CRAN Package Check Results for Package hyperSpec

Last updated on 2015-07-07 14:48:14.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.98-20150304 3.44 154.02 157.46 NOTE
r-devel-linux-x86_64-debian-gcc 0.98-20150304 3.32 153.16 156.48 NOTE
r-devel-linux-x86_64-fedora-clang 0.98-20150304 317.72 NOTE
r-devel-linux-x86_64-fedora-gcc 0.98-20150304 304.04 NOTE
r-devel-osx-x86_64-clang 0.98-20150304 262.53 NOTE
r-devel-windows-ix86+x86_64 0.98-20150304 19.00 165.00 184.00 ERROR
r-patched-linux-x86_64 0.98-20150304 3.43 150.88 154.31 NOTE
r-patched-solaris-sparc 0.98-20150304 1379.70 NOTE
r-patched-solaris-x86 0.98-20150304 287.40 NOTE
r-release-linux-x86_64 0.98-20150304 3.48 152.72 156.19 NOTE
r-release-osx-x86_64-mavericks 0.98-20150304 NOTE
r-release-windows-ix86+x86_64 0.98-20150304 17.00 236.00 253.00 NOTE
r-oldrel-windows-ix86+x86_64 0.98-20150304 17.00 307.00 324.00 NOTE

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
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

Version: 0.98-20150304
Check: R code for possible problems
Result: NOTE
    Warning: local assignments to syntactic functions: ~
    Warning: local assignments to syntactic functions: ~
Flavors: r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

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
Flavor: r-devel-windows-ix86+x86_64

Version: 0.98-20150304
Check: examples
Result: ERROR
    Running examples in 'hyperSpec-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: as.data.frame
    > ### Title: Conversion of a hyperSpec object into a data.frame or matrix
    > ### 'as.data.frame' returns 'x@data' (as data.frame) 'as.matrix' returns
    > ### the spectra matrix 'x@data$spc' as matrix
    > ### Aliases: as.data.frame as.data.frame,hyperSpec-method
    > ### as.data.frame.hyperSpec as.long.df as.matrix
    > ### as.matrix,hyperSpec-method as.matrix.hyperSpec as.t.df as.wide.df
    > ### Keywords: methods
    >
    > ### ** Examples
    >
    > as.data.frame (chondro [1:3,, 600 ~ 620])
     y x clusters spc.602 spc.606 spc.610 spc.614 spc.618 .row
    1 -4.77 -11.55 matrix 501.8194 504.8868 488.6323 466.1774 492.0016 1
    2 -4.77 -10.55 matrix 500.4552 507.8126 489.4758 465.0506 490.5329 2
    3 -4.77 -9.55 matrix 465.9614 474.6263 456.0324 436.6220 458.0576 3
    > as.matrix (chondro [1:3,, 600 ~ 620])
     602 606 610 614 618
    [1,] 501.8194 504.8868 488.6323 466.1774 492.0016
    [2,] 500.4552 507.8126 489.4758 465.0506 490.5329
    [3,] 465.9614 474.6263 456.0324 436.6220 458.0576
    > lm (c ~ spc, data = flu [,,450])
    
    Call:
    lm(formula = c ~ spc, data = flu[, , 450])
    
    Coefficients:
    (Intercept) spc
     0.0038493 0.0004407
    
    > as.wide.df (chondro [1:5,, 600 ~ 610])
     y x clusters 602 606 610
    1 -4.77 -11.55 matrix 501.8194 504.8868 488.6323
    2 -4.77 -10.55 matrix 500.4552 507.8126 489.4758
    3 -4.77 -9.55 matrix 465.9614 474.6263 456.0324
    4 -4.77 -8.55 matrix 477.4786 481.7259 464.8207
    5 -4.77 -7.55 matrix 439.3865 445.0571 428.6620
    > summary (as.wide.df (chondro [1:5,, 600 ~ 610]))
     y x clusters 602 606
     Min. :-4.77 Min. :-11.55 matrix:5 Min. :439.4 Min. :445.1
     1st Qu.:-4.77 1st Qu.:-10.55 lacuna:0 1st Qu.:466.0 1st Qu.:474.6
     Median :-4.77 Median : -9.55 cell :0 Median :477.5 Median :481.7
     Mean :-4.77 Mean : -9.55 Mean :477.0 Mean :482.8
     3rd Qu.:-4.77 3rd Qu.: -8.55 3rd Qu.:500.5 3rd Qu.:504.9
     Max. :-4.77 Max. : -7.55 Max. :501.8 Max. :507.8
     610
     Min. :428.7
     1st Qu.:456.0
     Median :464.8
     Mean :465.5
     3rd Qu.:488.6
     Max. :489.5
    > as.long.df (flu [,, 405 ~ 410])
     .wavelength spc file c
    1 405.0 27.15000 rawdata/flu1.txt 0.05
    2 405.0 66.80133 rawdata/flu2.txt 0.10
    3 405.0 93.14433 rawdata/flu3.txt 0.15
    4 405.0 130.66367 rawdata/flu4.txt 0.20
    5 405.0 167.26667 rawdata/flu5.txt 0.25
    6 405.0 198.43033 rawdata/flu6.txt 0.30
    1.1 405.5 32.34467 rawdata/flu1.txt 0.05
    2.1 405.5 63.71533 rawdata/flu2.txt 0.10
    3.1 405.5 103.06767 rawdata/flu3.txt 0.15
    4.1 405.5 139.99833 rawdata/flu4.txt 0.20
    5.1 405.5 171.89833 rawdata/flu5.txt 0.25
    6.1 405.5 209.45800 rawdata/flu6.txt 0.30
    1.2 406.0 33.37867 rawdata/flu1.txt 0.05
    2.2 406.0 66.71200 rawdata/flu2.txt 0.10
    3.2 406.0 106.19367 rawdata/flu3.txt 0.15
    4.2 406.0 143.79767 rawdata/flu4.txt 0.20
    5.2 406.0 177.47067 rawdata/flu5.txt 0.25
    6.2 406.0 215.78500 rawdata/flu6.txt 0.30
    1.3 406.5 34.41933 rawdata/flu1.txt 0.05
    2.3 406.5 69.58233 rawdata/flu2.txt 0.10
    3.3 406.5 110.18633 rawdata/flu3.txt 0.15
    4.3 406.5 148.42000 rawdata/flu4.txt 0.20
    5.3 406.5 184.62467 rawdata/flu5.txt 0.25
    6.3 406.5 224.58700 rawdata/flu6.txt 0.30
    1.4 407.0 36.53133 rawdata/flu1.txt 0.05
    2.4 407.0 72.52967 rawdata/flu2.txt 0.10
    3.4 407.0 113.24867 rawdata/flu3.txt 0.15
    4.4 407.0 152.13267 rawdata/flu4.txt 0.20
    5.4 407.0 189.75233 rawdata/flu5.txt 0.25
    6.4 407.0 232.52800 rawdata/flu6.txt 0.30
    1.5 407.5 37.64767 rawdata/flu1.txt 0.05
    2.5 407.5 74.55833 rawdata/flu2.txt 0.10
    3.5 407.5 119.17300 rawdata/flu3.txt 0.15
    4.5 407.5 159.31033 rawdata/flu4.txt 0.20
    5.5 407.5 198.11533 rawdata/flu5.txt 0.25
    6.5 407.5 240.77133 rawdata/flu6.txt 0.30
    1.6 408.0 38.13700 rawdata/flu1.txt 0.05
    2.6 408.0 77.04800 rawdata/flu2.txt 0.10
    3.6 408.0 121.31333 rawdata/flu3.txt 0.15
    4.6 408.0 165.05233 rawdata/flu4.txt 0.20
    5.6 408.0 205.56267 rawdata/flu5.txt 0.25
    6.6 408.0 248.04667 rawdata/flu6.txt 0.30
    1.7 408.5 39.17700 rawdata/flu1.txt 0.05
    2.7 408.5 80.25967 rawdata/flu2.txt 0.10
    3.7 408.5 124.67533 rawdata/flu3.txt 0.15
    4.7 408.5 168.68967 rawdata/flu4.txt 0.20
    5.7 408.5 208.41933 rawdata/flu5.txt 0.25
    6.7 408.5 256.89133 rawdata/flu6.txt 0.30
    1.8 409.0 40.73567 rawdata/flu1.txt 0.05
    2.8 409.0 82.53867 rawdata/flu2.txt 0.10
    3.8 409.0 129.56867 rawdata/flu3.txt 0.15
    4.8 409.0 175.45900 rawdata/flu4.txt 0.20
    5.8 409.0 217.55267 rawdata/flu5.txt 0.25
    6.8 409.0 262.73900 rawdata/flu6.txt 0.30
    1.9 409.5 41.38133 rawdata/flu1.txt 0.05
    2.9 409.5 84.49167 rawdata/flu2.txt 0.10
    3.9 409.5 134.11733 rawdata/flu3.txt 0.15
    4.9 409.5 181.58100 rawdata/flu4.txt 0.20
    5.9 409.5 224.74633 rawdata/flu5.txt 0.25
    6.9 409.5 270.27133 rawdata/flu6.txt 0.30
    1.10 410.0 44.25133 rawdata/flu1.txt 0.05
    2.10 410.0 88.15167 rawdata/flu2.txt 0.10
    3.10 410.0 139.98667 rawdata/flu3.txt 0.15
    4.10 410.0 185.69233 rawdata/flu4.txt 0.20
    5.10 410.0 231.03567 rawdata/flu5.txt 0.25
    6.10 410.0 281.82867 rawdata/flu6.txt 0.30
    > summary (as.long.df (flu [,, 405 ~ 410]))
     .wavelength spc file c
     Min. :405.0 Min. : 27.15 rawdata/flu1.txt:11 Min. :0.050
     1st Qu.:406.0 1st Qu.: 75.18 rawdata/flu2.txt:11 1st Qu.:0.100
     Median :407.5 Median :137.05 rawdata/flu3.txt:11 Median :0.175
     Mean :407.5 Mean :137.80 rawdata/flu4.txt:11 Mean :0.175
     3rd Qu.:409.0 3rd Qu.:196.02 rawdata/flu5.txt:11 3rd Qu.:0.250
     Max. :410.0 Max. :281.83 rawdata/flu6.txt:11 Max. :0.300
    > summary (as.long.df (flu [,, 405 ~ 410], rownames = TRUE))
     .rownames .wavelength spc file
     1:11 Min. :405.0 Min. : 27.15 rawdata/flu1.txt:11
     2:11 1st Qu.:406.0 1st Qu.: 75.18 rawdata/flu2.txt:11
     3:11 Median :407.5 Median :137.05 rawdata/flu3.txt:11
     4:11 Mean :407.5 Mean :137.80 rawdata/flu4.txt:11
     5:11 3rd Qu.:409.0 3rd Qu.:196.02 rawdata/flu5.txt:11
     6:11 Max. :410.0 Max. :281.83 rawdata/flu6.txt:11
     c
     Min. :0.050
     1st Qu.:0.100
     Median :0.175
     Mean :0.175
     3rd Qu.:0.250
     Max. :0.300
    > summary (as.long.df (flu [,, 405 ~ 410], wl.factor = TRUE))
     .wavelength spc file c
     405 : 6 Min. : 27.15 rawdata/flu1.txt:11 Min. :0.050
     405.5 : 6 1st Qu.: 75.18 rawdata/flu2.txt:11 1st Qu.:0.100
     406 : 6 Median :137.05 rawdata/flu3.txt:11 Median :0.175
     406.5 : 6 Mean :137.80 rawdata/flu4.txt:11 Mean :0.175
     407 : 6 3rd Qu.:196.02 rawdata/flu5.txt:11 3rd Qu.:0.250
     407.5 : 6 Max. :281.83 rawdata/flu6.txt:11 Max. :0.300
     (Other):30
    > df <- as.t.df (apply (chondro, 2, mean_pm_sd))
    > head (df)
     .wavelength mean.minus.sd mean mean.plus.sd
    spc.602 602 297.8472 343.0481 388.2489
    spc.606 606 300.0874 345.9178 391.7482
    spc.610 610 290.3887 334.0423 377.6959
    spc.614 614 280.1190 321.3384 362.5578
    spc.618 618 297.8204 342.4266 387.0328
    spc.622 622 314.7000 363.2688 411.8375
    >
    > if (require (ggplot2)){
    + ggplot (df, aes (x = .wavelength)) +
    + geom_ribbon (aes (ymin = mean.minus.sd, ymax = mean.plus.sd),
    + fill = "#00000040") +
    + geom_line (aes (y = mean))
    + }
    Warning in initialize(value, ...) :
     Class definition for Class "Scales" doesn't have a parent environment for objects defined. Bug??
    Error in match.fun(FUN) : object 'scale_clone' not found
    Calls: +.gg ... add_ggplot -> plot_clone -> <Anonymous> -> lapply -> match.fun
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.98-20150304
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in 'introduction.Rnw'
     ...
    + require(ggplot2)
    + ggplot(as.long.df(chondro[1]), aes(x = .wavelength, y = spc)) +
    + geom_line()
    + gg .... [TRUNCATED]
    Warning in initialize(value, ...) :
     Class definition for Class "Scales" doesn't have a parent environment for objects defined. Bug??
    
     When sourcing 'introduction.R':
    Error: object 'scale_clone' not found
    Execution halted
    when running code in 'plotting.Rnw'
     ...
    > if (require(ggplot2)) {
    + qplotspc(flu) + aes(colour = c)
    + ggsave("plotting-fig--ggplotspc.pdf", width = 4, height = 2.6)
    + qplotmap(ch .... [TRUNCATED]
    Warning in initialize(value, ...) :
     Class definition for Class "Scales" doesn't have a parent environment for objects defined. Bug??
    
     When sourcing 'plotting.R':
    Error: object 'scale_clone' not found
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.98-20150304
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    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
    Warning in initialize(value, ...) :
     Class definition for Class "Scales" doesn't have a parent environment for objects defined. Bug??
    
    Error: processing vignette 'introduction.Rnw' failed with diagnostics:
     chunk 110 (label = ggplot-do)
    Error in match.fun(FUN) : object 'scale_clone' not found
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.98-20150304
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    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: ~
Flavors: r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64