CRAN Package Check Results for Package GMD

Last updated on 2018-05-22 22:48:31 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.3 4.78 55.69 60.47 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.3 4.85 43.07 47.92 ERROR
r-devel-linux-x86_64-fedora-clang 0.3.3 79.43 WARN
r-devel-linux-x86_64-fedora-gcc 0.3.3 77.67 WARN
r-devel-windows-ix86+x86_64 0.3.3 19.00 311.00 330.00 NOTE
r-patched-linux-x86_64 0.3.3 6.06 54.56 60.62 ERROR
r-patched-solaris-x86 0.3.3 97.70 WARN
r-release-linux-x86_64 0.3.3 5.28 54.23 59.51 ERROR
r-release-windows-ix86+x86_64 0.3.3 14.00 303.00 317.00 NOTE
r-release-osx-x86_64 0.3.3 NOTE
r-oldrel-windows-ix86+x86_64 0.3.3 13.00 245.00 258.00 NOTE
r-oldrel-osx-x86_64 0.3.3 NOTE

Check Details

Version: 0.3.3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.elbow plot.gmdm plot.gmdp plot.mhist plot.mhist.summary
     print.gmdm print.gmdp summary.gmdp
    See section ‘Registering S3 methods’ 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-patched-solaris-x86, r-release-linux-x86_64

Version: 0.3.3
Check: R code for possible problems
Result: NOTE
    .file_path_as_absolute: no visible global function definition for
     ‘file_test’
    .plot.text: no visible global function definition for ‘par’
    .plot.text: no visible global function definition for ‘plot’
    .plot.text: no visible global function definition for ‘rect’
    .plot.text: no visible global function definition for ‘text’
    bedgraph.to.depth: no visible global function definition for
     ‘read.table’
    ghist: no visible global function definition for ‘hist’
    heatmap.3: no visible global function definition for ‘par’
    heatmap.3: no visible global function definition for ‘flush.console’
    heatmap.3: no visible global function definition for ‘layout’
    heatmap.3: no visible global function definition for ‘image’
    heatmap.3: no visible global function definition for ‘axis’
    heatmap.3: no visible global function definition for ‘text’
    heatmap.3: no visible global function definition for ‘mtext’
    heatmap.3: no visible global function definition for ‘rect’
    heatmap.3: no visible global function definition for ‘abline’
    heatmap.3: no visible global function definition for ‘lines’
    heatmap.3: no visible global function definition for ‘plot’
    heatmap.3: no visible global function definition for ‘title’
    heatmap.3: no visible global function definition for ‘hist’
    legend: no visible global function definition for ‘par’
    legend : rect2: no visible global function definition for ‘rect’
    legend : segments2: no visible global function definition for
     ‘segments’
    legend : points2: no visible global function definition for ‘points’
    legend : text2: no visible global function definition for ‘text’
    legend: no visible global function definition for ‘strwidth’
    legend: no visible global function definition for ‘xinch’
    legend: no visible global function definition for ‘yinch’
    legend: no visible global function definition for ‘strheight’
    plot.elbow: no visible global function definition for ‘par’
    plot.elbow: no visible global function definition for ‘plot’
    plot.elbow: no visible global function definition for ‘abline’
    plot.elbow: no visible global function definition for ‘mtext’
    plot.elbow: no visible global function definition for ‘text’
    plot.elbow: no visible global function definition for ‘title’
    plot.gmdm: no visible global function definition for ‘par’
    plot.gmdm: no visible global function definition for ‘plot’
    plot.gmdm: no visible global function definition for ‘text’
    plot.gmdm: no visible global function definition for ‘rect’
    plot.gmdm: no visible global function definition for ‘mtext’
    plot.mhist: no visible global function definition for ‘plot’
    plot.mhist: no visible global function definition for ‘abline’
    plot.mhist: no visible global function definition for ‘mtext’
    plot.mhist: no visible global function definition for ‘axis’
    plot.mhist: no visible global function definition for ‘rect’
    plot.mhist: no visible global function definition for ‘lines’
    plot.mhist: no visible global function definition for ‘par’
    plot.mhist.summary: no visible global function definition for ‘par’
    ts2df: no visible global function definition for ‘is’
    Undefined global functions or variables:
     abline axis file_test flush.console hist image is layout lines mtext
     par plot points read.table rect segments strheight strwidth text
     title xinch yinch
    Consider adding
     importFrom("graphics", "abline", "axis", "hist", "image", "layout",
     "lines", "mtext", "par", "plot", "points", "rect",
     "segments", "strheight", "strwidth", "text", "title",
     "xinch", "yinch")
     importFrom("methods", "is")
     importFrom("utils", "file_test", "flush.console", "read.table")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
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: 0.3.3
Check: compiled code
Result: NOTE
    File ‘GMD/libs/GMD.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: 0.3.3
Check: examples
Result: ERROR
    Running examples in ‘GMD-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: gmdp
    > ### Title: Generalized Minimum Distance between a pair of distributions
    > ### Aliases: gmdp print.gmdp summary.gmdp
    > ### Keywords: classes
    >
    > ### ** Examples
    >
    > require(GMD)
    > gmdp(c(4,1,1,0,0,0,3,1),c(2,1,1,0,0,0,3,3),sliding=FALSE)
    [1] 1.4
    attr(,"class")
    [1] "gmdp" "numeric"
    attr(,"meta")
    attr(,"meta")$labels
    [1] "v1" "v2"
    
    attr(,"meta")$v1.ori
    [1] 0.4 0.1 0.1 0.0 0.0 0.0 0.3 0.1
    
    attr(,"meta")$v2.ori
    [1] 0.2 0.1 0.1 0.0 0.0 0.0 0.3 0.3
    
    attr(,"meta")$resolution
    [1] 1
    
    attr(,"meta")$v1
    [1] 0.4 0.1 0.1 0.0 0.0 0.0 0.3 0.1
    
    attr(,"meta")$v2
    [1] 0.2 0.1 0.1 0.0 0.0 0.0 0.3 0.3
    
    attr(,"meta")$sliding
    [1] FALSE
    
    attr(,"meta")$pseudocount
    [1] 0
    
    attr(,"meta")$gap.pair
     [,1] [,2]
    [1,] 0 0
    
    attr(,"meta")$n.hit
    [1] 1
    
    > x <- gmdp(c(4,1,1,0,0,0,3,1), c(1,1,2,1,1,0,0,0,3,3,5,5),
    + pseudocount=1, sliding=TRUE)
    > print(x)
    [1] 1.156863
    attr(,"class")
    [1] "gmdp" "numeric"
    attr(,"meta")
    attr(,"meta")$labels
    [1] "v1" "v2"
    
    attr(,"meta")$v1.ori
    [1] 5 2 2 1 1 1 4 2
    
    attr(,"meta")$v2.ori
     [1] 2 2 3 2 2 1 1 1 4 4 6 6
    
    attr(,"meta")$resolution
    [1] 1
    
    attr(,"meta")$v1
    [1] 0.27777778 0.11111111 0.11111111 0.05555556 0.05555556 0.05555556 0.22222222
    [8] 0.11111111
    
    attr(,"meta")$v2
     [1] 0.05882353 0.05882353 0.08823529 0.05882353 0.05882353 0.02941176
     [7] 0.02941176 0.02941176 0.11764706 0.11764706 0.17647059 0.17647059
    
    attr(,"meta")$sliding
    [1] TRUE
    
    attr(,"meta")$pseudocount
    [1] 1
    
    attr(,"meta")$gap.pair
     [,1] [,2]
    [1,] 4 0
    
    attr(,"meta")$n.hit
    [1] 1
    
    > print(x, "full")
    Warning in print.default(x, "full") : NAs introduced by coercion
    Error in print.default(x, "full") : invalid 'digits' argument
    Calls: print -> print.default
    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: 0.3.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: GMD
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: row dendrogram is asked; Rowv is set to `TRUE'.
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: col dendrogram is asked; Colv is set to `TRUE'.
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
    heatmap.3 | From GMD 0.3.3, please use relative values for cexRow.
    heatmap.3 | From GMD 0.3.3, please use relative values for cexCol.
    The "ward" method has been renamed to "ward.D"; note new "ward.D2"
    Warning in plot.window(...) : "cex.text" is not a graphical parameter
    Warning in plot.window(...) :
     "if.plot.new" is not a graphical parameter
    Warning in plot.xy(xy, type, ...) :
     plot type ‘polygon’ will be truncated to first character
    Warning in plot.xy(xy, type, ...) :
     "cex.text" is not a graphical parameter
    Warning in plot.xy(xy, type, ...) :
     "if.plot.new" is not a graphical parameter
    Warning in axis(side = side, at = at, labels = labels, ...) :
     "cex.text" is not a graphical parameter
    Warning in axis(side = side, at = at, labels = labels, ...) :
     "if.plot.new" is not a graphical parameter
    Warning in axis(side = side, at = at, labels = labels, ...) :
     "cex.text" is not a graphical parameter
    Warning in axis(side = side, at = at, labels = labels, ...) :
     "if.plot.new" is not a graphical parameter
    Warning in box(...) : "cex.text" is not a graphical parameter
    Warning in box(...) : "if.plot.new" is not a graphical parameter
    Warning in title(...) : "cex.text" is not a graphical parameter
    Warning in title(...) : "if.plot.new" is not a graphical parameter
    
    Error: processing vignette ‘GMD-vignette.Rnw’ failed with diagnostics:
     chunk 6
    Error in xy.coords(x, y, xlabel, ylabel, log) :
     'x' is a list, but does not have components 'x' and 'y'
    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: 0.3.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: GMD
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: row dendrogram is asked; Rowv is set to `TRUE'.
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: col dendrogram is asked; Colv is set to `TRUE'.
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
    Warning in heatmap.3(x, dendrogram = "both", cexCol = 0.85, cexRow = 0.85) :
     Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
    heatmap.3 | From GMD 0.3.3, please use relative values for cexRow.
    heatmap.3 | From GMD 0.3.3, please use relative values for cexCol.
    The "ward" method has been renamed to "ward.D"; note new "ward.D2"
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'GMD-vignette.tex' failed.
    LaTeX errors:
    ! Package inputenc Error: Unicode character <c2><8a> (U+8A)
    (inputenc) not set up for use with LaTeX.
    
    See the inputenc package documentation for explanation.
    Type H <return> for immediate help.
    ! Package inputenc Error: Unicode character <c2><9a> (U+9A)
    (inputenc) not set up for use with LaTeX.
    
    See the inputenc package documentation for explanation.
    Type H <return> for immediate help.
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 0.3.3
Check: DESCRIPTION meta-information
Result: NOTE
    NeedsCompilation field should likely be 'yes'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3.3
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    
    Warning in as.mhist(tmp.x) :
     `bins' are not specified; use automatic numbering instead under assumption
    that memeber histograms have the same order of the bins.
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'GMD-data-processing.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `appendix.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ! Emergency stop.
    <read *>
    
    l.10 ^^M
    
    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-oldrel-osx-x86_64