CRAN Package Check Results for Package hyperSpec

Last updated on 2016-05-03 06:48:12.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-gcc 0.98-20150304 3.46 128.65 132.11 NOTE
r-devel-linux-x86_64-fedora-clang 0.98-20150304 280.65 NOTE
r-devel-linux-x86_64-fedora-gcc 0.98-20150304 240.54 NOTE
r-devel-osx-x86_64-clang 0.98-20150304 273.44 NOTE
r-devel-windows-ix86+x86_64 0.98-20150304 10.00 287.00 297.00 NOTE
r-patched-linux-x86_64 0.98-20150304 3.08 128.19 131.27 NOTE
r-patched-solaris-sparc 0.98-20150304 988.00 WARN
r-patched-solaris-x86 0.98-20150304 191.70 WARN
r-release-linux-x86_64 0.98-20150304 3.39 159.37 162.76 NOTE
r-release-osx-x86_64-mavericks 0.98-20150304 NOTE
r-release-windows-ix86+x86_64 0.98-20150304 12.00 322.00 334.00 NOTE
r-oldrel-windows-ix86+x86_64 0.98-20150304 24.00 493.00 517.00 WARN

Check Details

Version: 0.98-20150304
Check: R code for possible problems
Result: NOTE
    Warning: local assignments to syntactic functions: ~
    Warning: local assignments to syntactic functions: ~
    .cut.ticks: no visible global function definition for ‘head’
    .jdx.TABULAR.PAC: no visible global function definition for ‘head’
    .jdx.hdr.concentrations: no visible global function definition for
     ‘modifyList’
    .jdx.readhdr: no visible global function definition for ‘maintainer’
    .labels: no visible global function definition for ‘modifyList’
    .levelplot: no visible global function definition for ‘modifyList’
    .paste.row : .print.val: no visible global function definition for
     ‘head’
    .paste.row : .print.val: no visible global function definition for
     ‘tail’
    .plot: no visible global function definition for ‘modifyList’
    .rubberband: no visible global function definition for ‘chull’
    .spc.error: no visible global function definition for ‘str’
    .spc.filehdr: no visible global function definition for ‘maintainer’
    .spc.log: no visible global function definition for ‘tail’
    .spc.log: no visible global function definition for ‘head’
    alois.palette: no visible global function definition for
     ‘colorRampPalette’
    colmix.rgb: no visible global function definition for ‘col2rgb’
    colmix.rgb: no visible global function definition for ‘rgb’
    fitraster: no visible global function definition for ‘tail’
    hy.setOptions: no visible global function definition for ‘modifyList’
    map.identify: no visible global function definition for ‘modifyList’
    mark.dendrogram: no visible global function definition for ‘head’
    mark.dendrogram: no visible global function definition for ‘tail’
    matlab.dark.palette: no visible global function definition for
     ‘col2rgb’
    matlab.dark.palette: no visible global function definition for ‘rgb’
    plotc: no visible global function definition for ‘modifyList’
    plotmap: no visible global function definition for ‘modifyList’
    plotmat: no visible global function definition for ‘modifyList’
    plotspc: no visible global function definition for ‘relist’
    plotspc: no visible global function definition for ‘modifyList’
    plotspc: no visible global function definition for ‘rgb’
    plotspc: no visible global function definition for ‘col2rgb’
    plotspc: no visible global function definition for ‘head’
    plotspc: no visible global function definition for ‘tail’
    plotvoronoi: no visible global function definition for ‘modifyList’
    qplotmap: no visible global function definition for ‘tail’
    raw.split.nul: no visible global function definition for ‘tail’
    read.ENVI: no visible global function definition for ‘modifyList’
    read.ENVI.Nicolet: no visible global function definition for
     ‘modifyList’
    read.jdx: no visible global function definition for ‘modifyList’
    read.spc: no visible global function definition for ‘modifyList’
    read.txt.Shimadzu: no visible global function definition for
     ‘read.table’
    read.txt.long: no visible global function definition for ‘read.table’
    read.txt.long: no visible global function definition for ‘unstack’
    read.txt.wide: no visible global function definition for ‘read.table’
    read.txt.wide: no visible global function definition for ‘head’
    scan.txt.Renishaw: no visible global function definition for ‘head’
    sel.poly: no visible global function definition for ‘tail’
    trellis.factor.key: no visible global function definition for
     ‘modifyList’
    wc: no visible global function definition for ‘read.table’
    write.txt.long: no visible global function definition for ‘write.table’
    write.txt.wide: no visible global function definition for ‘write.table’
    labels,hyperSpec: no visible global function definition for
     ‘modifyList’
    levelplot,formula-hyperSpec: no visible global function definition for
     ‘modifyList’
    plot,hyperSpec-character: no visible global function definition for
     ‘modifyList’
    Undefined global functions or variables:
     chull col2rgb colorRampPalette head maintainer modifyList read.table
     relist rgb str tail unstack write.table
    Consider adding
     importFrom("grDevices", "chull", "col2rgb", "colorRampPalette", "rgb")
     importFrom("utils", "head", "maintainer", "modifyList", "read.table",
     "relist", "str", "tail", "unstack", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 0.98-20150304
Check: R code for possible problems
Result: NOTE
    Warning: local assignments to syntactic functions: ~
    .cut.ticks: no visible global function definition for 'head'
    .jdx.TABULAR.PAC: no visible global function definition for 'head'
    .jdx.hdr.concentrations: no visible global function definition for
     'modifyList'
    .jdx.readhdr: no visible global function definition for 'maintainer'
    .labels: no visible global function definition for 'modifyList'
    .levelplot: no visible global function definition for 'modifyList'
    .paste.row : .print.val: no visible global function definition for
     'head'
    .paste.row : .print.val: no visible global function definition for
     'tail'
    .plot: no visible global function definition for 'modifyList'
    .rubberband: no visible global function definition for 'chull'
    .spc.error: no visible global function definition for 'str'
    .spc.filehdr: no visible global function definition for 'maintainer'
    .spc.log: no visible global function definition for 'tail'
    .spc.log: no visible global function definition for 'head'
    alois.palette: no visible global function definition for
     'colorRampPalette'
    colmix.rgb: no visible global function definition for 'col2rgb'
    colmix.rgb: no visible global function definition for 'rgb'
    fitraster: no visible global function definition for 'tail'
    hy.setOptions: no visible global function definition for 'modifyList'
    map.identify: no visible global function definition for 'modifyList'
    mark.dendrogram: no visible global function definition for 'head'
    mark.dendrogram: no visible global function definition for 'tail'
    matlab.dark.palette: no visible global function definition for
     'col2rgb'
    matlab.dark.palette: no visible global function definition for 'rgb'
    plotc: no visible global function definition for 'modifyList'
    plotmap: no visible global function definition for 'modifyList'
    plotmat: no visible global function definition for 'modifyList'
    plotspc: no visible global function definition for 'relist'
    plotspc: no visible global function definition for 'modifyList'
    plotspc: no visible global function definition for 'rgb'
    plotspc: no visible global function definition for 'col2rgb'
    plotspc: no visible global function definition for 'head'
    plotspc: no visible global function definition for 'tail'
    plotvoronoi: no visible global function definition for 'modifyList'
    qplotmap: no visible global function definition for 'tail'
    raw.split.nul: no visible global function definition for 'tail'
    read.ENVI: no visible global function definition for 'modifyList'
    read.ENVI.Nicolet: no visible global function definition for
     'modifyList'
    read.jdx: no visible global function definition for 'modifyList'
    read.spc: no visible global function definition for 'modifyList'
    read.txt.Shimadzu: no visible global function definition for
     'read.table'
    read.txt.long: no visible global function definition for 'read.table'
    read.txt.long: no visible global function definition for 'unstack'
    read.txt.wide: no visible global function definition for 'read.table'
    read.txt.wide: no visible global function definition for 'head'
    scan.txt.Renishaw: no visible global function definition for 'head'
    sel.poly: no visible global function definition for 'tail'
    trellis.factor.key: no visible global function definition for
     'modifyList'
    wc: no visible global function definition for 'read.table'
    write.txt.long: no visible global function definition for 'write.table'
    write.txt.wide: no visible global function definition for 'write.table'
    labels,hyperSpec: no visible global function definition for
     'modifyList'
    levelplot,formula-hyperSpec: no visible global function definition for
     'modifyList'
    plot,hyperSpec-character: no visible global function definition for
     'modifyList'
    Undefined global functions or variables:
     chull col2rgb colorRampPalette head maintainer modifyList read.table
     relist rgb str tail unstack write.table
    Consider adding
     importFrom("grDevices", "chull", "col2rgb", "colorRampPalette", "rgb")
     importFrom("utils", "head", "maintainer", "modifyList", "read.table",
     "relist", "str", "tail", "unstack", "write.table")
    to your NAMESPACE file.
Flavor: r-devel-windows-ix86+x86_64

Version: 0.98-20150304
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: lattice
    Loading required package: grid
    Loading required package: ggplot2
    Loading required package: mvtnorm
    Package hyperSpec, version 0.98-20150304
    
    To get started, try
     vignette ("introduction", package = "hyperSpec")
     package?hyperSpec
     vignette (package = "hyperSpec")
    
    If you use this package please cite it appropriately.
     citation("hyperSpec")
    will give you the correct reference.
    
    The project homepage is http://hyperspec.r-forge.r-project.org
    
    
    Tracing function "spc.fit.poly.below" in package "hyperSpec"
    Warning in spc.fit.poly.below(chondro[1], poly.order = 1, npts.min = npts[iter] - :
     npts.min too small: adjusted to 2
    Warning in spc.fit.poly.below(chondro[1], poly.order = 1, npts.min = npts - :
     npts.min too small: adjusted to 2
    Tracing function "spc.fit.poly.below" in package "hyperSpec"
    Untracing function "spc.fit.poly.below" in package "hyperSpec"
    Tracing function "spc.fit.poly.below" in package "hyperSpec"
    Untracing function "spc.fit.poly.below" in package "hyperSpec"
    Tracing function "spc.fit.poly.below" in package "hyperSpec"
    Tracing function "spc.fit.poly.below" in package "hyperSpec"
    Tracing function "spc.fit.poly.below" in package "hyperSpec"
    Tracing function "spc.fit.poly.below" in package "hyperSpec"
    Untracing function "spc.fit.poly.below" in package "hyperSpec"
    Read 362 items
    Read 362 items
    Read 362 items
    Read 362 items
    Read 362 items
    Read 362 items
    Loading required package: MASS
    Warning in predict.lda(lda, chondro) :
     variable names in 'newdata' do not match those in 'object'
    Loading required namespace: plotrix
    Warning in rm(chondro) : object 'chondro' not found
    Loading required package: baseline
    
    Attaching package: ‘baseline’
    
    The following object is masked from ‘package:stats’:
    
     getCall
    
    Warning in scores[, , 1:10] %*% loadings[1:10] :
     Dropping column(s) of y: measurement
    The "ward" method has been renamed to "ward.D"; note new "ward.D2"
    Loading required package: rgl
    Warning in (function (object, model = spc ~ c, groups = NULL, func = NULL, :
     Intensity at first wavelengh only is used.
    Warning in hyperSpec:::.levelplot(x, data, ...) :
     Only first wavelength is used for plotting
    Loading required namespace: deldir
    
     PLEASE NOTE: The components "delsgs" and "summary" of the
     object returned by deldir() are now DATA FRAMES rather than
     matrices (as they were prior to release 0.0-18).
     See help("deldir").
    
     PLEASE NOTE: The process that deldir() uses for determining
     duplicated points has changed from that used in version
     0.0-9 of this package (and previously). See help("deldir").
    
    
    Warning in plotc(x, ...) : Intensity at first wavelengh only is used.
    Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col, :
     'x' values are not equispaced; output may be wrong
    Warning in hyperSpec:::.levelplot(x, data, ...) :
     Only first wavelength is used for plotting
    Loading required package: latticeExtra
    Loading required package: RColorBrewer
    
    Attaching package: ‘latticeExtra’
    
    The following object is masked from ‘package:ggplot2’:
    
     layer
    
    Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col, :
     'x' values are not equispaced; output may be wrong
    Warning in (function (x, y, z, subscripts, at = pretty(z), ..., col.regions = regions$col, :
     'y' values are not equispaced; output may be wrong
    "/home/ripley/R/cc/bin/R" CMD Sweave --pdf --encoding=utf8 --compact-vignettes=both
    Warning: unknown option ‘--compact-vignettes=both’
    Usage: R CMD Sweave [options] file
    
    A front-end for Sweave and other vignette engines, via buildVignette()
    
    Options:
     -h, --help print this help message and exit
     -v, --version print version info and exit
     --driver=name use named Sweave driver
     --engine=pkg::engine use named vignette engine
     --encoding=enc default encoding 'enc' for file
     --clean corresponds to --clean=default
     --clean= remove some of the created files:
     "default" removes those the same initial name;
     "keepOuts" keeps e.g. *.tex even when PDF is produced
     --options= comma-separated list of Sweave/engine options
     --pdf convert to PDF document
     --compact= try to compact PDF document:
     "no" (default), "qpdf", "gs", "gs+qpdf", "both"
     --compact same as --compact=qpdf
    
    Report bugs at bugs.r-project.org .
    *** Error code 1
    make: Fatal error: Command failed for target `baseline.pdf'
    Current working directory /home/ripley/R/packages/tests32/hyperSpec.Rcheck/vign_test/hyperSpec/vignettes
    Error in buildVignettes(dir = "/home/ripley/R/packages/tests32/hyperSpec.Rcheck/vign_test/hyperSpec") :
     running 'make' failed
    Execution halted
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86

Version: 0.98-20150304
Check: R code for possible problems
Result: NOTE
    Warning: local assignments to syntactic functions: ~
    Warning: local assignments to syntactic functions: ~
Flavor: r-release-linux-x86_64

Version: 0.98-20150304
Check: R code for possible problems
Result: NOTE
    Warning: local assignments to syntactic functions: ~
Flavors: r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.98-20150304
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: replacing previous import by 'grid::unit' when loading 'hyperSpec'
Flavor: r-oldrel-windows-ix86+x86_64