Package: AnimalHabitatNetwork
Check: examples
New result: ERROR
  Running examples in ‘AnimalHabitatNetwork-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ahn_gen
  > ### Title: Generate networks characterising habitat physical configurations
  > ### Aliases: ahn_gen
  > 
  > ### ** Examples
  > 
  > # generate a connected and weighted network
  > ahn_gen(N = 10, L = 5, mu = 1, lamda = 5)
  Error in `graph_from_adjacency_matrix()`:
  ! Cannot create a graph object because the adjacency matrix contains
    NAs.
  Backtrace:
      ▆
   1. └─AnimalHabitatNetwork::ahn_gen(N = 10, L = 5, mu = 1, lamda = 5)
   2.   └─igraph::graph_from_adjacency_matrix(ahn_wei_matrix, mode = "undirected", diag = FALSE, weighted = TRUE)
   3.     └─igraph:::ensure_no_na(adjmatrix, "adjacency matrix")
   4.       └─cli::cli_abort(...)
   5.         └─rlang::abort(...)
  Execution halted

Package: archeofrag
Check: examples
New result: ERROR
  Running examples in ‘archeofrag-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: frag.cycles
  > ### Title: Count the k-cycles in a graph, for cycles =< k
  > ### Aliases: frag.cycles
  > ### Keywords: measurement
  > 
  > ### ** Examples
  > 
  > g <- frag.simul.process(n.components=20, vertices=50, disturbance=.15)
  Error in `vctrs::vec_c()`:
  ! Can't combine `..1` <double> and `..2` <character>.
  Backtrace:
       ▆
    1. ├─archeofrag::frag.simul.process(...)
    2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
    3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
    4. └─vctrs (local) `<fn>`()
    5.   └─vctrs::vec_default_ptype2(...)
    6.     ├─base::withRestarts(...)
    7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
    8.     │   └─base (local) doWithOneRestart(return(expr), restart)
    9.     └─vctrs::stop_incompatible_type(...)
   10.       └─vctrs:::stop_incompatible(...)
   11.         └─vctrs:::stop_vctrs(...)
   12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  Execution halted

Package: archeofrag
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘archeofrag-vignette.Rmd’ using rmarkdown
  
  Quitting from archeofrag-vignette.Rmd:167-169 [make-simulatd-graph]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'archeofrag-vignette.Rmd' failed with diagnostics:
  Can't combine `..1` <double> and `..2` <character>.
  --- failed re-building ‘archeofrag-vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘archeofrag-vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: archeofrag
Check: tests
New result: ERROR
    Running ‘testthat.R’ [10s/10s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(archeofrag)
    > 
    > test_check("archeofrag")
    More than 2 layers: the 'frag.edges.weighting' function is applied to each pair of layers.
    More than 2 layers: the 'frag.edges.weighting' function is applied to each pair of layers.
    More than 2 layers: the 'frag.edges.weighting' function is applied to each pair of layers.
    More than 2 layers: the 'frag.edges.weighting' function is applied to each pair of layers.
    [ FAIL 9 | WARN 0 | SKIP 0 | PASS 58 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-frag.graph.reduce.R:24:3'): reduce vertice number (not conserving objects nr) ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.graph.reduce.R:24:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.graph.reduce.R:33:3'): reduce vertice number (conserving objects nr, conserving fragments balance) ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.graph.reduce.R:33:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.graph.reduce.R:48:3'): reduce vertice number (conserving fragments balance and inter-units connection) ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.graph.reduce.R:48:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.simul.compare.R:5:3'): frag.simul.compare works ───────────
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.simul.compare.R:5:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.simul.process.R:44:3'): parameters of a generated graph with 2 initial layers are correct ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.simul.process.R:44:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.simul.process.R:56:3'): admixture and cohesion values of a graph with 2 initial layers are correct ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.simul.process.R:56:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.simul.process.R:67:3'): the optional asymmetric.transport.from parameter works ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.simul.process.R:67:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.simul.process.R:84:3'): the optional from.observed.graph parameter works ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.simul.process.R:84:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    ── Error ('test-frag.simul.summarise.R:4:3'): parameters of a constrained generated graph with 1 initial layer are correct ──
    <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
    Error in `vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])`: Can't combine `..1` <double> and `..2` <character>.
    Backtrace:
         ▆
      1. ├─archeofrag::frag.simul.process(...) at test-frag.simul.summarise.R:4:3
      2. │ └─igraph::disjoint_union(g.layer1, g.layer2)
      3. │   └─vctrs::vec_c(attr[[exattr[a]]], va[[exattr[a]]])
      4. └─vctrs (local) `<fn>`()
      5.   └─vctrs::vec_default_ptype2(...)
      6.     ├─base::withRestarts(...)
      7.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
      8.     │   └─base (local) doWithOneRestart(return(expr), restart)
      9.     └─vctrs::stop_incompatible_type(...)
     10.       └─vctrs:::stop_incompatible(...)
     11.         └─vctrs:::stop_vctrs(...)
     12.           └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
    
    [ FAIL 9 | WARN 0 | SKIP 0 | PASS 58 ]
    Error: Test failures
    Execution halted

Package: cglasso
Check: examples
New result: ERROR
  Running examples in ‘cglasso-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot.cglasso2igraph
  > ### Title: Plot Method for a cglasso2igraph Object"
  > ### Aliases: plot.cglasso2igraph
  > ### Keywords: graphs
  > 
  > ### ** Examples
  > 
  > set.seed(123)
  > # Y ~ N(0, Sigma) and probability of left/right censored values equal to 0.05
  > n <- 100L
  > p <- 3L
  > rho <- 0.3
  > Sigma <- outer(1L:p, 1L:p, function(i, j) rho^abs(i - j))
  > Z <- rcggm(n = n, Sigma = Sigma, probl = 0.05, probr = 0.05)
  > out <- cglasso(. ~ ., data = Z)
  > out.graph <- to_graph(out)
  > plot(out.graph, type = "Gyy")
  Warning: vertex attribute color contains NAs. Replacing with default value 1
  Warning: vertex attribute frame.color contains NAs. Replacing with default value black
  > 
  > out.graph <- to_graph(out, weighted = TRUE)
  > plot(out.graph,  type = "Gyy")
  Warning: Non-positive edge weight found, ignoring all weights during graph layout.
  Warning: vertex attribute color contains NAs. Replacing with default value 1
  Warning: vertex attribute frame.color contains NAs. Replacing with default value black
  > 
  > 
  > # Y ~ N(b0 +XB, Sigma)  and probability of left/right censored values equal to 0.05
  > n <- 100L
  > p <- 3L
  > q <- 2L
  > b0 <- runif(p)
  > B <- matrix(runif(q * p), nrow = q, ncol = p)
  > X <- matrix(rnorm(n * q), nrow = n, ncol = q)
  > rho <- 0.3
  > Sigma <- outer(1L:p, 1L:p, function(i, j) rho^abs(i - j))
  > Z <- rcggm(n = n, b0 = b0, X = X, B = B, Sigma = Sigma, probl = 0.05, probr = 0.05)
  > out <- cglasso(. ~ ., data = Z)
  > out.graph <- to_graph(out, lambda.id = 3, rho.id = 3, weighted = TRUE)
  > plot(out.graph, type = "Gyy")
  Warning: Non-positive edge weight found, ignoring all weights during graph layout.
  Error in (function (graph, root = numeric(), circular = FALSE, rootlevel = numeric(),  : 
    unused argument (weights = NA)
  Calls: plot ... i.postprocess.layout -> %in% -> params -> ret -> v -> do.call
  Execution halted

Package: CITMIC
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘CITMIC.Rmd’ using rmarkdown
  
  Quitting from CITMIC.Rmd:38-49 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'CITMIC.Rmd' failed with diagnostics:
  `name` must be a single string, not `TRUE`.
  --- failed re-building ‘CITMIC.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘CITMIC.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: dosearch
Check: tests
New result: ERROR
    Running ‘testthat.R’ [4s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > #' @srrstats {G5.2} Error and warning behavior is tested.
    > #' @srrstats {G5.2a} Messages are unique.
    > #' @srrstats {G5.2b} Conditions are demonstrated.
    > #' @srrstats {G5.4, G5.4a, G5.6} Output of dosearch is compared against known
    > #'   theoretical identifiability and non-identifiability results.
    > #'   In other words, correctness can be tested independently of the
    > #'   implementation.
    > #' @srrstats {G5.5} The algorithm is deterministic, so this could also be NA
    > #' @srrstats {G5.6a} Because the package output is symbolic, the recovery
    > #'   of e.g., a causal effect is exact.
    > #' @srrstats {G5.7} Performance and scalability have been demonstrated
    > #'   in the JSS paper, and the simulations are too large to run on a single
    > #'   PC and require a cluster. The replication materials for this simulation
    > #'   are included in the 'rep' directory. The algorithm has exponential
    > #'   time and memory complexity in the number of the vertices of the graph,
    > #'   and it has been hypothesized that the general identifiability problem
    > #'   itself is NP-hard.
    > #' @srrstats {G5.8, G5.8a G5.8b, G5.8c, G5.8d} Edge conditions are tested.
    > #' @srrstats {NW6.0} Inputs types are tested.
    > #' @noRd
    > library(testthat)
    > library(dosearch)
    > 
    > test_check("dosearch")
    [ FAIL 1 | WARN 3 | SKIP 0 | PASS 294 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-interface.R:32:3'): igraph graph without names gets named ──────
    Error in `FUN(X[[i]], ...)`: Error: Logical index length does not match the number of edges. Recycling is not allowed.
    Backtrace:
         ▆
      1. ├─testthat::expect_message(parse_graph(g_igraph), "Argument `graph` is not named, node names have been assigned") at test-interface.R:32:3
      2. │ └─testthat:::expect_condition_matching(...)
      3. │   └─testthat:::quasi_capture(...)
      4. │     ├─testthat (local) .capture(...)
      5. │     │ └─base::withCallingHandlers(...)
      6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      7. └─dosearch:::parse_graph(g_igraph)
      8.   ├─e[(is.na(description) | description != "U")]
      9.   └─igraph:::`[.igraph.es`(...)
     10.     └─base::lapply(...)
     11.       └─igraph (local) FUN(X[[i]], ...)
     12.         └─cli::cli_abort("Error: Logical index length does not match the number of edges. Recycling is not allowed.")
     13.           └─rlang::abort(...)
    
    [ FAIL 1 | WARN 3 | SKIP 0 | PASS 294 ]
    Error: Test failures
    Execution halted

Package: DrDimont
Check: examples
New result: ERROR
  Running examples in ‘DrDimont-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: generate_individual_graphs
  > ### Title: Builds graphs from specified network layers
  > ### Aliases: generate_individual_graphs
  > 
  > ### ** Examples
  > 
  > ## Don't show: 
  > WGCNA::disableWGCNAThreads()
  > ## End(Don't show)
  > 
  > data(layers_example)
  > data(correlation_matrices_example)
  > 
  > example_settings <- drdimont_settings(
  +                         handling_missing_data=list(
  +                             default="pairwise.complete.obs",
  +                             mrna="all.obs"),
  +                         reduction_method="pickHardThreshold",
  +                         r_squared=list(default=0.65, metabolite=0.1),
  +                         cut_vector=list(default=seq(0.2, 0.5, 0.01)))
  [25-09-24 13:21:36] WARNING: Python executable in virtual environment 'r-DrDimont' not found. Either run `install_python_dependencies(package_manager='pip') or set `conda=TRUE` in `drdimont_settings()` if conda installation was used.
  > 
  > example_individual_graphs <- generate_individual_graphs(
  +                                  correlation_matrices=correlation_matrices_example,
  +                                  layers=layers_example, 
  +                                  settings=example_settings)
  [25-09-24 13:21:36] Generating graph of layer mrna for groupA...
  [25-09-24 13:21:36] Reducing network by WGCNA::pickHardThreshold...
  [25-09-24 13:21:36] R2 cutoff: 0.65
  [25-09-24 13:21:37] Cut Threshold: 0.26
  Error in `graph_from_adjacency_matrix()`:
  ! Cannot create a graph object because the adjacency matrix contains
    NAs.
  Backtrace:
      ▆
   1. └─DrDimont::generate_individual_graphs(...)
   2.   └─DrDimont::generate_reduced_graph(...)
   3.     └─igraph::graph.adjacency(...)
   4.       └─igraph::graph_from_adjacency_matrix(...)
   5.         └─igraph:::ensure_no_na(adjmatrix, "adjacency matrix")
   6.           └─cli::cli_abort(...)
   7.             └─rlang::abort(...)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
  compute_correlation_matrices 6.002  0.311   6.319

Package: DrDimont
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘DrDimont_Vignette.Rmd’ using rmarkdown
  
  Quitting from DrDimont_Vignette.Rmd:327-333 [Individual graphs]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'DrDimont_Vignette.Rmd' failed with diagnostics:
  Cannot create a graph object because the adjacency matrix contains NAs.
  --- failed re-building ‘DrDimont_Vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘DrDimont_Vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: EGAnet
Check: examples
New result: ERROR
  Running examples in ‘EGAnet-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: EGA
  > ### Title: Exploratory Graph Analysis
  > ### Aliases: EGA
  > 
  > ### ** Examples
  > 
  > # Obtain data
  > wmt <- wmt2[,7:24]
  > 
  > # Estimate EGA
  > ega.wmt <- EGA(
  +   data = wmt,
  +   plot.EGA = FALSE # No plot for CRAN checks
  + )
  Error in `set_vertex_attr()`:
  ! `name` must be a single string, not `FALSE`.
  Backtrace:
       ▆
    1. └─EGAnet::EGA(data = wmt, plot.EGA = FALSE)
    2.   └─EGAnet::EGA.estimate(...)
    3.     ├─base::do.call(...)
    4.     └─EGAnet (local) `<fn>`(...)
    5.       └─EGAnet::convert2igraph(network)
    6.         ├─EGAnet:::silent_call(...)
    7.         │ ├─utils::capture.output(result <- suppressWarnings(suppressMessages(...)))
    8.         │ │ └─base::withVisible(...elt(i))
    9.         │ ├─base::suppressWarnings(suppressMessages(...))
   10.         │ │ └─base::withCallingHandlers(...)
   11.         │ └─base::suppressMessages(...)
   12.         │   └─base::withCallingHandlers(...)
   13.         └─igraph::graph_from_adjacency_matrix(...)
   14.           └─igraph::set_vertex_attr(name = add.colnames)
   15.             └─igraph:::check_string(name)
   16.               └─igraph:::stop_input_type(...)
   17.                 └─rlang::abort(message, ..., call = call, arg = arg)
  Execution halted

Package: egor
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘egor_allbus.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘egor_allbus.Rmd’
  
  --- re-building ‘qualtrics.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘qualtrics.Rmd’
  
  --- re-building ‘using_egor.Rmd’ using rmarkdown
  
  Quitting from using_egor.Rmd:221-241 [unnamed-chunk-16]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `gray()`:
  ! invalid gray level, must be in [0,1].
  ---
  Backtrace:
      ▆
   1. └─egor::vis_clustered_graphs(...)
   2.   └─egor (local) plotGraph(graph, center, this_layout)
   3.     └─grDevices::gray(1 - betw_grp_dens/max(betw_grp_dens), alpha = 0.7)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'using_egor.Rmd' failed with diagnostics:
  invalid gray level, must be in [0,1].
  --- failed re-building ‘using_egor.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘using_egor.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: FCMapper
Check: examples
New result: ERROR
  Running examples in ‘FCMapper-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: graph.fcm
  > ### Title: Fuzzy cognitive map graph
  > ### Aliases: graph.fcm
  > 
  > ### ** Examples
  > 
  > 
  > matrix = matrix(nrow=7,ncol=7)
  > matrix[1,] = c(0,-0.5,0,0,1,0,1)
  > matrix[2,] = c(1,0,1,0.2,0,0,0.6)
  > matrix[3,] = c(0,1,0,0,0,0,0)
  > matrix[4,] = c(0.6,0,0,1,0,0,0.1)
  > matrix[5,] = c(0,0.5,0,0,1,0,-0.6) 
  > matrix[6,] = c(0,0,-1,0,0,0,0)
  > matrix[7,] = c(0,0,0,-0.5,0,0,1)
  > concept.names = c("A","B","C","D","E","F","G")
  > 
  > results = nochanges.scenario(matrix,iter=25,concept.names)
  > 
  > graph.fcm(matrix,concept.sizes=results$Equilibrium_value,concept.names)
  Warning: Non-positive edge weight found, ignoring all weights during graph layout.
  Warning in rep(no, length.out = len) :
    'x' is NULL so the result will be NULL
  Error in ans[npos] <- rep(no, length.out = len)[npos] : 
    replacement has length zero
  Calls: graph.fcm ... .tkplot.update.vertex -> .tkplot.update.edge -> ifelse
  Execution halted

Package: GephiForR
Check: examples
New result: ERROR
  Running examples in ‘GephiForR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: rotate_layout
  > ### Title: Rotate layout positions by a custom angle
  > ### Aliases: rotate_layout
  > 
  > ### ** Examples
  > 
  > 
  > # Create a random graph
  > library(igraph)
  
  Attaching package: ‘igraph’
  
  The following objects are masked from ‘package:stats’:
  
      decompose, spectrum
  
  The following object is masked from ‘package:base’:
  
      union
  
  > g <- erdos.renyi.game(100, 0.05)
  > 
  > # Initializing position vector and plotting
  > position <- as.matrix(data.frame(X = c(1, 2, 3), Y = c(4, 5, 6)))
  > plot(g, layout = position)
  Error in `plot()`:
  ! The layout has 3 rows, but the graph has 100 vertices.
  ℹ It is recommended to store the layout as x and y vertex attributes and not as
    a matrix graph attribute.
  Backtrace:
      ▆
   1. ├─base::plot(g, layout = position)
   2. └─igraph::plot.igraph(g, layout = position)
   3.   └─cli::cli_abort(...)
   4.     └─rlang::abort(...)
  Execution halted

Package: incidentally
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘congress.Rmd’ using rmarkdown
  trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
  Content type 'application/zip' length 1883678 bytes (1.8 MB)
  ==================================================
  downloaded 1.8 MB
  
  trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
  Content type 'application/zip' length 1883678 bytes (1.8 MB)
  ==================================================
  downloaded 1.8 MB
  
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘congress.Rmd’
  
  --- re-building ‘incidentally.Rmd’ using rmarkdown
  
   *** caught segfault ***
  address 0x55cffffffff8, cause 'memory not mapped'
  
  Traceback:
   1: .Call(R_igraph_finalizer)
   2: graph_incidence_build(incidence, directed = directed, mode = mode,     multiple = multiple, weighted = weighted)
   3: graph_from_biadjacency_matrix(...)
   4: igraph::graph_from_incidence_matrix(I)
   5: incidence.from.adjacency(G, k = 1, p = 0.75, model = "team")
   6: eval(expr, envir)
   7: eval(expr, envir)
   8: withVisible(eval(expr, envir))
   9: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
  10: eval(call)
  11: eval(call)
  12: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
  13: doWithOneRestart(return(expr), restart)
  14: withOneRestart(expr, restarts[[1L]])
  15: withRestartList(expr, restarts[-nr])
  16: doWithOneRestart(return(expr), restart)
  17: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
  18: withRestartList(expr, restarts)
  19: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
  20: evaluate::evaluate(...)
  21: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
  22: in_dir(input_dir(), expr)
  23: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
  24: eng_r(options)
  25: block_exec(params)
  26: call_block(x)
  27: process_group(group)
  28: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (xfun::pkg_available("rlang", "1.0.0")) {            if (is_R_CMD_build() || is_R_CMD_check()) {                cnd = tryCatch(rlang::entrace(e), error = identity)                error <<- format(cnd)            }            else {                rlang::entrace(e)            }        }    })
  29: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (xfun::pkg_available("rlang", "1.0.0")) {            if (is_R_CMD_build() || is_R_CMD_check()) {                cnd = tryCatch(rlang::entrace(e), error = identity)                error <<- format(cnd)            }            else {                rlang::entrace(e)            }        }    }), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
  30: process_file(text, output)
  31: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  32: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
  33: vweave_rmarkdown(...)
  34: engine$weave(file, quiet = quiet, encoding = enc)
  35: doTryCatch(return(expr), name, parentenv, handler)
  36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  37: tryCatchList(expr, classes, parentenv, handlers)
  38: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
  39: tools:::.buildOneVignette("incidentally.Rmd", "/home/hornik/tmp/CRAN_recheck/incidentally.Rcheck/vign_test/incidentally",     TRUE, FALSE, "incidentally", "UTF-8", "/home/hornik/tmp/scratch/RtmpVcjrXI/file19230df3b25a9.rds")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault
  SUMMARY: processing the following file failed:
    ‘incidentally.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: IOHanalyzer
Check: examples
New result: ERROR
  Running examples in ‘IOHanalyzer-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: Plot.Stats.Significance_Graph
  > ### Title: Plot a network graph showing the statistically different
  > ###   algorithms
  > ### Aliases: Plot.Stats.Significance_Graph
  > ###   Plot.Stats.Significance_Graph.DataSetList
  > 
  > ### ** Examples
  > 
  > Plot.Stats.Significance_Graph(subset(dsl, funcId == 2), 16)
  Error in `igraph::graph_from_adjacency_matrix()`:
  ! Cannot create a graph object because the adjacency matrix contains
    NAs.
  Backtrace:
      ▆
   1. ├─IOHanalyzer::Plot.Stats.Significance_Graph(...)
   2. └─IOHanalyzer:::Plot.Stats.Significance_Graph.DataSetList(...)
   3.   └─igraph::graph_from_adjacency_matrix(p_matrix <= alpha, mode = "directed", diag = F)
   4.     └─igraph:::ensure_no_na(adjmatrix, "adjacency matrix")
   5.       └─cli::cli_abort(...)
   6.         └─rlang::abort(...)
  Execution halted

Package: klassR
Check: examples
New result: ERROR
  Running examples in ‘klassR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: update_klass_node
  > ### Title: Given a node and a graph, find the node at the end of a sequence
  > ###   of changes.
  > ### Aliases: update_klass_node
  > 
  > ### ** Examples
  > 
  > 
  > # Build a graph directed towards the most recent codes.
  > library(klassR)
  > klass_131 <- klass_graph(131)
  Error in `FUN()`:
  ! Error: Logical index length does not match the number of edges.
    Recycling is not allowed.
  Backtrace:
      ▆
   1. └─klassR::klass_graph(131)
   2.   ├─igraph::reverse_edges(...)
   3.   │ └─igraph:::as_igraph_es(graph, eids)
   4.   ├─igraph::E(graph)[igraph::E(graph)$changeOccurred > date]
   5.   └─igraph:::`[.igraph.es`(...)
   6.     └─base::lapply(...)
   7.       └─igraph (local) FUN(X[[i]], ...)
   8.         └─cli::cli_abort("Error: Logical index length does not match the number of edges. Recycling is not allowed.")
   9.           └─rlang::abort(...)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
  get_family 0.353  0.004    6.24

Package: manynet
Check: examples
New result: ERROR
  Running examples in ‘manynet-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: mark_features
  > ### Title: Marking networks features
  > ### Aliases: mark_features is_connected is_perfect_matching is_eulerian
  > ###   is_acyclic is_aperiodic
  > 
  > ### ** Examples
  > 
  > is_connected(ison_southern_women)
  [1] TRUE
  > is_perfect_matching(ison_southern_women)
  [1] FALSE
  > is_eulerian(ison_brandes)
  [1] FALSE
  > is_acyclic(ison_algebra)
  [1] FALSE
  > is_aperiodic(ison_algebra)
  
  Execution halted

Package: manynet
Check: tests
New result: ERROR
    Running ‘testthat.R’

Package: multinet [Old version: 4.3, New version: 4.3.1]
Check: examples
New result: ERROR
  Running examples in ‘multinet-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: multinet.conversion
  > ### Title: Conversion to a simple or multi graph
  > ### Aliases: multinet.conversion as.igraph.multinet
  > ###   as.igraph.Rcpp_RMLNetwork
  > 
  > ### ** Examples
  > 
  > net <- ml_aucs()
  > # using the default merge.actors=TRUE we create a multigraph,
  > # where each actor corresponds to a vertex in the result
  > multigraph <- as.igraph(net)
  Error in `make_empty_graph()`:
  ! `directed` must be a logical, not a number.
  Backtrace:
      ▆
   1. ├─igraph::as.igraph(net)
   2. └─multinet:::as.igraph.Rcpp_RMLNetwork(net)
   3.   └─igraph::graph_from_data_frame(vertices = a_df, e_df, directed = dir)
   4.     └─igraph::make_empty_graph(n = 0, directed = directed)
   5.       └─cli::cli_abort("{.arg directed} must be a logical, not {.obj_type_friendly {directed}}.")
   6.         └─rlang::abort(...)
  Execution halted

Package: mwcsr
Check: examples
New result: ERROR
  Running examples in ‘mwcsr-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: virgo_solver
  > ### Title: Construct a virgo solver
  > ### Aliases: virgo_solver
  > 
  > ### ** Examples
  > 
  > data("sgmwcs_small_instance")
  > approx_vs <- virgo_solver(mst=TRUE, threads = 1)
  > approx_vs$run_main("-h")
  Option (* = required)                  Description                            
  ---------------------                  -----------                            
  --benchmark, --bm                      Benchmark output file (default: )      
  -c <Integer>                           Threshold for CPE solver (default: 25) 
  * -e, --edges                          Edge list file                         
  -h, --help                             Print a short help message             
  -l, --log <Integer>                    Log level (default: 0)                 
  -m, --threads <Integer>                Number of threads (default: 1)         
  --mst                                  Use primal heuristic only              
  * -n, --nodes                          Node list file                         
  -o, --output-dir                       Solver output directory                
  -p, --epsilon <Double>                 Maximum allowed absolute score error   
                                           for solver (default: 0.0)            
  --pl, --preprocessing-level [Integer]  Preprocessing level (default: 2)       
  -s, --signals                          Signals file                           
  -t, --timelimit <Long>                 Timelimit in seconds (<= 0 -           
                                           unlimited) (default: 0)              
  --type                                 One of: SGMWCS, GMWCS (default: sgmwcs)
  --version                                                                     
  > sol <- solve_mwcsp(approx_vs, sgmwcs_small_instance)
  Error:
  ! The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
  Backtrace:
       ▆
    1. ├─mwcsr::solve_mwcsp(approx_vs, sgmwcs_small_instance)
    2. └─mwcsr:::solve_mwcsp.virgo_solver(approx_vs, sgmwcs_small_instance)
    3.   └─mwcsr:::solve_sgmwcs(solver, instance, ...)
    4.     └─mwcsr:::run_solver(...)
    5.       └─igraph::get.edge.ids(instance, t(edges[, 1:2]))
    6.         └─igraph::get_edge_ids(...)
    7.           └─igraph:::el_to_vec(vp, call = rlang::caller_env())
    8.             └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
    9.               └─lifecycle:::deprecate_stop0(msg)
   10.                 └─rlang::cnd_signal(...)
  Execution halted

Package: mwcsr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [17s/17s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(mwcsr)
    > 
    > test_check("mwcsr")
    [ FAIL 2 | WARN 10 | SKIP 5 | PASS 41 ]
    
    ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
    • No CPLEX available (3): 'test_virgo.R:5:9', 'test_virgo.R:15:9',
      'test_virgo.R:24:9'
    • SCIP is not available (2): 'test_scip.R:5:9', 'test_scip.R:16:9'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_virgo.R:48:5'): heuristic virgo_solver works on SGMWCS ─────────
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. ├─mwcsr::solve_mwcsp(solver, sgmwcs_small_instance) at test_virgo.R:48:5
      2. └─mwcsr:::solve_mwcsp.virgo_solver(solver, sgmwcs_small_instance)
      3.   └─mwcsr:::solve_sgmwcs(solver, instance, ...)
      4.     └─mwcsr:::run_solver(...)
      5.       └─igraph::get.edge.ids(instance, t(edges[, 1:2]))
      6.         └─igraph::get_edge_ids(...)
      7.           └─igraph:::el_to_vec(vp, call = rlang::caller_env())
      8.             └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
      9.               └─lifecycle:::deprecate_stop0(msg)
     10.                 └─rlang::cnd_signal(...)
    ── Error ('test_virgo.R:81:5'): heuristic virgo_solver works on SGMWCS ─────────
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. ├─mwcsr::solve_mwcsp(solver, si) at test_virgo.R:81:5
      2. └─mwcsr:::solve_mwcsp.virgo_solver(solver, si)
      3.   └─mwcsr:::solve_sgmwcs(solver, instance, ...)
      4.     └─mwcsr:::run_solver(...)
      5.       └─igraph::get.edge.ids(instance, t(edges[, 1:2]))
      6.         └─igraph::get_edge_ids(...)
      7.           └─igraph:::el_to_vec(vp, call = rlang::caller_env())
      8.             └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
      9.               └─lifecycle:::deprecate_stop0(msg)
     10.                 └─rlang::cnd_signal(...)
    
    [ FAIL 2 | WARN 10 | SKIP 5 | PASS 41 ]
    Error: Test failures
    Execution halted

Package: PopComm
Check: examples
New result: ERROR
  Running examples in ‘PopComm-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: circle_plot
  > ### Title: Plot Circular Ligand-Receptor Interaction Network
  > ### Aliases: circle_plot
  > 
  > ### ** Examples
  > 
  > # Plot Circular Cell-Cell Interaction Network
  > data(filtered_lr_eg)
  > p <- circle_plot(filtered_lr_eg, edge_width = "count", show_self_interactions = TRUE)
  Warning: edge attribute loop.angle contains NAs. Replacing with default value
  Error in p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] : 
    replacement has length zero
  Calls: circle_plot -> plot -> plot.igraph -> params
  Execution halted

Package: remify
Check: tests
New result: ERROR
    Running ‘tinytest.R’ [11s/20s]
  Running the tests in ‘tests/tinytest.R’ failed.
  Complete output:
    > if ( requireNamespace("tinytest", quietly=TRUE) ){
    +   tinytest::test_package("remify")
    + }
    
    test-rehshape.R...............    0 tests    
    test-rehshape.R...............    1 tests OK 
    test-rehshape.R...............    1 tests OK 
    test-rehshape.R...............    2 tests OK 
    test-rehshape.R...............    3 tests OK 
    test-rehshape.R...............    4 tests OK 
    test-rehshape.R...............    5 tests OK 
    test-rehshape.R...............    6 tests OK 
    test-rehshape.R...............    7 tests OK 
    test-rehshape.R...............    8 tests OK 
    test-rehshape.R...............    9 tests OK 
    test-rehshape.R...............   10 tests OK 
    test-rehshape.R...............   10 tests OK 
    test-rehshape.R...............   11 tests OK 
    test-rehshape.R...............   12 tests OK 
    test-rehshape.R...............   13 tests OK 
    test-rehshape.R...............   14 tests OK 
    test-rehshape.R...............   15 tests OK 
    test-rehshape.R...............   16 tests OK 
    test-rehshape.R...............   17 tests OK 
    test-rehshape.R...............   18 tests OK 
    test-rehshape.R...............   19 tests OK 
    test-rehshape.R...............   19 tests OK 
    test-rehshape.R...............   20 tests OK 
    test-rehshape.R...............   20 tests OK 
    test-rehshape.R...............   21 tests OK 
    test-rehshape.R...............   22 tests OK 
    test-rehshape.R...............   22 tests OK 
    test-rehshape.R...............   22 tests OK 
    test-rehshape.R...............   23 tests OK 
    test-rehshape.R...............   24 tests OK 
    test-rehshape.R...............   24 tests OK 
    test-rehshape.R...............   24 tests OK 
    test-rehshape.R...............   25 tests OK 
    test-rehshape.R...............   26 tests OK 2.8s
    
    test-remify-error-messages.R..    1 tests OK 
    test-remify-error-messages.R..    1 tests OK 
    test-remify-error-messages.R..    1 tests OK 
    test-remify-error-messages.R..    2 tests OK 
    test-remify-error-messages.R..    2 tests OK 
    test-remify-error-messages.R..    2 tests OK 
    test-remify-error-messages.R..    3 tests OK 
    test-remify-error-messages.R..    3 tests OK 
    test-remify-error-messages.R..    3 tests OK 
    test-remify-error-messages.R..    4 tests OK 
    test-remify-error-messages.R..    5 tests OK 
    test-remify-error-messages.R..    6 tests OK 
    test-remify-error-messages.R..    6 tests OK 
    test-remify-error-messages.R..    6 tests OK 
    test-remify-error-messages.R..    7 tests OK 
    test-remify-error-messages.R..    7 tests OK 
    test-remify-error-messages.R..    8 tests OK 
    test-remify-error-messages.R..    8 tests OK 
    test-remify-error-messages.R..    8 tests OK 
    test-remify-error-messages.R..    9 tests OK 
    test-remify-error-messages.R..    9 tests OK 
    test-remify-error-messages.R..    9 tests OK 
    test-remify-error-messages.R..   10 tests OK 
    test-remify-error-messages.R..   10 tests OK 
    test-remify-error-messages.R..   10 tests OK 
    test-remify-error-messages.R..   11 tests OK 
    test-remify-error-messages.R..   11 tests OK 
    test-remify-error-messages.R..   11 tests OK 
    test-remify-error-messages.R..   12 tests OK 
    test-remify-error-messages.R..   12 tests OK 
    test-remify-error-messages.R..   12 tests OK 
    test-remify-error-messages.R..   13 tests OK 
    test-remify-error-messages.R..   13 tests OK 
    test-remify-error-messages.R..   14 tests OK 
    test-remify-error-messages.R..   14 tests OK 
    test-remify-error-messages.R..   14 tests OK 
    test-remify-error-messages.R..   15 tests OK 
    test-remify-error-messages.R..   15 tests OK 
    test-remify-error-messages.R..   15 tests OK 
    test-remify-error-messages.R..   16 tests OK 
    test-remify-error-messages.R..   16 tests OK 
    test-remify-error-messages.R..   16 tests OK 
    test-remify-error-messages.R..   17 tests OK 
    test-remify-error-messages.R..   17 tests OK 
    test-remify-error-messages.R..   17 tests OK 
    test-remify-error-messages.R..   18 tests OK 
    test-remify-error-messages.R..   18 tests OK 
    test-remify-error-messages.R..   19 tests OK 
    test-remify-error-messages.R..   19 tests OK 
    test-remify-error-messages.R..   20 tests OK 
    test-remify-error-messages.R..   20 tests OK 
    test-remify-error-messages.R..   21 tests OK 0.3s
    
    test-remify-methods.R.........    0 tests    
    test-remify-methods.R.........    0 tests    
    test-remify-methods.R.........    1 tests OK 
    test-remify-methods.R.........    2 tests OK 
    test-remify-methods.R.........    3 tests OK 
    test-remify-methods.R.........    4 tests OK 
    test-remify-methods.R.........    4 tests OK 
    test-remify-methods.R.........    4 tests OK 
    test-remify-methods.R.........    4 tests OK 
    test-remify-methods.R.........    5 tests OK 
    test-remify-methods.R.........    6 tests OK 
    test-remify-methods.R.........    7 tests OK 
    test-remify-methods.R.........    8 tests OK 
    test-remify-methods.R.........    8 tests OK 
    test-remify-methods.R.........    8 tests OK 
    test-remify-methods.R.........    8 tests OK 
    test-remify-methods.R.........    8 tests OK 
    test-remify-methods.R.........    9 tests OK 
    test-remify-methods.R.........   10 tests OK 
    test-remify-methods.R.........   11 tests OK 
    test-remify-methods.R.........   12 tests OK 
    test-remify-methods.R.........   13 tests OK 
    test-remify-methods.R.........   13 tests OK 
    test-remify-methods.R.........   13 tests OK 
    test-remify-methods.R.........   13 tests OK 
    test-remify-methods.R.........   13 tests OK 
    test-remify-methods.R.........   13 tests OK 
    test-remify-methods.R.........   14 tests OK 
    test-remify-methods.R.........   15 tests OK 
    test-remify-methods.R.........   16 tests OK 
    test-remify-methods.R.........   17 tests OK 
    test-remify-methods.R.........   18 tests OK 
    test-remify-methods.R.........   18 tests OK 
    test-remify-methods.R.........   18 tests OK 
    test-remify-methods.R.........   18 tests OK 
    test-remify-methods.R.........   18 tests OK 
    test-remify-methods.R.........   19 tests OK 
    test-remify-methods.R.........   20 tests OK 
    test-remify-methods.R.........   21 tests OK 
    test-remify-methods.R.........   22 tests OK 
    test-remify-methods.R.........   23 tests OK 
    test-remify-methods.R.........   23 tests OK 
    test-remify-methods.R.........   23 tests OK 
    test-remify-methods.R.........   24 tests OK 
    test-remify-methods.R.........   25 tests OK 
    test-remify-methods.R.........   26 tests OK 
    test-remify-methods.R.........   27 tests OK 
    test-remify-methods.R.........   27 tests OK 
    test-remify-methods.R.........   27 tests OK 
    test-remify-methods.R.........   28 tests OK 
    test-remify-methods.R.........   29 tests OK 
    test-remify-methods.R.........   30 tests OK 
    test-remify-methods.R.........   31 tests OK 
    test-remify-methods.R.........   31 tests OK 
    test-remify-methods.R.........   31 tests OK 
    test-remify-methods.R.........   32 tests OK 
    test-remify-methods.R.........   33 tests OK 
    test-remify-methods.R.........   33 tests OK 
    test-remify-methods.R.........   33 tests OK 
    test-remify-methods.R.........   34 tests OK 
    test-remify-methods.R.........   35 tests OK 
    test-remify-methods.R.........   36 tests OK 
    test-remify-methods.R.........   37 tests OK 
    test-remify-methods.R.........   38 tests OK 
    test-remify-methods.R.........   39 tests OK 
    test-remify-methods.R.........   40 tests OK 
    test-remify-methods.R.........   41 tests OK 
    test-remify-methods.R.........   42 tests OK 
    test-remify-methods.R.........   43 tests OK 
    test-remify-methods.R.........   44 tests OK 
    test-remify-methods.R.........   45 tests OK 
    test-remify-methods.R.........   46 tests OK 
    test-remify-methods.R.........   47 tests OK 
    test-remify-methods.R.........   48 tests OK 
    test-remify-methods.R.........   49 tests OK 
    test-remify-methods.R.........   49 tests OK 
    test-remify-methods.R.........   50 tests OK 
    test-remify-methods.R.........   51 tests OK 
    test-remify-methods.R.........   52 tests OK 
    test-remify-methods.R.........   53 tests OK 
    test-remify-methods.R.........   54 tests OK 
    test-remify-methods.R.........   55 tests OK 
    test-remify-methods.R.........   56 tests OK 
    test-remify-methods.R.........   57 tests OK 
    test-remify-methods.R.........   58 tests OK 
    test-remify-methods.R.........   59 tests OK 
    test-remify-methods.R.........   60 tests OK 
    test-remify-methods.R.........   61 tests OK 
    test-remify-methods.R.........   62 tests OK 
    test-remify-methods.R.........   63 tests OK 
    test-remify-methods.R.........   64 tests OK 
    test-remify-methods.R.........   64 tests OK 
    test-remify-methods.R.........   65 tests OK 
    test-remify-methods.R.........   66 tests OK 
    test-remify-methods.R.........   67 tests OK 
    test-remify-methods.R.........   68 tests OK 
    test-remify-methods.R.........   69 tests OK 
    test-remify-methods.R.........   70 tests OK 
    test-remify-methods.R.........   71 tests OK 
    test-remify-methods.R.........   72 tests OK 
    test-remify-methods.R.........   73 tests OK 
    test-remify-methods.R.........   74 tests OK 
    test-remify-methods.R.........   75 tests OK 
    test-remify-methods.R.........   76 tests OK 
    test-remify-methods.R.........   76 tests OK 
    test-remify-methods.R.........   76 tests OK 
    test-remify-methods.R.........   77 tests OK 
    test-remify-methods.R.........   78 tests OK 
    test-remify-methods.R.........   79 tests OK 
    test-remify-methods.R.........   80 tests OK 
    test-remify-methods.R.........   81 tests OK 
    test-remify-methods.R.........   82 tests OK 
    test-remify-methods.R.........   82 tests OK 
    test-remify-methods.R.........   82 tests OK 
    test-remify-methods.R.........   83 tests OK 
    test-remify-methods.R.........   84 tests OK 
    test-remify-methods.R.........   85 tests OK 
    test-remify-methods.R.........   86 tests OK 
    test-remify-methods.R.........   87 tests OK 
    test-remify-methods.R.........   88 tests OK 
    test-remify-methods.R.........   89 tests OK 
    test-remify-methods.R.........   90 tests OK 
    test-remify-methods.R.........   90 tests OK 
    test-remify-methods.R.........   90 tests OK 
    test-remify-methods.R.........   90 tests OK 
    test-remify-methods.R.........   91 tests OK 
    test-remify-methods.R.........   91 tests OK 
    test-remify-methods.R.........   92 tests 1 fails 
    test-remify-methods.R.........   93 tests 2 fails 
    test-remify-methods.R.........   94 tests 3 fails 
    test-remify-methods.R.........   95 tests 4 fails 
    test-remify-methods.R.........   96 tests 5 fails 
    test-remify-methods.R.........   97 tests 6 fails 
    test-remify-methods.R.........   98 tests 7 fails 
    test-remify-methods.R.........   98 tests 7 fails 
    test-remify-methods.R.........   99 tests 8 fails 
    test-remify-methods.R.........  100 tests 9 fails 
    test-remify-methods.R.........  101 tests 10 fails 
    test-remify-methods.R.........  101 tests 10 fails 
    test-remify-methods.R.........  102 tests 10 fails 
    test-remify-methods.R.........  103 tests 10 fails 
    test-remify-methods.R.........  104 tests 10 fails 
    test-remify-methods.R.........  105 tests 10 fails 
    test-remify-methods.R.........  106 tests 10 fails 
    test-remify-methods.R.........  107 tests 10 fails 
    test-remify-methods.R.........  107 tests 10 fails 
    test-remify-methods.R.........  107 tests 10 fails 
    test-remify-methods.R.........  108 tests 10 fails 
    test-remify-methods.R.........  109 tests 10 fails 
    test-remify-methods.R.........  109 tests 10 fails 
    test-remify-methods.R.........  109 tests 10 fails 
    test-remify-methods.R.........  110 tests 10 fails 
    test-remify-methods.R.........  110 tests 10 fails 
    test-remify-methods.R.........  110 tests 10 fails 
    test-remify-methods.R.........  111 tests 10 fails 
    test-remify-methods.R.........  111 tests 10 fails 
    test-remify-methods.R.........  111 tests 10 fails 
    test-remify-methods.R.........  112 tests 10 fails 
    test-remify-methods.R.........  112 tests 10 fails 
    test-remify-methods.R.........  112 tests 10 fails 
    test-remify-methods.R.........  113 tests 10 fails 14.6s
    
    test-remify-warning-messages.R    0 tests    
    test-remify-warning-messages.R    0 tests    
    test-remify-warning-messages.R    1 tests OK 
    test-remify-warning-messages.R    1 tests OK 
    test-remify-warning-messages.R    2 tests OK 
    test-remify-warning-messages.R    2 tests OK 
    test-remify-warning-messages.R    2 tests OK 
    test-remify-warning-messages.R    3 tests OK 
    test-remify-warning-messages.R    3 tests OK 
    test-remify-warning-messages.R    3 tests OK 
    test-remify-warning-messages.R    4 tests OK 
    test-remify-warning-messages.R    4 tests OK 
    test-remify-warning-messages.R    4 tests OK 
    test-remify-warning-messages.R    5 tests OK 
    test-remify-warning-messages.R    5 tests OK 
    test-remify-warning-messages.R    5 tests OK 
    test-remify-warning-messages.R    6 tests OK 
    test-remify-warning-messages.R    6 tests OK 
    test-remify-warning-messages.R    6 tests OK 
    test-remify-warning-messages.R    7 tests OK 
    test-remify-warning-messages.R    7 tests OK 
    test-remify-warning-messages.R    7 tests OK 
    test-remify-warning-messages.R    7 tests OK 
    test-remify-warning-messages.R    8 tests OK 
    test-remify-warning-messages.R    9 tests OK 
    test-remify-warning-messages.R    9 tests OK 
    test-remify-warning-messages.R   10 tests OK 
    test-remify-warning-messages.R   11 tests OK 
    test-remify-warning-messages.R   11 tests OK 
    test-remify-warning-messages.R   11 tests OK 
    test-remify-warning-messages.R   12 tests OK 
    test-remify-warning-messages.R   13 tests OK 
    test-remify-warning-messages.R   13 tests OK 
    test-remify-warning-messages.R   14 tests OK 
    test-remify-warning-messages.R   15 tests OK 
    test-remify-warning-messages.R   15 tests OK 
    test-remify-warning-messages.R   15 tests OK 
    test-remify-warning-messages.R   15 tests OK 
    test-remify-warning-messages.R   15 tests OK 
    test-remify-warning-messages.R   16 tests OK 
    test-remify-warning-messages.R   17 tests OK 
    test-remify-warning-messages.R   17 tests OK 
    test-remify-warning-messages.R   18 tests OK 
    test-remify-warning-messages.R   19 tests OK 
    test-remify-warning-messages.R   19 tests OK 
    test-remify-warning-messages.R   19 tests OK 
    test-remify-warning-messages.R   19 tests OK 
    test-remify-warning-messages.R   20 tests OK 
    test-remify-warning-messages.R   21 tests OK 
    test-remify-warning-messages.R   21 tests OK 
    test-remify-warning-messages.R   22 tests OK 
    test-remify-warning-messages.R   23 tests OK 
    test-remify-warning-messages.R   23 tests OK 
    test-remify-warning-messages.R   23 tests OK 
    test-remify-warning-messages.R   23 tests OK 
    test-remify-warning-messages.R   23 tests OK 
    test-remify-warning-messages.R   24 tests OK 
    test-remify-warning-messages.R   25 tests OK 
    test-remify-warning-messages.R   25 tests OK 
    test-remify-warning-messages.R   26 tests OK 
    test-remify-warning-messages.R   27 tests OK 
    test-remify-warning-messages.R   27 tests OK 
    test-remify-warning-messages.R   27 tests OK 
    test-remify-warning-messages.R   27 tests OK 
    test-remify-warning-messages.R   28 tests OK 
    test-remify-warning-messages.R   29 tests OK 
    test-remify-warning-messages.R   29 tests OK 
    test-remify-warning-messages.R   30 tests OK 
    test-remify-warning-messages.R   31 tests OK 0.8s
    
    test-remify.R.................    0 tests    
    test-remify.R.................    1 tests OK 
    test-remify.R.................    2 tests OK 
    test-remify.R.................    3 tests OK 
    test-remify.R.................    4 tests OK 
    test-remify.R.................    5 tests OK 
    test-remify.R.................    6 tests OK 
    test-remify.R.................    7 tests OK 
    test-remify.R.................    8 tests OK 
    test-remify.R.................    9 tests OK 
    test-remify.R.................   10 tests OK 
    test-remify.R.................   10 tests OK 
    test-remify.R.................   10 tests OK 
    test-remify.R.................   10 tests OK 
    test-remify.R.................   11 tests OK 
    test-remify.R.................   12 tests OK 
    test-remify.R.................   13 tests OK 
    test-remify.R.................   13 tests OK 
    test-remify.R.................   13 tests OK 
    test-remify.R.................   14 tests OK 
    test-remify.R.................   15 tests OK 
    test-remify.R.................   15 tests OK 
    test-remify.R.................   15 tests OK 
    test-remify.R.................   15 tests OK 
    test-remify.R.................   16 tests OK 
    test-remify.R.................   17 tests OK 
    test-remify.R.................   17 tests OK 
    test-remify.R.................   17 tests OK 
    test-remify.R.................   17 tests OK 
    test-remify.R.................   18 tests OK 
    test-remify.R.................   19 tests OK 
    test-remify.R.................   19 tests OK 
    test-remify.R.................   19 tests OK 
    test-remify.R.................   19 tests OK 
    test-remify.R.................   20 tests OK 
    test-remify.R.................   20 tests OK 
    test-remify.R.................   21 tests OK 
    test-remify.R.................   21 tests OK 
    test-remify.R.................   21 tests OK 
    test-remify.R.................   21 tests OK 
    test-remify.R.................   21 tests OK 
    test-remify.R.................   22 tests OK 
    test-remify.R.................   22 tests OK 
    test-remify.R.................   23 tests OK 
    test-remify.R.................   23 tests OK 
    test-remify.R.................   23 tests OK 
    test-remify.R.................   23 tests OK 
    test-remify.R.................   24 tests OK 
    test-remify.R.................   24 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   25 tests OK 
    test-remify.R.................   26 tests OK 
    test-remify.R.................   26 tests OK 
    test-remify.R.................   26 tests OK 
    test-remify.R.................   27 tests OK 
    test-remify.R.................   27 tests OK 
    test-remify.R.................   27 tests OK 
    test-remify.R.................   27 tests OK 
    test-remify.R.................   28 tests OK 
    test-remify.R.................   29 tests OK 
    test-remify.R.................   30 tests OK 
    test-remify.R.................   30 tests OK 
    test-remify.R.................   31 tests OK 
    test-remify.R.................   31 tests OK 
    test-remify.R.................   32 tests OK 
    test-remify.R.................   32 tests OK 
    test-remify.R.................   33 tests OK 
    test-remify.R.................   33 tests OK 
    test-remify.R.................   34 tests OK 
    test-remify.R.................   34 tests OK 
    test-remify.R.................   34 tests OK 
    test-remify.R.................   34 tests OK 
    test-remify.R.................   34 tests OK 
    test-remify.R.................   35 tests OK 
    test-remify.R.................   35 tests OK 
    test-remify.R.................   36 tests OK 
    test-remify.R.................   37 tests OK 
    test-remify.R.................   38 tests OK 
    test-remify.R.................   39 tests OK 
    test-remify.R.................   40 tests OK 
    test-remify.R.................   41 tests OK 
    test-remify.R.................   42 tests OK 
    test-remify.R.................   43 tests OK 
    test-remify.R.................   44 tests OK 
    test-remify.R.................   45 tests OK 
    test-remify.R.................   45 tests OK 
    test-remify.R.................   45 tests OK 
    test-remify.R.................   46 tests OK 
    test-remify.R.................   47 tests OK 
    test-remify.R.................   47 tests OK 
    test-remify.R.................   47 tests OK 
    test-remify.R.................   48 tests OK 
    test-remify.R.................   49 tests OK 
    test-remify.R.................   49 tests OK 
    test-remify.R.................   50 tests OK 
    test-remify.R.................   51 tests OK 
    test-remify.R.................   51 tests OK 
    test-remify.R.................   52 tests OK 
    test-remify.R.................   53 tests OK 
    test-remify.R.................   53 tests OK 
    test-remify.R.................   54 tests OK 
    test-remify.R.................   55 tests OK 
    test-remify.R.................   55 tests OK 
    test-remify.R.................   55 tests OK 
    test-remify.R.................   55 tests OK 
    test-remify.R.................   55 tests OK 
    test-remify.R.................   56 tests OK 
    test-remify.R.................   56 tests OK 
    test-remify.R.................   57 tests OK 
    test-remify.R.................   57 tests OK 
    test-remify.R.................   57 tests OK 
    test-remify.R.................   58 tests OK 
    test-remify.R.................   58 tests OK 
    test-remify.R.................   59 tests OK 
    test-remify.R.................   59 tests OK 
    test-remify.R.................   59 tests OK 
    test-remify.R.................   59 tests OK 
    test-remify.R.................   60 tests OK 
    test-remify.R.................   60 tests OK 
    test-remify.R.................   61 tests OK 
    test-remify.R.................   61 tests OK 
    test-remify.R.................   61 tests OK 
    test-remify.R.................   62 tests OK 
    test-remify.R.................   62 tests OK 
    test-remify.R.................   63 tests OK 1.1s
    ----- FAILED[xcpt]: test-remify-methods.R<349--349>
     call| expect_silent(plot(x = out))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<350--350>
     call| expect_silent(plot(x = out, breaks = NULL, palette = NULL, n_intervals = NULL, 
     call| -->    rev = NULL, actors = NULL, pch.degree = NULL, igraph.edge.color = NULL, 
     call| -->    igraph.vertex.color = NULL))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<351--351>
     call| expect_silent(plot(x = out, pch.degree = -1))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<352--352>
     call| expect_silent(plot(x = out, igraph.edge.color = "#000000000", 
     call| -->    igraph.vertex.color = "#000000000"))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<353--353>
     call| expect_silent(plot(x = out, igraph.edge.color = "magenta", igraph.vertex.color = "cyan4"))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<354--354>
     call| expect_silent(plot(x = out, n_intervals = 5))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<355--355>
     call| expect_silent(plot(x = out, actors = attr(out, "dictionary")$actors$actorName[1:5]))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<362--362>
     call| expect_silent(plot(x = out))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<363--363>
     call| expect_silent(plot(x = out, n_intervals = 5))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    ----- FAILED[xcpt]: test-remify-methods.R<364--364>
     call| expect_silent(plot(x = out, actors = attr(out, "dictionary")$actors$actorName[1:5]))
     diff| Execution was not silent. A warning was thrown with message
     diff| 'vertex attribute frame.color contains NAs. Replacing with default value black'
    Error: 10 out of 254 tests failed
    Execution halted

Package: rsetse
Check: examples
New result: ERROR
  Running examples in ‘rsetse-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: calc_spring_area
  > ### Title: Calculate the cross sectional area of the edge
  > ### Aliases: calc_spring_area
  > 
  > ### ** Examples
  > 
  >  
  > 
  > library(igraph)
  
  Attaching package: ‘igraph’
  
  The following objects are masked from ‘package:stats’:
  
      decompose, spectrum
  
  The following object is masked from ‘package:base’:
  
      union
  
  > set.seed(234)
  > g_prep <- generate_peels_network("A") %>%
  +  set.edge.attribute(., name = "edge_characteristic", value = rep(1:16, each = 10))
  Warning: `set.edge.attribute()` was deprecated in igraph 2.0.0.
  ℹ Please use `set_edge_attr()` instead.
  Error in `igraph::graph_from_adjacency_matrix()`:
  ! Cannot create a graph object because the adjacency matrix contains
    NAs.
  Backtrace:
       ▆
    1. ├─generate_peels_network("A") %>% ...
    2. ├─igraph::set.edge.attribute(...)
    3. │ ├─igraph::set_edge_attr(...)
    4. │ │ └─igraph:::is_complete_iterator(index)
    5. │ └─igraph::E(graph)
    6. │   └─igraph:::ensure_igraph(graph)
    7. └─rsetse::generate_peels_network("A")
    8.   └─rsetse:::generate_peels_network_internal(type, k_values)
    9.     └─igraph::graph_from_adjacency_matrix(...)
   10.       └─igraph:::ensure_no_na(adjmatrix, "adjacency matrix")
   11.         └─cli::cli_abort(...)
   12.           └─rlang::abort(...)
  Execution halted

Package: rsetse
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Categorical-and-continuous-features.Rmd’ using rmarkdown
  [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
  --- finished re-building ‘Categorical-and-continuous-features.Rmd’
  
  --- re-building ‘separate-peels-quintet.Rmd’ using rmarkdown
  
  Quitting from separate-peels-quintet.Rmd:44-74 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'separate-peels-quintet.Rmd' failed with diagnostics:
  ℹ In index: 1.
  Caused by error in `igraph::graph_from_adjacency_matrix()`:
  ! Cannot create a graph object because the adjacency matrix contains
    NAs.
  --- failed re-building ‘separate-peels-quintet.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘separate-peels-quintet.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: SEMID
Check: examples
New result: ERROR
  Running examples in ‘SEMID-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: SEMID-package
  > ### Title: SEMID package documentation.
  > ### Aliases: SEMID-package SEMID
  > 
  > ### ** Examples
  > 
  > ###
  > # Checking the generic identifiability of parameters in a mixed graph.
  > ###
  > 
  > # Mixed graphs are specified by their directed adjacency matrix L and
  > # bidirected adjacency matrix O.
  > L = t(matrix(
  +  c(0, 1, 1, 0, 0,
  +    0, 0, 1, 1, 1,
  +    0, 0, 0, 1, 0,
  +    0, 0, 0, 0, 1,
  +    0, 0, 0, 0, 0), 5, 5))
  > 
  > O = t(matrix(
  +  c(0, 0, 0, 1, 0,
  +    0, 0, 1, 0, 1,
  +    0, 0, 0, 0, 0,
  +    0, 0, 0, 0, 0,
  +    0, 0, 0, 0, 0), 5, 5)); O=O+t(O)
  > 
  > # Create a mixed graph object
  > graph = MixedGraph(L, O)
  > 
  > # We can plot what this mixed graph looks like, blue edges are directed
  > # red edges are bidirected.
  > plot(graph)
  > 
  > # Without using decomposition techniques we can't identify all nodes
  > # just using the half-trek criterion
  > htcID(graph, tianDecompose = FALSE)
  Warning: The `vp` argument of `get_edge_ids()` supplied as a matrix should be a n times
  2 matrix, not 2 times n as of igraph 2.1.5.
  ℹ either transpose the matrix with t() or convert it to a data.frame with two
    columns.
  ℹ The deprecated feature was likely used in the igraph package.
    Please report the issue at <https://github.com/igraph/rigraph/issues>.
  Call: htcID(mixedGraph = graph, tianDecompose = FALSE)
  
  Mixed Graph Info.
  # nodes: 5 
  # dir. edges: 7 
  # bi. edges: 3 
  
  Generic Identifiability Summary
  # dir. edges shown gen. identifiable: 1 
  # bi. edges shown gen. identifiable: 0 
  
  Generically identifiable dir. edges:
  1->2 
  
  Generically identifiable bi. edges:
  None
  > 
  > # The edgewiseTSID function can show that all edges are generically
  > # identifiable without proprocessing with decomposition techniques
  > edgewiseTSID(graph, tianDecompose = FALSE)
  Error:
  ! The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
  Backtrace:
       ▆
    1. └─SEMID::edgewiseTSID(graph, tianDecompose = FALSE)
    2.   └─SEMID::generalGenericID(...)
    3.     └─SEMID (local) idStepFunction(mixedGraph, unsolvedParents, solvedParents, identifier)
    4.       └─SEMID::trekSeparationIdentifyStep(...)
    5.         └─mixedGraph$getTrekSystem(sources, c(targets, i), avoidRightEdges = toRemoveOnRight)
    6.           ├─SEMID::getTrekSystem(this, ...)
    7.           └─SEMID:::getTrekSystem.MixedGraph(this, ...)
    8.             └─this$.internalGraph$getTrekSystem(...)
    9.               ├─SEMID::getTrekSystem(this, ...)
   10.               └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
   11.                 └─this$.internalGraph$getTrekSystem(...)
   12.                   ├─SEMID::getTrekSystem(this, ...)
   13.                   └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
   14.                     └─this$.trekFlowGraph$updateEdgeCapacities(...)
   15.                       ├─SEMID::updateEdgeCapacities(this, ...)
   16.                       └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...)
   17.                         └─igraph::get.edge.ids(...)
   18.                           └─igraph::get_edge_ids(...)
   19.                             └─igraph:::el_to_vec(vp, call = rlang::caller_env())
   20.                               └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
   21.                                 └─lifecycle:::deprecate_stop0(msg)
   22.                                   └─rlang::cnd_signal(...)
  Execution halted

Package: SEMID
Check: tests
New result: ERROR
    Running ‘testthat.R’ [45s/46s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(SEMID)
    > 
    > test_check("SEMID")
    [ FAIL 7 | WARN 11 | SKIP 0 | PASS 965 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_LatentDigraph.R:67:3'): Single node graph works properly ───────
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. ├─testthat::expect_equal(...) at test_LatentDigraph.R:67:3
      2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
      3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
      4. └─g$getTrekSystem(1, 1)
      5.   ├─SEMID::getTrekSystem(this, ...)
      6.   └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
      7.     └─this$.internalGraph$getTrekSystem(...)
      8.       ├─SEMID::getTrekSystem(this, ...)
      9.       └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
     10.         └─this$createTrekFlowGraph()
     11.           ├─SEMID::createTrekFlowGraph(this, ...)
     12.           └─SEMID:::createTrekFlowGraph.LatentDigraphFixedOrder(this, ...)
     13.             └─SEMID::FlowGraph(adjMat, 1, adjMat)
     14.               └─igraph::get.edge.ids(flowGraph, rbind(1:m, 1:m + m))
     15.                 └─igraph::get_edge_ids(...)
     16.                   └─igraph:::el_to_vec(vp, call = rlang::caller_env())
     17.                     └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
     18.                       └─lifecycle:::deprecate_stop0(msg)
     19.                         └─rlang::cnd_signal(...)
    ── Error ('test_ancestral.R:19:17'): Ancestral identification does not identify edges erroneously. ──
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. └─SEMID::ancestralID(g) at test_ancestral.R:19:17
      2.   └─SEMID::generalGenericID(...)
      3.     └─SEMID::generalGenericID(...)
      4.       └─SEMID (local) idStepFunction(mixedGraph, unsolvedParents, solvedParents, identifier)
      5.         └─tianAncGraph$getHalfTrekSystem(allowedNodes, nodeParents)
      6.           ├─SEMID::getHalfTrekSystem(this, ...)
      7.           └─SEMID:::getHalfTrekSystem.MixedGraph(this, ...)
      8.             └─this$getTrekSystem(...)
      9.               ├─SEMID::getTrekSystem(this, ...)
     10.               └─SEMID:::getTrekSystem.MixedGraph(this, ...)
     11.                 └─this$.internalGraph$getTrekSystem(...)
     12.                   ├─SEMID::getTrekSystem(this, ...)
     13.                   └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
     14.                     └─this$.internalGraph$getTrekSystem(...)
     15.                       ├─SEMID::getTrekSystem(this, ...)
     16.                       └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
     17.                         └─this$.trekFlowGraph$updateEdgeCapacities(...)
     18.                           ├─SEMID::updateEdgeCapacities(this, ...)
     19.                           └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...)
     20.                             └─igraph::get.edge.ids(...)
     21.                               └─igraph::get_edge_ids(...)
     22.                                 └─igraph:::el_to_vec(vp, call = rlang::caller_env())
     23.                                   └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
     24.                                     └─lifecycle:::deprecate_stop0(msg)
     25.                                       └─rlang::cnd_signal(...)
    ── Error ('test_ancestral.R:44:17'): Old and new ancestralID implementations agree. ──
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. └─SEMID::ancestralID(MixedGraph(L, O)) at test_ancestral.R:44:17
      2.   └─SEMID::generalGenericID(...)
      3.     └─SEMID::generalGenericID(...)
      4.       └─SEMID (local) idStepFunction(mixedGraph, unsolvedParents, solvedParents, identifier)
      5.         └─tianAncGraph$getHalfTrekSystem(allowedNodes, nodeParents)
      6.           ├─SEMID::getHalfTrekSystem(this, ...)
      7.           └─SEMID:::getHalfTrekSystem.MixedGraph(this, ...)
      8.             └─this$getTrekSystem(...)
      9.               ├─SEMID::getTrekSystem(this, ...)
     10.               └─SEMID:::getTrekSystem.MixedGraph(this, ...)
     11.                 └─this$.internalGraph$getTrekSystem(...)
     12.                   ├─SEMID::getTrekSystem(this, ...)
     13.                   └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
     14.                     └─this$.internalGraph$getTrekSystem(...)
     15.                       ├─SEMID::getTrekSystem(this, ...)
     16.                       └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
     17.                         └─this$.trekFlowGraph$updateEdgeCapacities(...)
     18.                           ├─SEMID::updateEdgeCapacities(this, ...)
     19.                           └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...)
     20.                             └─igraph::get.edge.ids(...)
     21.                               └─igraph::get_edge_ids(...)
     22.                                 └─igraph:::el_to_vec(vp, call = rlang::caller_env())
     23.                                   └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
     24.                                     └─lifecycle:::deprecate_stop0(msg)
     25.                                       └─rlang::cnd_signal(...)
    ── Error ('test_edgewiseID.R:18:17'): Edgewise identification does not identify edges erroneously. ──
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. └─SEMID::htcID(g) at test_edgewiseID.R:18:17
      2.   └─SEMID::generalGenericID(mixedGraph, list(htcIdentifyStep), tianDecompose = tianDecompose)
      3.     └─SEMID::generalGenericID(...)
      4.       └─SEMID (local) idStepFunction(mixedGraph, unsolvedParents, solvedParents, identifier)
      5.         └─mixedGraph$getHalfTrekSystem(allowedNodes, nodeParents)
      6.           ├─SEMID::getHalfTrekSystem(this, ...)
      7.           └─SEMID:::getHalfTrekSystem.MixedGraph(this, ...)
      8.             └─this$getTrekSystem(...)
      9.               ├─SEMID::getTrekSystem(this, ...)
     10.               └─SEMID:::getTrekSystem.MixedGraph(this, ...)
     11.                 └─this$.internalGraph$getTrekSystem(...)
     12.                   ├─SEMID::getTrekSystem(this, ...)
     13.                   └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
     14.                     └─this$.internalGraph$getTrekSystem(...)
     15.                       ├─SEMID::getTrekSystem(this, ...)
     16.                       └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
     17.                         └─this$.trekFlowGraph$updateEdgeCapacities(...)
     18.                           ├─SEMID::updateEdgeCapacities(this, ...)
     19.                           └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...)
     20.                             └─igraph::get.edge.ids(...)
     21.                               └─igraph::get_edge_ids(...)
     22.                                 └─igraph:::el_to_vec(vp, call = rlang::caller_env())
     23.                                   └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
     24.                                     └─lifecycle:::deprecate_stop0(msg)
     25.                                       └─rlang::cnd_signal(...)
    ── Error ('test_edgewiseID.R:44:9'): TO DELETE ─────────────────────────────────
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. └─SEMID::htcID(g, tianDecompose = F) at test_edgewiseID.R:44:9
      2.   └─SEMID::generalGenericID(mixedGraph, list(htcIdentifyStep), tianDecompose = tianDecompose)
      3.     └─SEMID (local) idStepFunction(mixedGraph, unsolvedParents, solvedParents, identifier)
      4.       └─mixedGraph$getHalfTrekSystem(allowedNodes, nodeParents)
      5.         ├─SEMID::getHalfTrekSystem(this, ...)
      6.         └─SEMID:::getHalfTrekSystem.MixedGraph(this, ...)
      7.           └─this$getTrekSystem(...)
      8.             ├─SEMID::getTrekSystem(this, ...)
      9.             └─SEMID:::getTrekSystem.MixedGraph(this, ...)
     10.               └─this$.internalGraph$getTrekSystem(...)
     11.                 ├─SEMID::getTrekSystem(this, ...)
     12.                 └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
     13.                   └─this$.internalGraph$getTrekSystem(...)
     14.                     ├─SEMID::getTrekSystem(this, ...)
     15.                     └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
     16.                       └─this$.trekFlowGraph$updateEdgeCapacities(...)
     17.                         ├─SEMID::updateEdgeCapacities(this, ...)
     18.                         └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...)
     19.                           └─igraph::get.edge.ids(...)
     20.                             └─igraph::get_edge_ids(...)
     21.                               └─igraph:::el_to_vec(vp, call = rlang::caller_env())
     22.                                 └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
     23.                                   └─lifecycle:::deprecate_stop0(msg)
     24.                                     └─rlang::cnd_signal(...)
    ── Error ('test_lfhtcID.R:8:5'): lfhtcID returns correct value for known examples. ──
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. └─SEMID::lfhtcID(digraphExamples[[i]]$graph) at test_lfhtcID.R:8:5
      2.   └─SEMID::lfhtcIdentifyStep(...)
      3.     └─graph$getTrekSystem(...)
      4.       ├─SEMID::getTrekSystem(this, ...)
      5.       └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
      6.         └─this$.internalGraph$getTrekSystem(...)
      7.           ├─SEMID::getTrekSystem(this, ...)
      8.           └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
      9.             └─this$.trekFlowGraph$updateEdgeCapacities(...)
     10.               ├─SEMID::updateEdgeCapacities(this, ...)
     11.               └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...)
     12.                 └─igraph::get.edge.ids(...)
     13.                   └─igraph::get_edge_ids(...)
     14.                     └─igraph:::el_to_vec(vp, call = rlang::caller_env())
     15.                       └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
     16.                         └─lifecycle:::deprecate_stop0(msg)
     17.                           └─rlang::cnd_signal(...)
    ── Error ('test_trekSepID.R:25:17'): Edgewise identification does not identify edges erroneously. ──
    <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
    Error: The `vp` argument of `get_edge_ids()` is not allowed to be a 2 times 2
    matrix as of igraph 2.1.5.
    Backtrace:
         ▆
      1. └─SEMID (local) trekSepId(MixedGraph(L, O)) at test_trekSepID.R:25:17
      2.   └─SEMID::generalGenericID(mixedGraph, list(tsIdStep)) at test_trekSepID.R:11:5
      3.     └─SEMID::generalGenericID(...)
      4.       └─SEMID (local) idStepFunction(mixedGraph, unsolvedParents, solvedParents, identifier)
      5.         └─SEMID::trekSeparationIdentifyStep(...) at test_trekSepID.R:8:9
      6.           └─mixedGraph$getTrekSystem(sources, c(targets, i), avoidRightEdges = toRemoveOnRight)
      7.             ├─SEMID::getTrekSystem(this, ...)
      8.             └─SEMID:::getTrekSystem.MixedGraph(this, ...)
      9.               └─this$.internalGraph$getTrekSystem(...)
     10.                 ├─SEMID::getTrekSystem(this, ...)
     11.                 └─SEMID:::getTrekSystem.LatentDigraph(this, ...)
     12.                   └─this$.internalGraph$getTrekSystem(...)
     13.                     ├─SEMID::getTrekSystem(this, ...)
     14.                     └─SEMID:::getTrekSystem.LatentDigraphFixedOrder(this, ...)
     15.                       └─this$.trekFlowGraph$updateEdgeCapacities(...)
     16.                         ├─SEMID::updateEdgeCapacities(this, ...)
     17.                         └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...)
     18.                           └─igraph::get.edge.ids(...)
     19.                             └─igraph::get_edge_ids(...)
     20.                               └─igraph:::el_to_vec(vp, call = rlang::caller_env())
     21.                                 └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')")
     22.                                   └─lifecycle:::deprecate_stop0(msg)
     23.                                     └─rlang::cnd_signal(...)
    
    [ FAIL 7 | WARN 11 | SKIP 0 | PASS 965 ]
    Error: Test failures
    Execution halted

Package: sharpshootR
Check: examples
New result: ERROR
  Running examples in ‘sharpshootR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: table5.2
  > ### Title: Table 5.2 from Hole and Campbell, 1985.
  > ### Aliases: table5.2
  > ### Keywords: datasets
  > 
  > ### ** Examples
  > 
  > 
  > data("table5.2")
  > 
  > if(requireNamespace("igraph")) {
  +   
  +   # note special incantation to get the "correct" graph structure
  +   g <- igraph::graph_from_adjacency_matrix(table5.2, mode = 'upper', diag = FALSE, weighted = TRUE)
  +   
  +   # visualize
  +   op <- par(no.readonly = TRUE)
  +   
  +   par(mar = c(0,0,0,0))
  +   plot(g)
  +   
  +   plot(g, vertex.size = sqrt(igraph::degree(g) * 25), vertex.label.family = 'sans')
  +   
  +   # find communities
  +   cm <- igraph::cluster_walktrap(g)
  +   plot(cm, g, vertex.label.family = 'sans')
  +   
  +   par(op)
  + }
  Error in `igraph::graph_from_adjacency_matrix()`:
  ! Cannot create a graph object because the adjacency matrix contains
    NAs.
  Backtrace:
      ▆
   1. └─igraph::graph_from_adjacency_matrix(table5.2, mode = "upper", diag = FALSE, weighted = TRUE)
   2.   └─igraph:::ensure_no_na(adjmatrix, "adjacency matrix")
   3.     └─cli::cli_abort(...)
   4.       └─rlang::abort(...)
  Execution halted

Package: TDApplied
Check: examples
New result: ERROR
  Running examples in ‘TDApplied-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_vr_graph
  > ### Title: Plot a VR graph using the igraph package.
  > ### Aliases: plot_vr_graph
  > 
  > ### ** Examples
  > 
  > 
  > if(require("TDAstats") & require("igraph"))
  + {
  +   # simulate data from the unit circle and calculate 
  +   # its diagram
  +   df <- TDAstats::circle2d[sample(1:100,25),]
  +   diag <- TDAstats::calculate_homology(df,
  +                                        dim = 1,
  +                                        threshold = 2)
  +   
  +   # get minimum death radius of any data cluster
  +   min_death_H0 <- 
  +   min(diag[which(diag[,1] == 0),3L])
  +   
  +   # get birth and death radius of the loop
  +   loop_birth <- as.numeric(diag[nrow(diag),2L])
  +   loop_death <- as.numeric(diag[nrow(diag),3L])
  + 
  +   # compute VR graphs at radii half of 
  +   # min_death_H0 and the mean of loop_birth and 
  +   # loop_death, returning clusters
  +   graphs <- vr_graphs(X = df,eps = 
  +   c(0.5*min_death_H0,(loop_birth + loop_death)/2))
  +   
  +   # plot graph of smaller (first) radius
  +   plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0,
  +                   plot_isolated_vertices = TRUE)
  +   
  +   # plot graph of larger (second) radius
  +   plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2)
  +   
  +   # repeat but with rownames for df, each vertex
  +   # will be plotted with its rownames
  +   rownames(df) <- paste0("V",1:25)
  +   graphs <- vr_graphs(X = df,eps = 
  +   c(0.5*min_death_H0,(loop_birth + loop_death)/2))
  +   plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0,
  +                   plot_isolated_vertices = TRUE)
  +   
  +   # plot without vertex labels
  +   plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2,
  +                   vertex_labels = FALSE)
  +                  
  +   # plot only the graph component containing vertex "1"
  +   plot_vr_graph(graphs = graphs,eps = 0.5*min_death_H0,
  +                   component_of = "V1",plot_isolated_vertices = TRUE)
  +  
  +   # save the layout of the graph for adding features to 
  +   # the same graph layout, like color
  +   layout <- plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2,
  +                             return_layout = TRUE,vertex_labels = TRUE)
  +   cols <- rep("blue",25)
  +   cols[1:5] <- "red"
  +   plot_vr_graph(graphs = graphs,eps = (loop_birth + loop_death)/2,cols = cols,
  +                   layout = layout)
  +   
  + }
  Loading required package: TDAstats
  
  Attaching package: ‘TDAstats’
  
  The following object is masked from ‘package:TDApplied’:
  
      permutation_test
  
  Loading required package: igraph
  
  Attaching package: ‘igraph’
  
  The following objects are masked from ‘package:stats’:
  
      decompose, spectrum
  
  The following object is masked from ‘package:base’:
  
      union
  
  Error in if (vr[1] == vr[2]) { : missing value where TRUE/FALSE needed
  Calls: plot_vr_graph -> <Anonymous> -> norm_coords -> .layout.norm.col
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
  bootstrap_persistence_thresholds 1.270  0.033   5.409
  permutation_model_inference      0.627  0.115  16.673
  diagram_kkmeans                  0.220  0.073   5.984

Package: tidygraph
Check: tests
New result: ERROR
    Running ‘testthat.R’ [12s/12s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # This file is part of the standard setup for testthat.
    > # It is recommended that you do not modify it.
    > #
    > # Where should you do additional test configuration?
    > # Learn more about the roles of various files in:
    > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
    > # * https://testthat.r-lib.org/articles/special-files.html
    > 
    > library(testthat)
    > library(tidygraph)
    
    Attaching package: 'tidygraph'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following object is masked from 'package:stats':
    
        filter
    
    > 
    > test_check("tidygraph")
    Ungrouping `.data`...
    Splitting by nodes
    Unfocusing graph...
    `focus()` selected all nodes. Returning unfocused graph
    `focus()` didn't select any nodes. Returning unfocused graph
    Unfocusing graph...
    Unfocusing prior to grouping
    Unfocusing prior to morphing
    Unfocusing graph...
    Joining with `by = join_by(from, to)`
    Joining with `by = join_by(from, to)`
    Joining with `by = join_by(from, to)`
    Joining with `by = join_by(from, to)`
    Joining with `by = join_by(from, to)`
    Joining with `by = join_by(from, to)`
    Ungrouping `.data`...
    Subsetting by nodes
    Splitting by nodes
    Unfocusing prior to morphing
    [ FAIL 2 | WARN 20 | SKIP 1 | PASS 428 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test-random-walk.R:19:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-group.R:18:3'): grouping returns integer vector ────────────────
    <dplyr:::mutate_error/rlang_error/error/condition>
    Error in `mutate(d_tmp, ...)`: i In argument: `group = fn`.
    Caused by error in `modularity.igraph()`:
    ! At vendor/cigraph/src/community/modularity.c:177 : Weight vector size differs from number of edges. Invalid value
    Backtrace:
         ▆
      1. ├─testthat::expect_type(get_group(gr, group_label_prop()), "integer") at test-group.R:18:3
      2. │ └─testthat::quasi_label(enquo(object), arg = "object")
      3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─tidygraph (local) get_group(gr, group_label_prop())
      5. │ └─gr %>% mutate(group = fn) %>% pull(group) at test-group.R:2:3
      6. ├─dplyr::pull(., group)
      7. ├─dplyr::mutate(., group = fn)
      8. ├─tidygraph:::mutate.tbl_graph(., group = fn)
      9. │ └─tidygraph::mutate_as_tbl(.data, !!!dot)
     10. │   ├─dplyr::mutate(d_tmp, ...)
     11. │   └─dplyr:::mutate.data.frame(d_tmp, ...)
     12. │     └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
     13. │       ├─base::withCallingHandlers(...)
     14. │       └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
     15. │         └─mask$eval_all_mutate(quo)
     16. │           └─dplyr (local) eval()
     17. ├─tidygraph::group_label_prop()
     18. │ ├─igraph::membership(...)
     19. │ └─igraph::cluster_label_prop(...)
     20. │   └─igraph:::cluster_label_prop0(graph, weights, mode, initial, fixed)
     21. │     ├─igraph::modularity(...)
     22. │     └─igraph:::modularity.igraph(...)
     23. └─base::.handleSimpleError(...)
     24.   └─dplyr (local) h(simpleError(msg, call))
     25.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
    ── Error ('test-group.R:38:3'): grouping returns integer of correct length ─────
    <dplyr:::mutate_error/rlang_error/error/condition>
    Error in `mutate(d_tmp, ...)`: i In argument: `group = fn`.
    Caused by error in `modularity.igraph()`:
    ! At vendor/cigraph/src/community/modularity.c:177 : Weight vector size differs from number of edges. Invalid value
    Backtrace:
         ▆
      1. ├─testthat::expect_length(get_group(gr, group_label_prop()), igraph::gorder(gr)) at test-group.R:38:3
      2. │ └─testthat::quasi_label(enquo(object), arg = "object")
      3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
      4. ├─tidygraph (local) get_group(gr, group_label_prop())
      5. │ └─gr %>% mutate(group = fn) %>% pull(group) at test-group.R:2:3
      6. ├─dplyr::pull(., group)
      7. ├─dplyr::mutate(., group = fn)
      8. ├─tidygraph:::mutate.tbl_graph(., group = fn)
      9. │ └─tidygraph::mutate_as_tbl(.data, !!!dot)
     10. │   ├─dplyr::mutate(d_tmp, ...)
     11. │   └─dplyr:::mutate.data.frame(d_tmp, ...)
     12. │     └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
     13. │       ├─base::withCallingHandlers(...)
     14. │       └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
     15. │         └─mask$eval_all_mutate(quo)
     16. │           └─dplyr (local) eval()
     17. ├─tidygraph::group_label_prop()
     18. │ ├─igraph::membership(...)
     19. │ └─igraph::cluster_label_prop(...)
     20. │   └─igraph:::cluster_label_prop0(graph, weights, mode, initial, fixed)
     21. │     ├─igraph::modularity(...)
     22. │     └─igraph:::modularity.igraph(...)
     23. └─base::.handleSimpleError(...)
     24.   └─dplyr (local) h(simpleError(msg, call))
     25.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
    
    [ FAIL 2 | WARN 20 | SKIP 1 | PASS 428 ]
    Error: Test failures
    Execution halted

Package: tilemaps
Check: examples
New result: ERROR
  Running examples in ‘tilemaps-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: create_island
  > ### Title: Create a Tile for an Island
  > ### Aliases: create_island
  > 
  > ### ** Examples
  > 
  > library(sf)
  Linking to GEOS 3.14.0, GDAL 3.11.4, PROJ 9.6.2; sf_use_s2() is TRUE
  WARNING: different compile-time and runtime versions for GEOS found:
  Linked against: 3.14.0-CAPI-1.20.4 compiled against: 3.13.1-CAPI-1.19.2
  It is probably a good idea to reinstall sf (and maybe lwgeom too)
  > northeast <- governors[c(6,7,17,18,19,27,28,30,36,37,43),]
  > tile_map <- generate_map(northeast$geometry, square = FALSE)
  Error:
  ! The `neimode` argument of `bfs()` was deprecated in igraph 1.3.0 and
    is now defunct.
  ℹ Please use the `mode` argument instead.
  Backtrace:
      ▆
   1. └─tilemaps::generate_map(northeast$geometry, square = FALSE)
   2.   └─igraph::bfs(neighbor_graph, 1, neimode = "all", unreachable = FALSE)
   3.     └─lifecycle::deprecate_stop("1.3.0", "bfs(neimode = )", "bfs(mode = )")
   4.       └─lifecycle:::deprecate_stop0(msg)
   5.         └─rlang::cnd_signal(...)
  Execution halted

Package: tilemaps
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘tilemaps.Rmd’ using rmarkdown
  
  Quitting from tilemaps.Rmd:32-41 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'tilemaps.Rmd' failed with diagnostics:
  ℹ In argument: `tile_map = generate_map(geometry, square = FALSE,
    flat_topped = TRUE)`.
  Caused by error:
  ! The `neimode` argument of `bfs()` was deprecated in igraph 1.3.0 and
    is now defunct.
  ℹ Please use the `mode` argument instead.
  --- failed re-building ‘tilemaps.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘tilemaps.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: timeordered
Check: examples
New result: ERROR
  Running examples in ‘timeordered-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: transformspreadbyindividual
  > ### Title: A helper function to assess differences in spreading potential
  > ###   by vertex.
  > ### Aliases: transformspreadbyindividual
  > 
  > ### ** Examples
  > 
  > data(ants)
  > allindivs <- c(union(as.character(ants$VertexFrom), as.character(ants$VertexTo)), "NULL1", "NULL2")
  > g <- generatetonetwork(ants, allindivs)
  > sa <- spreadanalysis(g, seq(0,1000,by=50), 20)
  [1] 0.05
  [1] 0.1
  [1] 0.15
  [1] 0.2
  [1] 0.25
  [1] 0.3
  [1] 0.35
  [1] 0.4
  [1] 0.45
  [1] 0.5
  [1] 0.55
  [1] 0.6
  [1] 0.65
  [1] 0.7
  [1] 0.75
  [1] 0.8
  [1] 0.85
  [1] 0.9
  [1] 0.95
  [1] 1
  > b <- transformspreadbyindividual(sa)
  > plot(ts(b),plot.type="single",col=rainbow(ncol(b)),xlab="Time",ylab="Fraction reached")
  Error in xy.coords(x, NULL, log = log, setLab = FALSE) : 
    'list' object cannot be coerced to type 'double'
  Calls: plot -> plot.ts -> plotts -> xy.coords
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
  shortesttimepath      3.476  0.663  23.375
  generatetonetwork     3.055  0.461  24.955
  randomizetimes        3.134  0.378  25.405
  randomizeidentities   2.880  0.288  13.726
  plottonet             2.631  0.188  11.294
  shortesthoppath       2.597  0.187  11.329
  generatelatencies     1.422  0.675  16.096
  spreadanalysis        0.890  0.506  30.643
  generatenetworkslices 1.032  0.067   7.615