CRAN Package Check Results for Package occ

Last updated on 2018-05-14 01:46:50 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 0.77 15.76 16.53 ERROR
r-devel-linux-x86_64-debian-gcc 1.0 0.75 13.81 14.56 ERROR
r-devel-linux-x86_64-fedora-clang 1.0 21.92 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 20.63 NOTE
r-devel-windows-ix86+x86_64 1.0 4.00 27.00 31.00 NOTE
r-patched-linux-x86_64 1.0 0.98 16.09 17.07 ERROR
r-patched-solaris-x86 1.0 35.50 NOTE
r-release-linux-x86_64 1.0 0.93 15.80 16.73 ERROR
r-release-windows-ix86+x86_64 1.0 4.00 27.00 31.00 NOTE
r-release-osx-x86_64 1.0 NOTE
r-oldrel-windows-ix86+x86_64 1.0 2.00 26.00 28.00 NOTE
r-oldrel-osx-x86_64 1.0 NOTE

Check Details

Version: 1.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.occ print.occ print.summary.occ summary.occ
    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: 1.0
Check: R code for possible problems
Result: NOTE
    occ.ols: no visible global function definition for ‘lm’
    occ.reml: no visible global function definition for ‘nlm’
    occ.reml: no visible global function definition for ‘sd’
    plot.occ: no visible global function definition for ‘par’
    plot.occ: no visible global function definition for ‘barplot’
    plot.occ: no visible global function definition for ‘lines’
    plot.occ: no visible global function definition for ‘title’
    plot.occ: no visible global function definition for ‘frame’
    plot.occ: no visible global function definition for ‘legend’
    Undefined global functions or variables:
     barplot frame legend lines lm nlm par sd title
    Consider adding
     importFrom("graphics", "barplot", "frame", "legend", "lines", "par",
     "title")
     importFrom("stats", "lm", "nlm", "sd")
    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: 1.0
Check: examples
Result: ERROR
    Running examples in ‘occ-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: occ
    > ### Title: Estimates PET neuroreceptor occupancies
    > ### Aliases: occ occ.ols occ.ref occ.reml plot.occ print.occ
    > ### print.summary.occ summary.occ
    > ### Keywords: maximum likelihood estimation neuroreceptor neuroreceptor
    > ### occupancy occupancy occupancy plot PET positron emission tomography
    > ### receptor receptor occupancy reference region restricted maximum
    > ### likelihood estimation
    >
    > ### ** Examples
    >
    > ## Total volumes of distribution (VT) from a simulated PET study
    > ## including a baseline scan, as well as two other scans after
    > ## administration of a drug. Note that each row in the matrix
    > ## represents a ROI, whilst each column represents a scan.
    >
    > data(occ.example)
    > occ.example
     Baseline 1st postdose 2nd postdose
    Cerebellum 0.39 0.28 0.30
    Frontal cortex 0.72 0.35 0.47
    Occipital cortex 0.96 0.43 0.62
    Parietal cortex 0.75 0.34 0.50
    Temporal cortex 0.44 0.26 0.31
    >
    > # Baseline 1st postdose 2nd postdose
    > # Cerebellum 0.39 0.28 0.30
    > # Frontal cortex 0.72 0.35 0.47
    > # Occipital cortex 0.96 0.43 0.62
    > # Parietal cortex 0.75 0.34 0.50
    > # Temporal cortex 0.44 0.26 0.31
    >
    >
    > ## Default REML fitting of these simulated data:
    >
    > m = occ(occ.example)
    >
    > print(m) # Prints the neuroreceptor occupancy coefficients
    $VT
     Baseline 1st postdose 2nd postdose
    Cerebellum 0.39 0.28 0.30
    Frontal cortex 0.72 0.35 0.47
    Occipital cortex 0.96 0.43 0.62
    Parietal cortex 0.75 0.34 0.50
    Temporal cortex 0.44 0.26 0.31
    
    $coefficients
     Baseline 1st postdose 2nd postdose
    Cerebellum 0 0.7086362 0.4598614
    Frontal cortex 0 0.7086362 0.4598614
    Occipital cortex 0 0.7086362 0.4598614
    Parietal cortex 0 0.7086362 0.4598614
    Temporal cortex 0 0.7086362 0.4598614
    
    $VND
     Baseline 1st postdose 2nd postdose
    VND 0.1982597 0.1982597 0.1982597
    
    $VS
     Baseline 1st postdose 2nd postdose
    Cerebellum 0.1964995 0.1964995 0.1964995
    Frontal cortex 0.5177297 0.5177297 0.5177297
    Occipital cortex 0.7678527 0.7678527 0.7678527
    Parietal cortex 0.5491762 0.5491762 0.5491762
    Temporal cortex 0.2325105 0.2325105 0.2325105
    
    $sigma
     Baseline 1st postdose 2nd postdose
    sigma 0.01016802 0.01016802 0.01016802
    
    $fitted.values
     Baseline 1st postdose 2nd postdose
    Cerebellum 0.3947592 0.2555125 0.3043966
    Frontal cortex 0.7159894 0.3491074 0.4779055
    Occipital cortex 0.9661124 0.4219841 0.6130065
    Parietal cortex 0.7474358 0.3582697 0.4948909
    Temporal cortex 0.4307701 0.2660048 0.3238475
    
    $residuals
     Baseline 1st postdose 2nd postdose
    Cerebellum -0.004759197 0.0244874808 -0.004396649
    Frontal cortex 0.004010596 0.0008926295 -0.007905481
    Occipital cortex -0.006112358 0.0080158574 0.006993459
    Parietal cortex 0.002564154 -0.0182697251 0.005109082
    Temporal cortex 0.009229865 -0.0060048025 -0.013847546
    
    $call
    occ(VT = occ.example)
    
    attr(,"class")
    [1] "occ"
    >
    > summary(m) # Also prints the non-displaceable volume of
     Length Class Mode
    VT 15 -none- numeric
    coefficients 15 -none- numeric
    VND 3 -none- numeric
    VS 15 -none- numeric
    sigma 3 -none- numeric
    fitted.values 15 -none- numeric
    residuals 15 -none- numeric
    call 2 -none- call
    > # distribution (VND), the specific volumes of
    > # distribution (VS) and the measurement error
    >
    > fitted(m) # Prints the fitted values
     Baseline 1st postdose 2nd postdose
    Cerebellum 0.3947592 0.2555125 0.3043966
    Frontal cortex 0.7159894 0.3491074 0.4779055
    Occipital cortex 0.9661124 0.4219841 0.6130065
    Parietal cortex 0.7474358 0.3582697 0.4948909
    Temporal cortex 0.4307701 0.2660048 0.3238475
    >
    > residuals(m) # Prints the residuals
     Baseline 1st postdose 2nd postdose
    Cerebellum -0.004759197 0.0244874808 -0.004396649
    Frontal cortex 0.004010596 0.0008926295 -0.007905481
    Occipital cortex -0.006112358 0.0080158574 0.006993459
    Parietal cortex 0.002564154 -0.0182697251 0.005109082
    Temporal cortex 0.009229865 -0.0060048025 -0.013847546
    >
    > plot(m) # Plots the estimated and observed volumes of
    Error in xy.coords(x, y, xlabel, ylabel, log) :
     'x' is a list, but does not have components 'x' and 'y'
    Calls: plot -> plot.default -> xy.coords
    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