CRAN Package Check Results for Package biclust

Last updated on 2018-05-14 01:46:23 CEST.

Additional issues

valgrind

Check Details

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.2.0
Check: R code for possible problems
Result: NOTE
    biclustbarchart: no visible global function definition for ‘plot’
    biclustmember: no visible global function definition for ‘plot.new’
    biclustmember: no visible global function definition for ‘rect’
    biclustmember: no visible global function definition for ‘axis’
    biclustmember: no visible global function definition for ‘title’
    bigquestmetmotif: no visible global function definition for ‘qnorm’
    bimaxbiclust: no visible global function definition for ‘flush.console’
    bubbleplot: no visible global function definition for ‘rgb’
    bubbleplot: no visible global function definition for ‘par’
    bubbleplot: no visible global function definition for ‘dist’
    bubbleplot: no visible global function definition for ‘cmdscale’
    bubbleplot: no visible global function definition for ‘plot’
    bubbleplot: no visible global function definition for ‘text’
    ccbiclust: no visible global function definition for ‘runif’
    clustmember: no visible global function definition for ‘plot.new’
    clustmember: no visible global function definition for ‘rect’
    clustmember: no visible global function definition for ‘axis’
    clustmember: no visible global function definition for ‘title’
    computeObservedFstat: no visible global function definition for ‘anova’
    computeObservedFstat: no visible global function definition for ‘aov’
    computeObservedFstat: no visible global function definition for ‘pf’
    corappr: no visible global function definition for ‘cor’
    diagnoseColRow: no visible global function definition for ‘anova’
    diagnoseColRow: no visible global function definition for ‘aov’
    diagnosticPlot: no visible global function definition for ‘par’
    diagnosticPlot: no visible global function definition for ‘density’
    diagnosticPlot: no visible global function definition for ‘hist’
    diagnosticPlot: no visible global function definition for ‘lines’
    discretize: no visible global function definition for ‘quantile’
    drawHeatmap: no visible global function definition for ‘rgb’
    drawHeatmap: no visible global function definition for ‘par’
    drawHeatmap: no visible global function definition for ‘image’
    drawHeatmap: no visible global function definition for ‘axis’
    drawHeatmap2: no visible global function definition for ‘rgb’
    drawHeatmap2: no visible global function definition for ‘par’
    drawHeatmap2: no visible global function definition for ‘image’
    hcl: no visible global function definition for ‘hclust’
    hcl: no visible global function definition for ‘as.dist’
    hcl: no visible global function definition for ‘plot’
    hcl: no visible global function definition for ‘cutree’
    heatmapBC: no visible global function definition for ‘image’
    heatmapBC: no visible global function definition for ‘rect’
    iterativeKmeans: no visible global function definition for ‘kmeans’
    kmeansClassStart: no visible global function definition for ‘kmeans’
    kmeansStart: no visible global function definition for ‘kmeans’
    parallelCoordinates: no visible global function definition for ‘par’
    parallelCoordinates: no visible global function definition for
     ‘matplot’
    parallelCoordinates: no visible global function definition for ‘gray’
    parallelCoordinates: no visible global function definition for ‘axis’
    parallelCoordinates: no visible global function definition for ‘title’
    plaid: no visible global function definition for ‘terms’
    plaid.grid: no visible global function definition for ‘as.formula’
    plotclust: no visible global function definition for ‘par’
    plotclust: no visible binding for global variable ‘median’
    plotclust: no visible global function definition for ‘barplot’
    plotclust: no visible global function definition for ‘title’
    prequest: no visible binding for global variable ‘sd’
    prequest: no visible binding for global variable ‘median’
    printrect: no visible global function definition for ‘rect’
    variance: no visible global function definition for ‘dist’
    Undefined global functions or variables:
     anova aov as.dist as.formula axis barplot cmdscale cor cutree density
     dist flush.console gray hclust hist image kmeans lines matplot median
     par pf plot plot.new qnorm quantile rect rgb runif sd terms text
     title
    Consider adding
     importFrom("grDevices", "gray", "rgb")
     importFrom("graphics", "axis", "barplot", "hist", "image", "lines",
     "matplot", "par", "plot", "plot.new", "rect", "text",
     "title")
     importFrom("stats", "anova", "aov", "as.dist", "as.formula",
     "cmdscale", "cor", "cutree", "density", "dist", "hclust",
     "kmeans", "median", "pf", "qnorm", "quantile", "runif",
     "sd", "terms")
     importFrom("utils", "flush.console")
    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-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: 1.2.0
Check: compiled code
Result: NOTE
    File ‘biclust/libs/biclust.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-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.2.0
Check: examples
Result: ERROR
    Running examples in ‘biclust-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: biclustmember
    > ### Title: Bicluster Membership Graph
    > ### Aliases: clustmember biclustmember bicorder
    > ### Keywords: hplot cluster
    >
    > ### ** Examples
    >
    > set.seed(1)
    > x=matrix(rnorm(900),30,30)
    > x[1:5,1:5]=rnorm(25,3,0.3)
    > x[11:15,11:15]=rnorm(25,-3,0.3)
    > x[21:25,21:25]=rnorm(25,6,0.3)
    > colnames(x)<-paste("Var.",1:30)
    > bics <- biclust(x,BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,
    + iter.startup = 5, iter.layer = 30, verbose = TRUE)
    layer: 0
     436.0833
    layer: 1
    [1] 0 5 5
    [1] 30 5 5
    [1] 31 5 5
    [1] 60 5 5
    [1] 1
    [1] 437.8929 0.0000 0.0000 0.0000
    back fitting 2 times
    layer: 2
    [1] 0 5 5
    [1] 1 9 12
    [1] 2 10 9
    [1] 3 8 7
    [1] 4 7 6
    [1] 30 7 6
    [1] 31 5 6
    [1] 32 5 5
    [1] 33 5 5
    [1] 60 5 5
    [1] 5
    [1] 113.3975 0.0000 0.0000 0.0000
    back fitting 2 times
    layer: 3
    [1] 0 6 5
    [1] 30 6 5
    [1] 31 5 5
    [1] 32 5 5
    [1] 33 5 5
    [1] 60 5 5
    [1] 1
    [1] 112.1011 0.0000 0.0000 0.0000
    back fitting 2 times
    layer: 4
    [1] 0 15 12
    [1] 1 14 11
    [1] 2 14 10
    [1] 3 13 9
    [1] 4 15 9
    [1] 30 15 9
    [1] 31 0 9
    [1] 32
    [1] 0 0 0 0
    
    Layer Rows Cols Df SS MS Convergence Rows Released Cols Released
     0 30 30 59 69.55 1.18 NA NA NA
     1 5 5 9 897.09 99.68 1 0 0
     2 5 5 9 244.29 27.14 1 2 1
     3 5 5 9 219.44 24.38 1 1 0
    >
    > biclustmember(bics,x)
    >
    > ord<-bicorder(bics, cols=TRUE, rev=TRUE)
    >
    > biclustmember(bics,x,which=ord)
    Error in if (is.na(which)) which <- 1:ny : the condition has length > 1
    Calls: biclustmember
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-clang/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-devel/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See 'd:/Rcompile/CRANpkg/local/3.5/biclust.Rcheck/00install.out' for details.
    Information on the location(s) of code generating the 'Note's can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to 'yes'.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-linux-x86_64

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/ripley/R/packages/tests32/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-solaris-x86

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-linux-x86_64

Version: 1.2.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/biclust.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-osx-x86_64