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: 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: 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))) [25-10-10 01:46:53] 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) [25-10-10 01:46:53] Generating graph of layer mrna for groupA... [25-10-10 01:46:53] Reducing network by WGCNA::pickHardThreshold... [25-10-10 01:46:53] R2 cutoff: 0.65 [25-10-10 01:46:54] 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 6.808 0.308 7.116 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: 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 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 0x560dfffffff8, 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/RtmpN9XxXN/filed2e617074f58.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 0.350 0 5.946 search_klass 0.011 0 60.138 Package: multinet 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 Threshold for CPE solver (default: 25) * -e, --edges Edge list file -h, --help Print a short help message -l, --log Log level (default: 0) -m, --threads Number of threads (default: 1) --mst Use primal heuristic only * -n, --nodes Node list file -o, --output-dir Solver output directory -p, --epsilon Maximum allowed absolute score error for solver (default: 0.0) --pl, --preprocessing-level [Integer] Preprocessing level (default: 2) -s, --signals Signals file -t, --timelimit 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/16s] 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 ───────── 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 ───────── 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: 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 . 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’ [44s/44s] 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 ─────── 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. ── 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. ── 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. ── 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 ───────────────────────────────── 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. ── 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. ── 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$updateEdgeCapacities(...) 16. ├─SEMID::updateEdgeCapacities(this, ...) 17. └─SEMID:::updateEdgeCapacities.FlowGraph(this, ...) 18. └─igraph::get.edge.ids(...) 19. └─igraph::get_edge_ids(...) 20. └─igraph:::el_to_vec(vp, call = rlang::caller_env()) 21. └─lifecycle::deprecate_stop("2.1.5", "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')") 22. └─lifecycle:::deprecate_stop0(msg) 23. └─rlang::cnd_signal(...) [ FAIL 7 | WARN 11 | SKIP 0 | PASS 965 ] Error: Test failures Execution halted Package: timeordered Check: examples New result: ERROR Running examples in ‘timeordered-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: transformspreadbyindividual > ### Title: A helper function to assess differences in spreading potential > ### by vertex. > ### Aliases: transformspreadbyindividual > > ### ** Examples > > data(ants) > allindivs <- c(union(as.character(ants$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) > heatmap(b, Rowv=NA, Colv=NA, scale='none', xlab="Individual", ylab="Time") Error in heatmap(b, Rowv = NA, Colv = NA, scale = "none", xlab = "Individual", : 'x' must be a numeric matrix Execution halted Package: zoomerjoin Check: whether package can be installed New result: ERROR Installation failed.