yet -- it needs SEMgraph (and therefore Bioconductor's graph/Rgraphviz),
+# which is why the .md beside it carries the check log rather than reprex
+# output.
+
+library(SEMgraph)
+library(igraph)
+
+# SEMml()'s own preprocessing, up to the call that fails
+ig <- alsData$graph
+data <- transformData(alsData$exprs)$data
+
+nodes <- colnames(data)[colnames(data) %in% V(ig)$name]
+graph <- induced_subgraph(ig, vids = which(V(ig)$name %in% nodes))
+dag <- graph2dag(graph, data, bap = FALSE)
+data <- data[, V(dag)$name]
+
+# SEMdeep::SEMml(..., algo = "sem") does exactly this:
+fit <- SEMrun(dag, data = data, algo = "cggm")
+
+# Or, from the package itself:
+# set.seed(123)
+# train <- sample(1:nrow(data), 0.5 * nrow(data))
+# SEMml(alsData$graph, data[train, ], algo = "sem")
+
+# Triage notes -- what to compare between CRAN igraph and the dev version,
+# since the error is a column subscript running past the end of a data frame:
+#   vcount(dag); ecount(dag)
+#   V(dag)$name                      # names and their order
+#   setdiff(V(dag)$name, colnames(data))
+#   igraph::degree(dag, mode = "in") # SEMml() splits Vx/Vy on this
+#   is_dag(dag)
+# A graph2dag() that now drops, renames or reorders vertices would produce
+# exactly this failure downstream.
+
+# Assessment:
+# - Not yet traced to a specific igraph change. It is the same shape as
+#   SEMgraph's own open item in #2646 (subscript out of bounds in
+#   buildLevels()), and SEMdeep Depends on SEMgraph, so one cause may explain
+#   both.
+
+# Recommendation:
+# - Bisect against the ellipsis-move PRs (#2757-#2778, #2784) before
+#   contacting the maintainer: the shape of the failure -- a silently
+#   different result with no warning -- is what a positional argument no
+#   longer binding where it used to looks like.