revdeps

[maelle]

https://win-builder.r-project.org/incoming_pretest/igraph_2.1.0_20240929_085818/reverseDependencies/summary.txt

Will add one comment per non as.undirected() problem.

[maelle]

Package: CePa Check: Rd cross-references New result: WARNING Missing link or links in Rd file 'cepa.Rd': ‘[igraph:igraph_test]{igraphtest}’

Missing link or links in Rd file 'cepa.ora.Rd': ‘[igraph:igraph_test]{igraphtest}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

I did remove that function in https://github.com/igraph/rigraph/pull/1501 but I can't understand why that package used it?

https://github.com/cran/CePa/blob/09e893dbc471c8fd4768857c6561515b31d876f3/R/ora_extension.R#L162

https://github.com/jokergoo/CePa/issues/3

[maelle]

All those errors related to as.undirected() show it'll be a long time before we can remove it (in favor of as_undirected())

[maelle]

Package: linkprediction
Check: tests
New result: ERROR
    Running ‘testthat.R’ [4s/4s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(linkprediction)
    > 
    > test_check("linkprediction")
    [ FAIL 2 | WARN 11 | SKIP 0 | PASS 58 ]

    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_proxfun.R:51:7'): Checking calculating 'jaccard' ───────────────
    Error in `score[v1, v2]`: incorrect number of dimensions
    Backtrace:
        ▆
     1. ├─testthat::expect_is(...) at test_proxfun.R:51:7
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─linkprediction::proxfun(g, method = m, value = "matrix")
     5. └─linkprediction:::proxfun.igraph(g, method = m, value = "matrix")
     6.   ├─base::do.call(method, list(graph = graph, v1 = v1, v2 = v2, ...))
     7.   └─linkprediction:::similarity_jaccard(...)
    ── Error ('test_proxfun.R:51:7'): Checking calculating 'sor' ───────────────────
    Error in `score[v1, v2]`: incorrect number of dimensions
    Backtrace:
        ▆
     1. ├─testthat::expect_is(...) at test_proxfun.R:51:7
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─linkprediction::proxfun(g, method = m, value = "matrix")
     5. └─linkprediction:::proxfun.igraph(g, method = m, value = "matrix")
     6.   ├─base::do.call(method, list(graph = graph, v1 = v1, v2 = v2, ...))
     7.   └─linkprediction:::similarity_sor(...)

    [ FAIL 2 | WARN 11 | SKIP 0 | PASS 58 ]
    Error: Test failures
    Execution halted

I'll look into this

[maelle]

Package: MetaNet
Check: examples
New result: ERROR
  Running examples in ‘MetaNet-Ex.R’ failed
  The error most likely occurred in:

  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: anno_vertex
  > ### Title: Use data.frame to annotate vertexes of metanet
  > ### Aliases: anno_vertex anno_node
  > 
  > ### ** Examples
  > 
  > data("c_net")
  > data("otutab", package = "pcutils")
  > anno_vertex(co_net, taxonomy)
  7 attributes will be overwrited:
  Kingdom, Phylum, Class, Order, Family, Genus, Species

  =================================== metanet ==================================== 
  IGRAPH 74bfffd UNW- 451 740 -- 
  + attr: n_type (g/c), name (v/c), v_group (v/c), v_class (v/c), size
  | (v/n), label (v/c), shape (v/c), color (v/c), Abundance (v/n),
  | Kingdom (v/c), Phylum (v/c), Class (v/c), Order (v/c), Family (v/c),
  | Genus (v/c), Species (v/c), id (e/n), from (e/c), to (e/c), weight
  | (e/n), cor (e/n), p.value (e/n), e_type (e/c), width (e/n),
  | v_group_from (e/c), v_group_to (e/c), e_class (e/c), color (e/c), lty
  | (e/n)
  + edges from 74bfffd (vertex names):
  Error in `FUN()`:
  ! `data` must be uniquely named but has duplicate columns
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─MetaNet:::print.metanet(x)
    3. │ └─igraph::print.igraph(x)
    4. │   └─igraph:::.print.edges.compressed(...)
    5. │     └─igraph:::.print.edges.compressed.limit(x, edges, names, max.lines)
    6. │       └─igraph::head_print(fun, max_lines = max.lines)
    7. │         └─igraph:::head_print_callback(...)
    8. │           └─igraph (local) x("width", no = can_max)
    9. │             ├─igraph::ends(x, edges[seq_len(no)], names = names)
   10. │             │ ├─igraph:::as_igraph_es(graph, na.omit(es))
   11. │             │ └─stats::na.omit(es)
   12. │             ├─edges[seq_len(no)]
   13. │             └─igraph:::`[.igraph.es`(edges, seq_len(no))
   14. │               └─base::lapply(...)
   15. │                 └─rlang (local) FUN(X[[i]], ...)
   16. └─rlang::abort(message = message)
  Execution halted

[maelle]

simcausal https://github.com/osofr/simcausal/pull/22#issuecomment-2396115962

[maelle]

skynet https://github.com/ropensci/skynet/pull/11#issuecomment-2396126932

[maelle]

https://github.com/recon-icm/linkprediction/pull/37

[maelle]

the error in linkprediction must have come from the similarity functions

[maelle]

ooooh there's an error in igraph PR coming right now! I put the deprecation after the return :woman_facepalming:

[maelle]

https://github.com/igraph/rigraph/pull/1549