CRAN Package Check Results for Maintainer ‘Alex T. Kalinka <alex.t.kalinka at gmail.com>’

Last updated on 2020-01-20 23:50:36 CET.

Package ERROR NOTE
hint 13
linkcomm 1 12

Package hint

Current CRAN status: NOTE: 13

Version: 0.1-1
Check: R code for possible problems
Result: NOTE
    overlay.sim: no visible global function definition for 'points'
    plotDistr: no visible global function definition for 'dev.hold'
    plotDistr: no visible global function definition for 'dev.flush'
    plotDistr: no visible global function definition for 'plot'
    plotDistr: no visible global function definition for 'segments'
    Undefined global functions or variables:
     dev.flush dev.hold plot points segments
    Consider adding
     importFrom("grDevices", "dev.flush", "dev.hold")
     importFrom("graphics", "plot", "points", "segments")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.1-1
Check: compiled code
Result: NOTE
    File ‘hint/libs/hint.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Package linkcomm

Current CRAN status: ERROR: 1, NOTE: 12

Version: 1.0-11
Check: R code for possible problems
Result: NOTE
    .COL: no visible global function definition for 'is.leaf'
    corLinkcommCentrality: no visible global function definition for 'lm'
    corLinkcommCentrality: no visible global function definition for
     'abline'
    corLinkcommCentrality: no visible global function definition for 'cor'
    cutDendrogramAt: no visible global function definition for
     'as.dendrogram'
    cutDendrogramAt: no visible global function definition for
     'colorRampPalette'
    cutDendrogramAt: no visible global function definition for 'dendrapply'
    cutDendrogramAt: no visible global function definition for 'abline'
    cutDendrogramAt: no visible global function definition for 'mtext'
    getClusterRelatedness: no visible global function definition for
     'as.dist'
    getClusterRelatedness: no visible global function definition for
     'hclust'
    getLinkCommunities: no visible global function definition for 'as.dist'
    getLinkCommunities: no visible global function definition for 'hclust'
    getLinkCommunities: no visible global function definition for 'par'
    getLinkCommunities: no visible global function definition for 'abline'
    getLinkCommunities: no visible global function definition for 'lines'
    layout.spencer.circle: no visible global function definition for
     'runif'
    meta.communities: no visible global function definition for 'hclust'
    meta.communities: no visible global function definition for 'as.dist'
    plotLinkCommDend: no visible global function definition for
     'as.dendrogram'
    plotLinkCommDend: no visible global function definition for
     'colorRampPalette'
    plotLinkCommDend: no visible global function definition for
     'dendrapply'
    plotLinkCommDend: no visible global function definition for 'plot'
    plotLinkCommDend: no visible global function definition for 'abline'
    plotLinkCommDend: no visible global function definition for 'mtext'
    plotLinkCommGraph: no visible global function definition for
     'colorRampPalette'
    plotLinkCommGraph: no visible global function definition for 'dev.hold'
    plotLinkCommGraph: no visible global function definition for
     'dev.flush'
    plotLinkCommGraph: no visible global function definition for 'par'
    plotLinkCommGraph: no visible global function definition for 'plot'
    plotLinkCommGraph: no visible global function definition for 'polygon'
    plotLinkCommGraph: no visible global function definition for 'text'
    plotLinkCommGraph: no visible global function definition for 'points'
    plotLinkCommMembers: no visible global function definition for
     'colorRampPalette'
    plotLinkCommSumm: no visible global function definition for 'par'
    plotLinkCommSumm: no visible global function definition for
     'as.dendrogram'
    plotLinkCommSumm: no visible global function definition for
     'colorRampPalette'
    plotLinkCommSumm: no visible global function definition for
     'dendrapply'
    plotLinkCommSumm: no visible global function definition for 'plot.new'
    plotLinkCommSumm: no visible global function definition for 'plot'
    plotLinkCommSummComm: no visible global function definition for
     'colorRampPalette'
    plotLinkCommSummComm: no visible global function definition for
     'barplot'
    plotLinkCommSummComm: no visible global function definition for
     'abline'
    plotOCGraph: no visible global function definition for
     'colorRampPalette'
    plotOCGraph: no visible global function definition for 'dev.hold'
    plotOCGraph: no visible global function definition for 'dev.flush'
    plotOCGraph: no visible global function definition for 'plot'
    plotOCGraph: no visible global function definition for 'polygon'
    plotOCGraph: no visible global function definition for 'text'
    Undefined global functions or variables:
     abline as.dendrogram as.dist barplot colorRampPalette cor dendrapply
     dev.flush dev.hold hclust is.leaf lines lm mtext par plot plot.new
     points polygon runif text
    Consider adding
     importFrom("grDevices", "colorRampPalette", "dev.flush", "dev.hold")
     importFrom("graphics", "abline", "barplot", "lines", "mtext", "par",
     "plot", "plot.new", "points", "polygon", "text")
     importFrom("stats", "as.dendrogram", "as.dist", "cor", "dendrapply",
     "hclust", "is.leaf", "lm", "runif")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0-11
Check: examples
Result: ERROR
    Running examples in 'linkcomm-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: linkcomm-package
    > ### Title: The 'linkcomm' package
    > ### Aliases: linkcomm-package linkcomm
    >
    > ### ** Examples
    >
    > ## Generate graph and extract link communities.
    > g <- swiss[,3:4]
    > lc <- getLinkCommunities(g)
    
     Checking for loops and duplicate edges... 0.000%
     Checking for loops and duplicate edges... 2.174%
     Checking for loops and duplicate edges... 4.348%
     Checking for loops and duplicate edges... 6.522%
     Checking for loops and duplicate edges... 8.696%
     Checking for loops and duplicate edges... 10.870%
     Checking for loops and duplicate edges... 13.043%
     Checking for loops and duplicate edges... 15.217%
     Checking for loops and duplicate edges... 17.391%
     Checking for loops and duplicate edges... 19.565%
     Checking for loops and duplicate edges... 21.739%
     Checking for loops and duplicate edges... 23.913%
     Checking for loops and duplicate edges... 26.087%
     Checking for loops and duplicate edges... 28.261%
     Checking for loops and duplicate edges... 30.435%
     Checking for loops and duplicate edges... 32.609%
     Checking for loops and duplicate edges... 34.783%
     Checking for loops and duplicate edges... 36.957%
     Checking for loops and duplicate edges... 39.130%
     Checking for loops and duplicate edges... 41.304%
     Checking for loops and duplicate edges... 43.478%
     Checking for loops and duplicate edges... 45.652%
     Checking for loops and duplicate edges... 47.826%
     Checking for loops and duplicate edges... 50.000%
     Checking for loops and duplicate edges... 52.174%
     Checking for loops and duplicate edges... 54.348%
     Checking for loops and duplicate edges... 56.522%
     Checking for loops and duplicate edges... 58.696%
     Checking for loops and duplicate edges... 60.870%
     Checking for loops and duplicate edges... 63.043%
     Checking for loops and duplicate edges... 65.217%
     Checking for loops and duplicate edges... 67.391%
     Checking for loops and duplicate edges... 69.565%
     Checking for loops and duplicate edges... 71.739%
     Checking for loops and duplicate edges... 73.913%
     Checking for loops and duplicate edges... 76.087%
     Checking for loops and duplicate edges... 78.261%
     Checking for loops and duplicate edges... 80.435%
     Checking for loops and duplicate edges... 82.609%
     Checking for loops and duplicate edges... 84.783%
     Checking for loops and duplicate edges... 86.957%
     Checking for loops and duplicate edges... 89.130%
     Checking for loops and duplicate edges... 91.304%
     Checking for loops and duplicate edges... 93.478%
     Checking for loops and duplicate edges... 95.652%
     Checking for loops and duplicate edges... 97.826%
     Checking for loops and duplicate edges... 100.000%
     Found and removed 4 loop(s)
     Found and removed 2 duplicate edge(s)
    
     Calculating edge similarities for 41 edges... 0.00%
     Calculating edge similarities for 41 edges... 2.56%
     Calculating edge similarities for 41 edges... 5.13%
     Calculating edge similarities for 41 edges... 7.69%
     Calculating edge similarities for 41 edges... 10.26%
     Calculating edge similarities for 41 edges... 12.82%
     Calculating edge similarities for 41 edges... 15.38%
     Calculating edge similarities for 41 edges... 17.95%
     Calculating edge similarities for 41 edges... 20.51%
     Calculating edge similarities for 41 edges... 23.08%
     Calculating edge similarities for 41 edges... 25.64%
     Calculating edge similarities for 41 edges... 28.21%
     Calculating edge similarities for 41 edges... 30.77%
     Calculating edge similarities for 41 edges... 33.33%
     Calculating edge similarities for 41 edges... 35.90%
     Calculating edge similarities for 41 edges... 38.46%
     Calculating edge similarities for 41 edges... 41.03%
     Calculating edge similarities for 41 edges... 43.59%
     Calculating edge similarities for 41 edges... 46.15%
     Calculating edge similarities for 41 edges... 48.72%
     Calculating edge similarities for 41 edges... 51.28%
     Calculating edge similarities for 41 edges... 53.85%
     Calculating edge similarities for 41 edges... 56.41%
     Calculating edge similarities for 41 edges... 58.97%
     Calculating edge similarities for 41 edges... 61.54%
     Calculating edge similarities for 41 edges... 64.10%
     Calculating edge similarities for 41 edges... 66.67%
     Calculating edge similarities for 41 edges... 69.23%
     Calculating edge similarities for 41 edges... 71.79%
     Calculating edge similarities for 41 edges... 74.36%
     Calculating edge similarities for 41 edges... 76.92%
     Calculating edge similarities for 41 edges... 79.49%
     Calculating edge similarities for 41 edges... 82.05%
     Calculating edge similarities for 41 edges... 84.62%
     Calculating edge similarities for 41 edges... 87.18%
     Calculating edge similarities for 41 edges... 89.74%
     Calculating edge similarities for 41 edges... 92.31%
     Calculating edge similarities for 41 edges... 94.87%
     Calculating edge similarities for 41 edges... 97.44%
     Calculating edge similarities for 41 edges... 100.00%
     Hierarchical clustering of edges...
    
     Calculating link densities... 0.00%
     Calculating link densities... 2.56%
     Calculating link densities... 5.13%
     Calculating link densities... 7.69%
     Calculating link densities... 10.26%
     Calculating link densities... 12.82%
     Calculating link densities... 15.38%
     Calculating link densities... 17.95%
     Calculating link densities... 20.51%
     Calculating link densities... 23.08%
     Calculating link densities... 25.64%
     Calculating link densities... 28.21%
     Calculating link densities... 30.77%
     Calculating link densities... 33.33%
     Calculating link densities... 35.90%
     Calculating link densities... 38.46%
     Calculating link densities... 41.03%
     Calculating link densities... 43.59%
     Calculating link densities... 46.15%
     Calculating link densities... 48.72%
     Calculating link densities... 51.28%
     Calculating link densities... 53.85%
     Calculating link densities... 56.41%
     Calculating link densities... 58.97%
     Calculating link densities... 61.54%
     Calculating link densities... 64.10%
     Calculating link densities... 66.67%
     Calculating link densities... 69.23%
     Calculating link densities... 71.79%
     Calculating link densities... 74.36%
     Calculating link densities... 76.92%
     Calculating link densities... 79.49%
     Calculating link densities... 82.05%
     Calculating link densities... 84.62%
     Calculating link densities... 87.18%
     Calculating link densities... 89.74%
     Calculating link densities... 92.31%
     Calculating link densities... 94.87%
     Calculating link densities... 97.44%
     Calculating link densities... 100.00%
     Maximum partition density = 0.2601626
     Finishing up...1/4... 12%
     Finishing up...1/4... 25%
     Finishing up...1/4... 37%
     Finishing up...1/4... 50%
     Finishing up...1/4... 62%
     Finishing up...1/4... 75%
     Finishing up...1/4... 87%
     Finishing up...1/4... 100%
     Finishing up...2/4... 12%
     Finishing up...2/4... 25%
     Finishing up...2/4... 37%
     Finishing up...2/4... 50%
     Finishing up...2/4... 62%
     Finishing up...2/4... 75%
     Finishing up...2/4... 87%
     Finishing up...2/4... 100%
     Finishing up...3/4... 12%
     Finishing up...3/4... 25%
     Finishing up...3/4... 37%
     Finishing up...3/4... 50%
     Finishing up...3/4... 62%
     Finishing up...3/4... 75%
     Finishing up...3/4... 87%
     Finishing up...3/4... 100%
    
     Finishing up...4/4... 0.00%
     Finishing up...4/4... 4.76%
     Finishing up...4/4... 9.52%
     Finishing up...4/4... 14.29%
     Finishing up...4/4... 19.05%
     Finishing up...4/4... 23.81%
     Finishing up...4/4... 28.57%
     Finishing up...4/4... 33.33%
     Finishing up...4/4... 38.10%
     Finishing up...4/4... 42.86%
     Finishing up...4/4... 47.62%
     Finishing up...4/4... 52.38%
     Finishing up...4/4... 57.14%
     Finishing up...4/4... 61.90%
     Finishing up...4/4... 66.67%
     Finishing up...4/4... 71.43%
     Finishing up...4/4... 76.19%
     Finishing up...4/4... 80.95%
     Finishing up...4/4... 85.71%
     Finishing up...4/4... 90.48%
     Finishing up...4/4... 95.24%
     Finishing up...4/4... 100.00%
     Plotting...
     Colouring dendrogram... 1%
     Colouring dendrogram... 2%
     Colouring dendrogram... 3%
     Colouring dendrogram... 4%
     Colouring dendrogram... 6%
     Colouring dendrogram... 7%
     Colouring dendrogram... 8%
     Colouring dendrogram... 9%
     Colouring dendrogram... 11%
     Colouring dendrogram... 12%
     Colouring dendrogram... 13%
     Colouring dendrogram... 14%
     Colouring dendrogram... 16%
     Colouring dendrogram... 17%
     Colouring dendrogram... 18%
     Colouring dendrogram... 19%
     Colouring dendrogram... 20%
     Colouring dendrogram... 22%
     Colouring dendrogram... 23%
     Colouring dendrogram... 24%
     Colouring dendrogram... 25%
     Colouring dendrogram... 27%
     Colouring dendrogram... 28%
     Colouring dendrogram... 29%
     Colouring dendrogram... 30%
     Colouring dendrogram... 32%
     Colouring dendrogram... 33%
     Colouring dendrogram... 34%
     Colouring dendrogram... 35%
     Colouring dendrogram... 37%
     Colouring dendrogram... 38%
     Colouring dendrogram... 39%
     Colouring dendrogram... 40%
     Colouring dendrogram... 41%
     Colouring dendrogram... 43%
     Colouring dendrogram... 44%
     Colouring dendrogram... 45%
     Colouring dendrogram... 46%
     Colouring dendrogram... 48%
     Colouring dendrogram... 49%
     Colouring dendrogram... 50%
     Colouring dendrogram... 51%
     Colouring dendrogram... 53%
     Colouring dendrogram... 54%
     Colouring dendrogram... 55%
     Colouring dendrogram... 56%
     Colouring dendrogram... 58%
     Colouring dendrogram... 59%
     Colouring dendrogram... 60%
     Colouring dendrogram... 61%
     Colouring dendrogram... 62%
     Colouring dendrogram... 64%
     Colouring dendrogram... 65%
     Colouring dendrogram... 66%
     Colouring dendrogram... 67%
     Colouring dendrogram... 69%
     Colouring dendrogram... 70%
     Colouring dendrogram... 71%
     Colouring dendrogram... 72%
     Colouring dendrogram... 74%
     Colouring dendrogram... 75%
     Colouring dendrogram... 76%
     Colouring dendrogram... 77%
     Colouring dendrogram... 79%
     Colouring dendrogram... 80%
     Colouring dendrogram... 81%
     Colouring dendrogram... 82%
     Colouring dendrogram... 83%
     Colouring dendrogram... 85%
     Colouring dendrogram... 86%
     Colouring dendrogram... 87%
     Colouring dendrogram... 88%
     Colouring dendrogram... 90%
     Colouring dendrogram... 91%
     Colouring dendrogram... 92%
     Colouring dendrogram... 93%
     Colouring dendrogram... 95%
     Colouring dendrogram... 96%
     Colouring dendrogram... 97%
     Colouring dendrogram... 98%
     Colouring dendrogram... 100%
    >
    > ## Plot a graph layout of the link communities.
    > plot(lc, type = "graph")
     Getting node community edge density...4%
     Getting node community edge density...9%
     Getting node community edge density...13%
     Getting node community edge density...18%
     Getting node community edge density...22%
     Getting node community edge density...27%
     Getting node community edge density...31%
     Getting node community edge density...36%
     Getting node community edge density...40%
     Getting node community edge density...45%
     Getting node community edge density...50%
     Getting node community edge density...54%
     Getting node community edge density...59%
     Getting node community edge density...63%
     Getting node community edge density...68%
     Getting node community edge density...72%
     Getting node community edge density...77%
     Getting node community edge density...81%
     Getting node community edge density...86%
     Getting node community edge density...90%
     Getting node community edge density...95%
     Getting node community edge density...100%
     Getting node layout...
     Constructing node pies...4%
     Constructing node pies...9%
     Constructing node pies...13%
     Constructing node pies...18%
     Constructing node pies...22%
     Constructing node pies...27%
     Constructing node pies...31%
     Constructing node pies...36%
     Constructing node pies...40%
     Constructing node pies...45%
     Constructing node pies...50%
     Constructing node pies...54%
     Constructing node pies...59%
     Constructing node pies...63%
     Constructing node pies...68%
     Constructing node pies...72%
     Constructing node pies...77%
     Constructing node pies...81%
     Constructing node pies...86%
     Constructing node pies...90%
     Constructing node pies...95%
     Constructing node pies...100%
    >
    > ## Use a Spencer circle layout.
    > plot(lc, type = "graph", layout = "spencer.circle")
     Ordering communities according to dendrogram...12%
     Ordering communities according to dendrogram...25%
     Ordering communities according to dendrogram...37%
     Ordering communities according to dendrogram...50%
     Ordering communities according to dendrogram...62%
     Ordering communities according to dendrogram...75%
     Ordering communities according to dendrogram...87%
     Ordering communities according to dendrogram...100%
     Calculating node co-ordinates for Spencer circle...4%
     Calculating node co-ordinates for Spencer circle...9%
     Calculating node co-ordinates for Spencer circle...13%
     Calculating node co-ordinates for Spencer circle...18%
     Calculating node co-ordinates for Spencer circle...22%
     Calculating node co-ordinates for Spencer circle...27%
     Calculating node co-ordinates for Spencer circle...31%
     Calculating node co-ordinates for Spencer circle...36%
     Calculating node co-ordinates for Spencer circle...40%
     Calculating node co-ordinates for Spencer circle...45%
     Calculating node co-ordinates for Spencer circle...50%
     Calculating node co-ordinates for Spencer circle...54%
     Calculating node co-ordinates for Spencer circle...59%
     Calculating node co-ordinates for Spencer circle...63%
     Calculating node co-ordinates for Spencer circle...68%
     Calculating node co-ordinates for Spencer circle...72%
     Calculating node co-ordinates for Spencer circle...77%
     Calculating node co-ordinates for Spencer circle...81%
     Calculating node co-ordinates for Spencer circle...86%
     Calculating node co-ordinates for Spencer circle...90%
     Calculating node co-ordinates for Spencer circle...95%
     Calculating node co-ordinates for Spencer circle...100%
     Getting node community edge density...4%
     Getting node community edge density...9%
     Getting node community edge density...13%
     Getting node community edge density...18%
     Getting node community edge density...22%
     Getting node community edge density...27%
     Getting node community edge density...31%
     Getting node community edge density...36%
     Getting node community edge density...40%
     Getting node community edge density...45%
     Getting node community edge density...50%
     Getting node community edge density...54%
     Getting node community edge density...59%
     Getting node community edge density...63%
     Getting node community edge density...68%
     Getting node community edge density...72%
     Getting node community edge density...77%
     Getting node community edge density...81%
     Getting node community edge density...86%
     Getting node community edge density...90%
     Getting node community edge density...95%
     Getting node community edge density...100%
     Getting node layout... ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    linkcomm
     --- call from context ---
    plotLinkCommGraph(x, ...)
     --- call from argument ---
    if (class(layout) == "function") {
     lay <- layout(ig)
    } else {
     lay <- layout
    }
     --- R stacktrace ---
    where 1: plotLinkCommGraph(x, ...)
    where 2: plot.linkcomm(lc, type = "graph", layout = "spencer.circle")
    where 3: plot(lc, type = "graph", layout = "spencer.circle")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (x, clusterids = 1:length(x$clusters), nodes = NULL,
     layout = layout.fruchterman.reingold, pal = brewer.pal(7,
     "Set2"), random = TRUE, node.pies = TRUE, pie.local = TRUE,
     vertex.radius = 0.03, scale.vertices = 0.05, edge.color = NULL,
     vshape = "none", vsize = 15, ewidth = 3, margin = 0, vlabel.cex = 0.8,
     vlabel.color = "black", vlabel.family = "Helvetica", vertex.color = "palegoldenrod",
     vlabel = TRUE, col.nonclusters = "black", jitter = 0.2, circle = TRUE,
     printids = TRUE, cid.cex = 1, shownodesin = 0, showall = FALSE,
     verbose = TRUE, ...)
    {
     if (length(nodes) > 0) {
     clusterids <- which.communities(x, nodes = nodes)
     }
     clusters <- x$clusters[clusterids]
     miss <- setdiff(x$hclust$order, unlist(clusters))
     crf <- colorRampPalette(pal, bias = 1)
     cols <- crf(length(clusters))
     if (random) {
     cols <- sample(cols, length(clusters), replace = FALSE)
     }
     if (showall) {
     single <- setdiff(1:x$numbers[1], unlist(clusters))
     ll <- length(clusters)
     for (i in 1:length(single)) {
     clusters[[(i + ll)]] <- single[i]
     }
     cols <- append(cols, rep(col.nonclusters, length(single)))
     }
     drawcircle <- FALSE
     if (class(layout) == "character") {
     if (layout == "spencer.circle") {
     if (length(clusters) > length(x$clusters[1:x$numbers[3]])) {
     clusterids <- 1:x$numbers[3]
     }
     ord <- orderCommunities(x, clusterids = clusterids,
     verbose = FALSE)
     clusters <- ord$ordered
     clusterids <- ord$clusids
     layout <- layout.spencer.circle(x, clusterids = clusterids,
     jitter = jitter, verbose = verbose)$nodes
     drawcircle <- TRUE
     }
     }
     names(cols) <- clusterids
     if (length(unlist(clusters)) < nrow(x$edgelist) || length(miss) ==
     0) {
     edges <- x$edgelist[unlist(clusters), ]
     ig <- graph.edgelist(edges, directed = x$directed)
     clen <- sapply(clusters, length)
     j <- 1
     for (i in 1:length(clusters)) {
     newcids <- j:sum(clen[1:i])
     E(ig)[newcids]$color <- cols[i]
     j <- tail(newcids, 1) + 1
     }
     }
     else {
     ig <- x$igraph
     for (i in 1:length(clusters)) {
     E(ig)[clusters[[i]]]$color <- cols[i]
     }
     }
     if (shownodesin == 0) {
     vnames <- V(ig)$name
     }
     else {
     vnames <- V(ig)$name
     inds <- NULL
     for (i in 1:length(vnames)) {
     if (x$numclusters[which(names(x$numclusters) == vnames[i])] <
     shownodesin) {
     inds <- append(inds, i)
     }
     }
     vnames[inds] <- ""
     }
     if (vlabel == FALSE) {
     vnames = NA
     }
     dev.hold()
     on.exit(dev.flush())
     oldpar <- par(no.readonly = TRUE)
     par(mar = c(4, 4, 2, 2))
     if (!node.pies) {
     plot(ig, layout = layout, vertex.shape = vshape, edge.width = ewidth,
     vertex.label = vnames, vertex.label.family = vlabel.family,
     vertex.label.color = vlabel.color, vertex.size = vsize,
     vertex.color = vertex.color, margin = margin, vertex.label.cex = vlabel.cex,
     ...)
     }
     else {
     nodes <- V(ig)$name
     if (pie.local) {
     edge.memb <- numberEdgesIn(x, clusterids = clusterids,
     nodes = nodes)
     }
     else {
     edge.memb <- numberEdgesIn(x, nodes = nodes)
     }
     cat(" Getting node layout...")
     if (class(layout) == "function") {
     lay <- layout(ig)
     }
     else {
     lay <- layout
     }
     lay <- layout.norm(lay, xmin = -1, xmax = 1, ymin = -1,
     ymax = 1)
     rownames(lay) <- V(ig)$name
     cat("\n")
     node.pies <- .nodePie(edge.memb = edge.memb, layout = lay,
     nodes = nodes, edges = 100, radius = vertex.radius,
     scale = scale.vertices)
     cat("\n")
     if (is.null(edge.color)) {
     plot(ig, layout = lay, vertex.shape = "none", vertex.label = NA,
     vertex.label.dist = 1, edge.width = ewidth, vertex.label.color = vlabel.color,
     ...)
     }
     else {
     plot(ig, layout = lay, vertex.shape = "none", vertex.label = NA,
     vertex.label.dist = 1, edge.width = ewidth, vertex.label.color = vlabel.color,
     edge.color = edge.color, ...)
     }
     labels <- list()
     for (i in 1:length(node.pies)) {
     yp <- NULL
     for (j in 1:length(node.pies[[i]])) {
     seg.col <- cols[which(names(cols) == names(edge.memb[[i]])[j])]
     polygon(node.pies[[i]][[j]][, 1], node.pies[[i]][[j]][,
     2], col = seg.col)
     yp <- append(yp, node.pies[[i]][[j]][, 2])
     }
     lx <- lay[which(rownames(lay) == names(node.pies[i])),
     1] + 0.1
     ly <- max(yp) + 0.02
     labels[[i]] <- c(lx, ly)
     }
     for (i in 1:length(labels)) {
     text(labels[[i]][1], labels[[i]][2], labels = vnames[which(nodes ==
     names(node.pies[i]))], cex = vlabel.cex, col = vlabel.color)
     }
     }
     if (circle && drawcircle) {
     cx <- NULL
     for (i in 1:100) {
     cx[i] <- 1.25 * cos(i * (2 * pi)/100)
     }
     cy <- NULL
     for (i in 1:100) {
     cy[i] <- 1.25 * sin(i * (2 * pi)/100)
     }
     polygon(cx - 0.08, cy - 0.08, border = "grey", lwd = 2)
     for (i in 1:length(clusters)) {
     px <- 1.1 * cos(i * (2 * pi)/length(clusters))
     py <- 1.1 * sin(i * (2 * pi)/length(clusters))
     points(px - 0.08, py - 0.08, pch = 20, col = cols[i])
     if (printids) {
     tx <- 1.3 * cos(i * (2 * pi)/length(clusters))
     ty <- 1.3 * sin(i * (2 * pi)/length(clusters))
     text(tx - 0.08, ty - 0.08, labels = clusterids[i],
     col = cols[i], cex = cid.cex, font = 2)
     }
     }
     }
     par(oldpar)
    }
    <bytecode: 0x4ddda48>
    <environment: namespace:linkcomm>
     --- function search by body ---
    Function plotLinkCommGraph in namespace linkcomm has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(layout) == "function") { :
     the condition has length > 1
    Calls: plot -> plot.linkcomm -> plotLinkCommGraph
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0-11
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘temp.cns’ ‘temp.ea’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0-11
Check: compiled code
Result: NOTE
    File ‘linkcomm/libs/linkcomm.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc