revdeps

[maelle]

revdeps

[maelle]

thomasp85/tidygraph#198

[maelle]

thomasp85/tidygraph#199

I get no failure for tidygraph with the current igraph version @krlmlr

[maelle]

ropensci/skynet#11

[maelle]

osofr/simcausal#22

[maelle]

rcmfs also uses from() instead of .from() but I could not locate the package source so we'll have to email the maintainer.

[maelle]

netropy error.

Error in igraph::distances(g) : 
  At vendor/cigraph/src/paths/dijkstra.c:128 : Weights must not contain NaN values. Invalid value
Backtrace:
  1. netropy::assoc_graph(df.att.ed, 0.15)
  2. ggraph::ggraph(ag, layout = "stress")
       at netropy/R/assoc_graph.R:45:3
  5. ggraph:::create_layout.default(graph, layout, ...)
  7. ggraph:::create_layout.tbl_graph(graph, layout, ...)
  9. ggraph:::layout_to_table.character(...)
 10. ggraph (local) layout_fun(graph, circular = circular, ...)
 11. graphlayouts::layout_with_stress(...)
 12. graphlayouts:::.layout_with_stress_dim(...)
 13. igraph::distances(g)

[maelle]

in netropy

structure(list(7, FALSE, c(1, 2, 3, 4, 5, 6, 2, 3, 4, 5, 6, 3, 
4, 5, 6, 4, 5, 6, 5, 6, 6), c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 
2, 2, 2, 2, 3, 3, 3, 4, 4, 5), NULL, NULL, NULL, NULL, list(c(1, 
0, 1), structure(list(), names = character(0)), list(name = c("status", 
"gender", "office", "years", "age", "practice", "lawschool")), 
    list(weight = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, 
    NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, 
    NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, 
    NA_real_, NA_real_, NA_real_, NA_real_))), <environment>), class = "igraph")

Error in igraph::distances(g) : 
  At vendor/cigraph/src/paths/dijkstra.c:128 : Weights must not contain NaN values. Invalid value
Backtrace:
  1. netropy::assoc_graph(df.att.ed, 0.15)
  2. ggraph::ggraph(ag, layout = "stress")
       at netropy/R/assoc_graph.R:45:3
  5. ggraph:::create_layout.default(graph, layout, ...)
  7. ggraph:::create_layout.tbl_graph(graph, layout, ...)
  9. ggraph:::layout_to_table.character(...)
 10. ggraph (local) layout_fun(graph, circular = circular, ...)
 11. graphlayouts::layout_with_stress(...)
 12. graphlayouts:::.layout_with_stress_dim(...)
 13. igraph::distances(g)

The error is somewhere in ggraph/graphlayouts. I don't understand when we changed what distances() accepts as input. Or did we change graph_from_adjacency_matrix() somehow? It's that call that creates the NA weights.

[maelle]

Reg BCT, I do not know where the package source is. I think #1431 will fix the problem on our side.

I however note that BCT should update its usage of igraph:

https://github.com/cran/BCT/blob/23e22470683b417c6da33cd3c55ab2c29d8670cf/R/process_bct.R#L46

should use make_lattice(), for instance.

[maelle]

https://github.com/termehs/netropy

library(netropy)
df.att <- lawdata[[4]]

df.att.ed <- data.frame(
  status = df.att$status,
  gender = df.att$gender,
  office = df.att$office - 1,
  years = ifelse(df.att$years <= 3, 0,
    ifelse(df.att$years <= 13, 1, 2)
  ),
  age = ifelse(df.att$age <= 35, 0,
    ifelse(df.att$age <= 45, 1, 2)
  ),
  practice = df.att$practice,
  lawschool = df.att$lawschool - 1
)

assoc_graph(df.att.ed, 0.15)
#> Error in igraph::distances(g): At vendor/cigraph/src/paths/dijkstra.c:128 : Weights must not contain NaN values. Invalid value

^{Created on 2024-07-18 with reprex v2.1.0}

[krlmlr]

BCT still shows failures, unfortunately.

[maelle]

Reg BCT

s <- c("2", "11", "00", "10", "12", "011", "020", "021", "012", "022", 
"0100", "0102", "0101") 
init_g=igraph::graph.empty(n=1)
#> Warning: `graph.empty()` was deprecated in igraph 2.0.4.
#> ℹ Please use `make_empty_graph()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
  igraph::V(init_g)$name=""
   g = init_g
     for(word in c(s)){
    # turns "10100" into c("1","10","101","1010", 10100")
    subwords = stringr::str_sub(word, 1, 1:nchar(word))
    # make a graph long enough to hold all those sub-words + start node
    subg = igraph::graph.lattice(length(subwords)+1,directed=TRUE)
    # set vertex nodes to start node plus sub-words
    igraph::V(subg)$name=c("",subwords)
    # merge *by name* into the existing graph
    g = igraph::graph.union(g, subg)
  }
#> Warning: `graph.lattice()` was deprecated in igraph 2.0.4.
#> ℹ Please use `make_lattice()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: `graph.union()` was deprecated in igraph 2.0.0.
#> ℹ Please use `union.igraph()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Error in getval(w, name): argument "newval" is missing, with no default

^{Created on 2024-07-19 with reprex v2.1.0}

Backtrace:
 1. igraph::graph.union(g, subg)
 2. igraph:::union.igraph(byname = byname, ...)
      at rigraph/R/operators.R:29:3
 3. igraph:::.igraph.graph.union.or.intersection(...)
      at rigraph/R/operators.R:448:3
 4. igraph:::rename.attr.if.needed("g", newgraphs)
      at rigraph/R/operators.R:320:5
 5. igraph (local) getval(w, name)
      at rigraph/R/operators.R:151:7

[maelle]

Replacing graph.lattice() with make_lattice() makes the error disappear!

s <- c("2", "11", "00", "10", "12", "011", "020", "021", "012", "022", 
"0100", "0102", "0101") 
init_g=igraph::graph.empty(n=1)
#> Warning: `graph.empty()` was deprecated in igraph 2.0.4.
#> ℹ Please use `make_empty_graph()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
  igraph::V(init_g)$name=""
   g = init_g
     for(word in c(s)){
    # turns "10100" into c("1","10","101","1010", 10100")
    subwords = stringr::str_sub(word, 1, 1:nchar(word))
    # make a graph long enough to hold all those sub-words + start node
    subg = igraph::make_lattice(length(subwords)+1,directed=TRUE)
    # set vertex nodes to start node plus sub-words
    igraph::V(subg)$name=c("",subwords)
    # merge *by name* into the existing graph
    g = igraph::graph.union(g, subg)
  }
#> Warning: `graph.union()` was deprecated in igraph 2.0.0.
#> ℹ Please use `union.igraph()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.

^{Created on 2024-07-19 with reprex v2.1.0}

[maelle]

so the remaining mystery is netropy I suppose