diff --git a/NAMESPACE b/NAMESPACE index 3ad0778d3fe..2237e9bca29 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -935,7 +935,6 @@ importFrom(utils,capture.output) importFrom(utils,edit) importFrom(utils,head) importFrom(utils,packageDescription) -importFrom(utils,packageName) importFrom(utils,read.table) importFrom(utils,setTxtProgressBar) importFrom(utils,tail) diff --git a/R/aaa-a-deprecate.R b/R/aaa-a-deprecate.R deleted file mode 100644 index 89a2285bce0..00000000000 --- a/R/aaa-a-deprecate.R +++ /dev/null @@ -1,29 +0,0 @@ - -# IGraph R package -# Copyright (C) 2014 Gabor Csardi -# 334 Harvard street, Cambridge, MA 02139 USA -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301 USA -# -################################################################### - -## For the future, right now, we do not warn or even message - -#' @importFrom utils packageName -deprecated <- function(old, new) { # nocov start - assign(old, new, envir = asNamespace(packageName())) -} # nocov end - diff --git a/R/make.R b/R/make.R index c1e7ac58199..3780d3c4752 100644 --- a/R/make.R +++ b/R/make.R @@ -1,4 +1,295 @@ +#' Create an igraph graph from a list of edges, or a notable graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph()` was renamed to `make_graph()` to create a more +#' consistent API. +#' @inheritParams make_graph +#' @keywords internal +#' @export +graph <- function(edges, ..., n = max(edges), isolates = NULL, directed = TRUE, dir = directed, simplify = TRUE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph()", "make_graph()") + if (!missing(dir) && missing(directed)) { + directed <- dir + } + current_call <- rlang::current_call() + current_args <- rlang::call_args(current_call) + current_args <- lapply(current_args, rlang::eval_tidy) + + if (missing(simplify)) { + rlang::exec("make_graph", !!!current_args) + } else { + current_args <- c(simplify = simplify, !!!current_args) + rlang::exec("make_graph", current_args) + } +} # nocov end + +#' Create an igraph graph from a list of edges, or a notable graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.famous()` was renamed to `make_graph()` to create a more +#' consistent API. +#' @inheritParams make_graph +#' @keywords internal +#' @export +graph.famous <- function(edges, ..., n = max(edges), isolates = NULL, directed = TRUE, dir = directed, simplify = TRUE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.famous()", "make_graph()") + if (!missing(dir) && missing(directed)) { + directed <- dir + } + + if (missing(simplify)) { + make_graph(edges = edges, n = n, isolates = isolates, directed = directed, ...) + } else { + make_graph(edges = edges, n = n, isolates = isolates, directed = directed, simplify = simplify, ...) + } +} # nocov end + +#' Line graph of a graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `line.graph()` was renamed to `make_line_graph()` to create a more +#' consistent API. +#' @inheritParams make_line_graph +#' @keywords internal +#' @export +line.graph <- function(graph) { # nocov start + lifecycle::deprecate_soft("2.0.0", "line.graph()", "make_line_graph()") + make_line_graph(graph = graph) +} # nocov end + +#' Create a ring graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.ring()` was renamed to `make_ring()` to create a more +#' consistent API. +#' @inheritParams make_ring +#' @keywords internal +#' @export +graph.ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.ring()", "make_ring()") + make_ring(n = n, directed = directed, mutual = mutual, circular = circular) +} # nocov end + +#' Create tree graphs +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.tree()` was renamed to `make_tree()` to create a more +#' consistent API. +#' @inheritParams make_tree +#' @keywords internal +#' @export +graph.tree <- function(n, children = 2, mode = c("out", "in", "undirected")) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.tree()", "make_tree()") + make_tree(n = n, children = children, mode = mode) +} # nocov end + +#' Create a star graph, a tree with n vertices and n - 1 leaves +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.star()` was renamed to `make_star()` to create a more +#' consistent API. +#' @inheritParams make_star +#' @keywords internal +#' @export +graph.star <- function(n, mode = c("in", "out", "mutual", "undirected"), center = 1) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.star()", "make_star()") + make_star(n = n, mode = mode, center = center) +} # nocov end + +#' Creating a graph from LCF notation +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.lcf()` was renamed to `graph_from_lcf()` to create a more +#' consistent API. +#' @inheritParams graph_from_lcf +#' @keywords internal +#' @export +graph.lcf <- function(n, shifts, repeats = 1) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.lcf()", "graph_from_lcf()") + graph_from_lcf(n = n, shifts = shifts, repeats = repeats) +} # nocov end + +#' Create a lattice graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.lattice()` was renamed to `make_lattice()` to create a more +#' consistent API. +#' @inheritParams make_lattice +#' @keywords internal +#' @export +graph.lattice <- function(dimvector = NULL, length = NULL, dim = NULL, nei = 1, directed = FALSE, mutual = FALSE, circular = FALSE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.lattice()", "make_lattice()") + make_lattice(dimvector = dimvector, length = length, dim = dim, nei = nei, directed = directed, mutual = mutual, circular = circular) +} # nocov end + +#' Kautz graphs +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.kautz()` was renamed to `make_kautz_graph()` to create a more +#' consistent API. +#' @inheritParams make_kautz_graph +#' @keywords internal +#' @export +graph.kautz <- function(m, n) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.kautz()", "make_kautz_graph()") + make_kautz_graph(m = m, n = n) +} # nocov end + +#' Create a complete (full) citation graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.full.citation()` was renamed to `make_full_citation_graph()` to create a more +#' consistent API. +#' @inheritParams make_full_citation_graph +#' @keywords internal +#' @export +graph.full.citation <- function(n, directed = TRUE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.full.citation()", "make_full_citation_graph()") + make_full_citation_graph(n = n, directed = directed) +} # nocov end + +#' Create a full bipartite graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.full.bipartite()` was renamed to `make_full_bipartite_graph()` to create a more +#' consistent API. +#' @inheritParams make_full_bipartite_graph +#' @keywords internal +#' @export +graph.full.bipartite <- function(n1, n2, directed = FALSE, mode = c("all", "out", "in")) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.full.bipartite()", "make_full_bipartite_graph()") + make_full_bipartite_graph(n1 = n1, n2 = n2, directed = directed, mode = mode) +} # nocov end + +#' Create a full graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.full()` was renamed to `make_full_graph()` to create a more +#' consistent API. +#' @inheritParams make_full_graph +#' @keywords internal +#' @export +graph.full <- function(n, directed = FALSE, loops = FALSE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.full()", "make_full_graph()") + make_full_graph(n = n, directed = directed, loops = loops) +} # nocov end + +#' Creating (small) graphs via a simple interface +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.formula()` was renamed to `graph_from_literal()` to create a more +#' consistent API. +#' @inheritParams graph_from_literal +#' @keywords internal +#' @export +graph.formula <- function(..., simplify = TRUE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.formula()", "graph_from_literal()") + mf <- as.list(match.call())[-1] + graph_from_literal_i(mf) +} # nocov end + +#' Create an extended chordal ring graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.extended.chordal.ring()` was renamed to `make_chordal_ring()` to create a more +#' consistent API. +#' @inheritParams make_chordal_ring +#' @keywords internal +#' @export +graph.extended.chordal.ring <- function(n, w, directed = FALSE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.extended.chordal.ring()", "make_chordal_ring()") + make_chordal_ring(n = n, w = w, directed = directed) +} # nocov end + +#' A graph with no edges +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.empty()` was renamed to `make_empty_graph()` to create a more +#' consistent API. +#' @inheritParams make_empty_graph +#' @keywords internal +#' @export +graph.empty <- function(n = 0, directed = TRUE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.empty()", "make_empty_graph()") + make_empty_graph(n = n, directed = directed) +} # nocov end + +#' De Bruijn graphs +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.de.bruijn()` was renamed to `make_de_bruijn_graph()` to create a more +#' consistent API. +#' @inheritParams make_de_bruijn_graph +#' @keywords internal +#' @export +graph.de.bruijn <- function(m, n) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.de.bruijn()", "make_de_bruijn_graph()") + make_de_bruijn_graph(m = m, n = n) +} # nocov end + +#' Create a bipartite graph +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.bipartite()` was renamed to `make_bipartite_graph()` to create a more +#' consistent API. +#' @inheritParams make_bipartite_graph +#' @keywords internal +#' @export +graph.bipartite <- function(types, edges, directed = FALSE) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.bipartite()", "make_bipartite_graph()") + make_bipartite_graph(types = types, edges = edges, directed = directed) +} # nocov end + +#' Create a graph from the Graph Atlas +#' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' `graph.atlas()` was renamed to `graph_from_atlas()` to create a more +#' consistent API. +#' @inheritParams graph_from_atlas +#' @keywords internal +#' @export +graph.atlas <- function(n) { # nocov start + lifecycle::deprecate_soft("2.0.0", "graph.atlas()", "graph_from_atlas()") + graph_from_atlas(n = n) +} # nocov end + ## ---------------------------------------------------------------- ## ## IGraph R package @@ -506,7 +797,6 @@ with_graph_ <- function(...) { #' groups, Journal of Anthropological Research 33, 452-473 (1977). } } #' #' @encoding UTF-8 -#' @aliases graph.famous graph #' @param edges A vector defining the edges, the first edge points #' from the first element to the second, the second edge from the third #' to the fourth, etc. For a numeric vector, these are interpreted @@ -687,7 +977,6 @@ undirected_graph <- function(...) constructor_spec(make_undirected_graph, ...) #' A graph with no edges #' -#' @aliases graph.empty #' @concept Empty graph. #' @param n Number of vertices. #' @param directed Whether to create a directed graph. @@ -797,7 +1086,6 @@ empty_graph <- function(...) constructor_spec(make_empty_graph, ...) #' #' See more examples below. #' -#' @aliases graph.formula #' @param ... For `graph_from_literal()` the formulae giving the #' structure of the graph, see details below. For `from_literal()` #' all arguments are passed to `graph_from_literal()`. @@ -959,7 +1247,6 @@ from_literal <- function(...) { #' `star()` creates a star graph, in this every single vertex is #' connected to the center vertex and nobody else. #' -#' @aliases graph.star #' @concept Star graph #' @param n Number of vertices. #' @param mode It defines the direction of the @@ -1011,7 +1298,6 @@ star <- function(...) constructor_spec(make_star, ...) #' Create a full graph #' -#' @aliases graph.full #' @concept Full graph #' @param n Number of vertices. #' @param directed Whether to create a directed graph. @@ -1051,7 +1337,6 @@ full_graph <- function(...) constructor_spec(make_full_graph, ...) #' `length` and `dim`. In the second form you omit #' `dimvector` and supply `length` and `dim`. #' -#' @aliases graph.lattice #' @concept Lattice #' @param dimvector A vector giving the size of the lattice in each #' dimension. @@ -1112,7 +1397,6 @@ lattice <- function(...) constructor_spec(make_lattice, ...) #' A ring is a one-dimensional lattice and this function is a special case #' of [make_lattice()]. #' -#' @aliases graph.ring #' @param n Number of vertices. #' @param directed Whether the graph is directed. #' @param mutual Whether directed edges are mutual. It is ignored in @@ -1153,7 +1437,6 @@ ring <- function(...) constructor_spec(make_ring, ...) #' Create a k-ary tree graph, where almost all vertices other than the leaves #' have the same number of children. #' -#' @aliases graph.tree #' @concept Trees. #' @param n Number of vertices. #' @param children Integer scalar, the number of children of a vertex @@ -1275,7 +1558,6 @@ from_prufer <- function(...) constructor_spec(make_from_prufer, ...) #' automorphisms. #' } #' -#' @aliases graph.atlas #' @concept Graph Atlas. #' @param n The id of the graph to create. #' @return An igraph graph. @@ -1317,7 +1599,6 @@ atlas <- function(...) constructor_spec(graph_from_atlas, ...) #' of total nodes. See also Kotsis, G: Interconnection Topologies for #' Parallel Processing Systems, PARS Mitteilungen 11, 1-6, 1993. #' -#' @aliases graph.extended.chordal.ring #' @param n The number of vertices. #' @param w A matrix which specifies the extended chordal ring. See #' details below. @@ -1366,7 +1647,6 @@ chordal_ring <- function(...) constructor_spec(make_chordal_ring, ...) #' the first vertex's corresponding edge is the same as the source of the #' second vertex's corresponding edge. #' -#' @aliases line.graph #' @param graph The input graph, it can be directed or undirected. #' @return A new graph object. #' @author Gabor Csardi \email{csardi.gabor@@gmail.com}, the first version of @@ -1417,7 +1697,6 @@ line_graph <- function(...) constructor_spec(make_line_graph, ...) #' De Bruijn graphs have some interesting properties, please see another #' source, e.g. Wikipedia for details. #' -#' @aliases graph.de.bruijn #' @param m Integer scalar, the size of the alphabet. See details below. #' @param n Integer scalar, the length of the labels. See details below. #' @return A graph object. @@ -1463,7 +1742,6 @@ de_bruijn_graph <- function(...) constructor_spec(make_de_bruijn_graph, ...) #' Kautz graphs have some interesting properties, see e.g. Wikipedia for #' details. #' -#' @aliases graph.kautz #' @param m Integer scalar, the size of the alphabet. See details below. #' @param n Integer scalar, the length of the labels. See details below. #' @return A graph object. @@ -1504,7 +1782,6 @@ kautz_graph <- function(...) constructor_spec(make_kautz_graph, ...) #' this is boolean and `FALSE` for the vertices of the first kind and #' `TRUE` for vertices of the second kind. #' -#' @aliases graph.full.bipartite #' @param n1 The number of vertices of the first kind. #' @param n2 The number of vertices of the second kind. #' @param directed Logical scalar, whether the graphs is directed. @@ -1574,7 +1851,6 @@ full_bipartite_graph <- function(...) constructor_spec(make_full_bipartite_graph #' `is_bipartite()` checks whether the graph is bipartite or not. It just #' checks whether the graph has a vertex attribute called `type`. #' -#' @aliases graph.bipartite is.bipartite #' @param types A vector giving the vertex types. It will be coerced into #' boolean. The length of the vector gives the number of vertices in the graph. #' When the vector is a named vector, the names will be attached to the graph @@ -1642,7 +1918,6 @@ bipartite_graph <- function(...) constructor_spec(make_bipartite_graph, ...) #' directed graph, where every `i->j` edge is present if and only if #' \eqn{j + +* Version: 1.3.15 +* GitHub: https://github.com/santikka/causaleffect +* Source code: https://github.com/cran/causaleffect +* Date/Publication: 2022-07-14 09:10:05 UTC +* Number of recursive dependencies: 17 + +Run `revdepcheck::cloud_details(, "causaleffect")` for more info + + + +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘causaleffect-Ex.R’ failed + The error most likely occurred in: + + > ### Name: causal.effect + > ### Title: Identify a causal effect + > ### Aliases: causal.effect + > + > ### ** Examples + > + > library(igraph) + ... + > # Here the bidirected edge between X and Z is set to be unobserved in graph g + > # This is denoted by giving them a description attribute with the value "U" + > # The edges in question are the fourth and the fifth edge + > g <- set.edge.attribute(graph = g, name = "description", index = c(4,5), value = "U") + Warning: `set.edge.attribute()` was deprecated in igraph 2.0.0. + ℹ Please use `set_edge_attr()` instead. + > causal.effect("y", "x", G = g) + Error in simple_es_index(x, ii) : Unknown edge selected + Calls: causal.effect ... [ -> [.igraph.es -> lapply -> FUN -> simple_es_index + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘causaleffect.ltx’ using tex + Error: processing vignette 'causaleffect.ltx' failed with diagnostics: + Running 'texi2dvi' on 'causaleffect.ltx' failed. + LaTeX errors: + ! LaTeX Error: File `thumbpdf.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + l.16 \usepackage + {csquotes}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘simplification.ltx’ + + SUMMARY: processing the following files failed: + ‘causaleffect.ltx’ ‘simplification.ltx’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# centiserve + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/centiserve +* Date/Publication: 2017-07-15 09:34:41 UTC +* Number of recursive dependencies: 14 + +Run `revdepcheck::cloud_details(, "centiserve")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘centiserve-Ex.R’ failed + The error most likely occurred in: + + > ### Name: averagedis + > ### Title: Find the average distance of a node + > ### Aliases: averagedis + > + > ### ** Examples + > + > g <- graph(c(1,2,2,3,3,4,4,2), directed=FALSE) + Warning: `graph()` was deprecated in igraph 2.0.0. + ℹ Please use `make_graph()` instead. + > averagedis(g) + Error in getIgraphOpt("add.vertex.names") && is.named(graph) : + invalid 'x' type in 'x && y' + Calls: averagedis + Execution halted + ``` + +# cfid + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/santikka/cfid +* Source code: https://github.com/cran/cfid +* Date/Publication: 2023-11-27 16:00:04 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "cfid")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cfid) + > + > test_check("cfid") + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 203 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─cfid::import_graph(ig) + 5. └─cfid::dag(paste0(c(g_obs, g_unobs), collapse = "; ")) + 6. └─cfid:::stopifnot_(nzchar(x), "Argument `x` contains only whitespace or special characters.") + 7. └─cfid:::stop_(message) + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 203 ] + Error: Test failures + Execution halted + ``` + +# CINNA + +
+ +* Version: 1.2.2 +* GitHub: NA +* Source code: https://github.com/cran/CINNA +* Date/Publication: 2023-08-08 16:40:02 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "CINNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CINNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dangalchev_closeness_centrality + > ### Title: Dangalchev Closeness Centrality + > ### Aliases: dangalchev_closeness_centrality + > + > ### ** Examples + > + > + ... + > data(zachary) + > + > dangalchev_closeness_centrality(zachary) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in getIgraphOpt("add.vertex.names") && is_named(x) : + invalid 'x' type in 'x && y' + Calls: dangalchev_closeness_centrality + Execution halted + ``` + +* checking re-building of vignette outputs ... ERROR + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CINNA.Rmd’ using rmarkdown + + Quitting from lines 247-250 [unnamed-chunk-13] (CINNA.Rmd) + Error: processing vignette 'CINNA.Rmd' failed with diagnostics: + perplexity is too large for the number of samples + --- failed re-building ‘CINNA.Rmd’ + + SUMMARY: processing the following file failed: + ‘CINNA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘circlize’ ‘utils’ + All declared Imports should be used. + ``` + # countland
@@ -65,7 +279,7 @@ Run `revdepcheck::cloud_details(, "DiagrammeR")` for more info > > suppressWarnings(RNGversion("3.5.0")) > test_check("DiagrammeR") - [ FAIL 2 | WARN 12 | SKIP 0 | PASS 2128 ] + [ FAIL 2 | WARN 13 | SKIP 0 | PASS 2128 ] ... 1/1 mismatches @@ -75,7 +289,7 @@ Run `revdepcheck::cloud_details(, "DiagrammeR")` for more info 1/1 mismatches [1] 2 - 4 == -2 - [ FAIL 2 | WARN 12 | SKIP 0 | PASS 2128 ] + [ FAIL 2 | WARN 13 | SKIP 0 | PASS 2128 ] Error: Test failures Execution halted ``` @@ -87,6 +301,122 @@ Run `revdepcheck::cloud_details(, "DiagrammeR")` for more info Note: found 1 marked UTF-8 string ``` +# dosearch + +
+ +* Version: 1.0.8 +* GitHub: NA +* Source code: https://github.com/cran/dosearch +* Date/Publication: 2021-08-19 16:40:02 UTC +* Number of recursive dependencies: 18 + +Run `revdepcheck::cloud_details(, "dosearch")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dosearch-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dosearch + > ### Title: Identify a causal effect from arbitrary experiments and + > ### observations + > ### Aliases: dosearch + > + > ### ** Examples + > + ... + + g_igraph <- igraph::set.edge.attribute(g_igraph, "description", 3:4, "U") + + dosearch(data2, query2, g_igraph) + + } + Warning: `graph.formula()` was deprecated in igraph 2.0.0. + ℹ Please use `graph_from_literal()` instead. + Warning: `set.edge.attribute()` was deprecated in igraph 2.0.0. + ℹ Please use `set_edge_attr()` instead. + Error in graph_split[[x]] : subscript out of bounds + Calls: dosearch -> get_derivation_dag -> lapply -> FUN + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + libs 6.2Mb + ``` + +# fanovaGraph + +
+ +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/fanovaGraph +* Date/Publication: 2020-10-07 12:10:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "fanovaGraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fanovaGraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estimateGraph + > ### Title: FANOVA graph estimation. + > ### Aliases: estimateGraph print.graphlist + > + > ### ** Examples + > + > # Ishigami function, true analytical values: D12 = D23 = 0, D13 =~ 3.374 + > q.arg = list(list(min=-pi, max=pi), list(min=-pi, max=pi), list(min=-pi, max=pi)) + > estimateGraph(f.mat=ishigami.fun, d=3, q.arg=q.arg, n.tot=10000, method="LiuOwen") + Error in (function (edges, n = max(edges), directed = TRUE) : + unused arguments (3, FALSE) + Calls: estimateGraph ... max_cliques -> ensure_igraph -> graph -> make_graph -> do.call + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘run-all.R’ + Running the tests in ‘tests/run-all.R’ failed. + Complete output: + > library(testthat) + > library(fanovaGraph) + Loading required package: sensitivity + Loading required package: igraph + + Attaching package: 'igraph' + + ... + 3. ├─igraph::maximal.cliques(graph(as.vector(t(E)), d, FALSE)) + 4. │ └─igraph::max_cliques(...) + 5. │ └─igraph:::ensure_igraph(graph) + 6. └─igraph::graph(as.vector(t(E)), d, FALSE) + 7. └─igraph::make_graph(...) + 8. └─base::do.call(old_graph, args) + + [ FAIL 6 | WARN 3 | SKIP 0 | PASS 6 ] + Error: Test failures + Execution halted + ``` + # ggnetwork
@@ -208,7 +538,7 @@ Run `revdepcheck::cloud_details(, "intergraph")` for more info > library(intergraph) > > test_check("intergraph") - [ FAIL 2 | WARN 138 | SKIP 0 | PASS 54 ] + [ FAIL 2 | WARN 141 | SKIP 0 | PASS 54 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ... @@ -219,7 +549,7 @@ Run `revdepcheck::cloud_details(, "intergraph")` for more info 1. └─testthat::expect_snapshot(print(r)) at test-netcompare.R:5:3 2. └─rlang::cnd_signal(state$error) - [ FAIL 2 | WARN 138 | SKIP 0 | PASS 54 ] + [ FAIL 2 | WARN 141 | SKIP 0 | PASS 54 ] Error: Test failures Execution halted ``` @@ -260,7 +590,7 @@ Run `revdepcheck::cloud_details(, "manynet")` for more info 1/4 mismatches [1] 0 - 1 == -1 - [ FAIL 1 | WARN 11 | SKIP 14 | PASS 329 ] + [ FAIL 1 | WARN 13 | SKIP 14 | PASS 329 ] Error: Test failures Execution halted ``` @@ -439,7 +769,7 @@ Run `revdepcheck::cloud_details(, "nat")` for more info 7. └─igraph::delete.vertices(g, verticestoprune) 8. └─igraph::delete_vertices(graph = graph, v = v) - [ FAIL 1 | WARN 11 | SKIP 5 | PASS 787 ] + [ FAIL 1 | WARN 21 | SKIP 5 | PASS 787 ] Error: Test failures Execution halted ``` @@ -843,3 +1173,37 @@ Run `revdepcheck::cloud_details(, "tidygraph")` for more info Execution halted ``` +# TreeDimensionTest + +
+ +* Version: 0.0.2 +* GitHub: NA +* Source code: https://github.com/cran/TreeDimensionTest +* Date/Publication: 2022-03-12 10:30:07 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "TreeDimensionTest")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... ERROR + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 46-56 [unnamed-chunk-5] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + At vendor/cigraph/src/graph/type_indexededgelist.c:101 : Number of vertices must not be negative. Invalid value + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` +