CRAN Package Check Results for Package amei

Last updated on 2018-06-17 19:49:28 CEST.

Flavor	Version	T_install	T_check	T_total	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0-7	4.40	26.72	31.12	ERROR
r-devel-linux-x86_64-debian-gcc	1.0-7	2.56	21.19	23.75	ERROR
r-devel-linux-x86_64-fedora-clang	1.0-7			684.22	WARN
r-devel-linux-x86_64-fedora-gcc	1.0-7			653.52	NOTE
r-devel-windows-ix86+x86_64	1.0-7	15.00	52.00	67.00	NOTE	--no-vignettes
r-patched-linux-x86_64	1.0-7	3.52	25.81	29.33	ERROR
r-patched-solaris-x86	1.0-7			761.70	NOTE	--no-build-vignettes
r-release-linux-x86_64	1.0-7	3.46	25.92	29.38	ERROR
r-release-windows-ix86+x86_64	1.0-7	15.00	53.00	68.00	NOTE	--no-vignettes
r-release-osx-x86_64	1.0-7				WARN
r-oldrel-windows-ix86+x86_64	1.0-7	11.00	52.00	63.00	NOTE	--no-vignettes
r-oldrel-osx-x86_64	1.0-7				NOTE

Check Details

Version: 1.0-7
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
     matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
     matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64

Version: 1.0-7
Check: DESCRIPTION meta-information
Result: NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
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, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-7
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.MCepi plot.epiman plot.optvac print.MCepi print.epiman
     print.optvac print.summary.MCepi print.summary.epiman
     print.summary.optvac summary.MCepi summary.epiman summary.optvac
    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-release-linux-x86_64

Version: 1.0-7
Check: R code for possible problems
Result: NOTE
    PlotCosts: no visible global function definition for ‘lines’
    PlotCosts: no visible global function definition for ‘plot’
    PlotEpi: no visible global function definition for ‘rgb’
    PlotEpi: no visible global function definition for ‘lines’
    PlotEpi: no visible global function definition for ‘plot’
    PlotEpi: no visible global function definition for ‘legend’
    PlotParams: no visible global function definition for ‘par’
    PlotParams: no visible global function definition for ‘density’
    PlotParams: no visible global function definition for ‘rgamma’
    PlotParams: no visible global function definition for ‘rbeta’
    PlotParams: no visible global function definition for ‘plot’
    PlotParams: no visible global function definition for ‘quantile’
    PlotParams: no visible global function definition for ‘polygon’
    PlotParams: no visible global function definition for ‘rgb’
    PlotParams: no visible global function definition for ‘lines’
    PlotParams: no visible global function definition for ‘points’
    SimulateEpidemicQuantiles: no visible binding for global variable
     ‘quantile’
    SimulateEpidemicQuantiles: no visible binding for global variable
     ‘median’
    SimulateManagementQuantiles: no visible binding for global variable
     ‘quantile’
    SimulateManagementQuantiles: no visible binding for global variable
     ‘median’
    TimeSeriesOfDensities: no visible global function definition for
     ‘density’
    TimeSeriesOfDensities: no visible global function definition for ‘plot’
    TimeSeriesOfDensities: no visible global function definition for
     ‘lines’
    TimeSeriesOfDensities: no visible global function definition for ‘rgb’
    TimeSeriesOfDensities: no visible global function definition for ‘axis’
    TimeSeriesOfDensities: no visible global function definition for ‘box’
    epi.gibbs.mu: no visible global function definition for ‘rbeta’
    epi.gibbs.nu: no visible global function definition for ‘rbeta’
    epi.log.post.b: no visible global function definition for ‘dbinom’
    epi.log.post.b: no visible global function definition for ‘dgamma’
    epi.log.post.k: no visible global function definition for ‘dbinom’
    epi.log.post.k: no visible global function definition for ‘dgamma’
    epistep: no visible global function definition for ‘rbinom’
    mcmc.bknumu: no visible global function definition for ‘runif’
    plot.MCepi: no visible global function definition for ‘plot’
    plot.MCepi: no visible global function definition for ‘lines’
    plot.epiman: no visible global function definition for ‘title’
    plot.optvac: no visible global function definition for ‘layout’
    plot.optvac: no visible global function definition for ‘image’
    plot.optvac: no visible global function definition for ‘heat.colors’
    plot.optvac: no visible global function definition for ‘grid’
    plot.optvac: no visible global function definition for ‘text’
    plot.optvac: no visible global function definition for ‘axis’
    plot.optvac: no visible global function definition for ‘mtext’
    propose: no visible global function definition for ‘runif’
    propose: no visible global function definition for ‘dunif’
    Undefined global functions or variables:
     axis box dbinom density dgamma dunif grid heat.colors image layout
     legend lines median mtext par plot points polygon quantile rbeta
     rbinom rgamma rgb runif text title
    Consider adding
     importFrom("grDevices", "heat.colors", "rgb")
     importFrom("graphics", "axis", "box", "grid", "image", "layout",
     "legend", "lines", "mtext", "par", "plot", "points",
     "polygon", "text", "title")
     importFrom("stats", "dbinom", "density", "dgamma", "dunif", "median",
     "quantile", "rbeta", "rbinom", "rgamma", "runif")
    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-patched-linux-x86_64, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.0-7
Check: compiled code
Result: NOTE
    File ‘amei/libs/amei.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: 1.0-7
Check: examples
Result: ERROR
    Running examples in ‘amei-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: MCepi
    > ### Title: Monte Carlo Epidemic Simulation with Static Vaccination
    > ### Aliases: MCepi
    > ### Keywords: methods iteration
    >
    > ### ** Examples
    >
    > ## true epidemic parameters, initial values, and
    > ## vaccination costs
    > truth <- list(b=0.00218, k=10, nu=0.4, mu=0)
    > init <- list(S0=762, I0=1, R0=0, D0=0)
    > costs <- list(vac=2, death=4, infect=1)
    >
    > ## trivial vaccination strategy -- dont vaccinate
    > vac <- list(frac=0, stop=0)
    >
    > ## simulate the resulting trajectories
    > init.MCepi <- MCepi(init, truth, vac, costs)
    >
    > ## plot the distribution of trajectories and costs
    > ## under no vaccination
    > plot(init.MCepi, main="no vaccination")
    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

Version: 1.0-7
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...

    Error: processing vignette ‘amei.Rnw’ failed with diagnostics:
     chunk 6 (label = epis)
    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: 1.0-7
Flags: --no-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
Checking should be performed on sources prepared by 'R CMD build'.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-7
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    PlotCosts: no visible global function definition for 'lines'
    PlotCosts: no visible global function definition for 'plot'
    PlotEpi: no visible global function definition for 'rgb'
    PlotEpi: no visible global function definition for 'lines'
    PlotEpi: no visible global function definition for 'plot'
    PlotEpi: no visible global function definition for 'legend'
    PlotParams: no visible global function definition for 'par'
    PlotParams: no visible global function definition for 'density'
    PlotParams: no visible global function definition for 'rgamma'
    PlotParams: no visible global function definition for 'rbeta'
    PlotParams: no visible global function definition for 'plot'
    PlotParams: no visible global function definition for 'quantile'
    PlotParams: no visible global function definition for 'polygon'
    PlotParams: no visible global function definition for 'rgb'
    PlotParams: no visible global function definition for 'lines'
    PlotParams: no visible global function definition for 'points'
    SimulateEpidemicQuantiles: no visible binding for global variable
     'quantile'
    SimulateEpidemicQuantiles: no visible binding for global variable
     'median'
    SimulateManagementQuantiles: no visible binding for global variable
     'quantile'
    SimulateManagementQuantiles: no visible binding for global variable
     'median'
    TimeSeriesOfDensities: no visible global function definition for
     'density'
    TimeSeriesOfDensities: no visible global function definition for 'plot'
    TimeSeriesOfDensities: no visible global function definition for
     'lines'
    TimeSeriesOfDensities: no visible global function definition for 'rgb'
    TimeSeriesOfDensities: no visible global function definition for 'axis'
    TimeSeriesOfDensities: no visible global function definition for 'box'
    epi.gibbs.mu: no visible global function definition for 'rbeta'
    epi.gibbs.nu: no visible global function definition for 'rbeta'
    epi.log.post.b: no visible global function definition for 'dbinom'
    epi.log.post.b: no visible global function definition for 'dgamma'
    epi.log.post.k: no visible global function definition for 'dbinom'
    epi.log.post.k: no visible global function definition for 'dgamma'
    epistep: no visible global function definition for 'rbinom'
    mcmc.bknumu: no visible global function definition for 'runif'
    plot.MCepi: no visible global function definition for 'plot'
    plot.MCepi: no visible global function definition for 'lines'
    plot.epiman: no visible global function definition for 'title'
    plot.optvac: no visible global function definition for 'layout'
    plot.optvac: no visible global function definition for 'image'
    plot.optvac: no visible global function definition for 'heat.colors'
    plot.optvac: no visible global function definition for 'grid'
    plot.optvac: no visible global function definition for 'text'
    plot.optvac: no visible global function definition for 'axis'
    plot.optvac: no visible global function definition for 'mtext'
    propose: no visible global function definition for 'runif'
    propose: no visible global function definition for 'dunif'
    Undefined global functions or variables:
     axis box dbinom density dgamma dunif grid heat.colors image layout
     legend lines median mtext par plot points polygon quantile rbeta
     rbinom rgamma rgb runif text title
    Consider adding
     importFrom("grDevices", "heat.colors", "rgb")
     importFrom("graphics", "axis", "box", "grid", "image", "layout",
     "legend", "lines", "mtext", "par", "plot", "points",
     "polygon", "text", "title")
     importFrom("stats", "dbinom", "density", "dgamma", "dunif", "median",
     "quantile", "rbeta", "rbinom", "rgamma", "runif")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-7
Flags: --no-build-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
Flavor: r-patched-solaris-x86

Version: 1.0-7
Flags: --no-build-vignettes
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.MCepi plot.epiman plot.optvac print.MCepi print.epiman
     print.optvac print.summary.MCepi print.summary.epiman
     print.summary.optvac summary.MCepi summary.epiman summary.optvac
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-patched-solaris-x86

Version: 1.0-7
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    PlotCosts: no visible global function definition for ‘lines’
    PlotCosts: no visible global function definition for ‘plot’
    PlotEpi: no visible global function definition for ‘rgb’
    PlotEpi: no visible global function definition for ‘lines’
    PlotEpi: no visible global function definition for ‘plot’
    PlotEpi: no visible global function definition for ‘legend’
    PlotParams: no visible global function definition for ‘par’
    PlotParams: no visible global function definition for ‘density’
    PlotParams: no visible global function definition for ‘rgamma’
    PlotParams: no visible global function definition for ‘rbeta’
    PlotParams: no visible global function definition for ‘plot’
    PlotParams: no visible global function definition for ‘quantile’
    PlotParams: no visible global function definition for ‘polygon’
    PlotParams: no visible global function definition for ‘rgb’
    PlotParams: no visible global function definition for ‘lines’
    PlotParams: no visible global function definition for ‘points’
    SimulateEpidemicQuantiles: no visible binding for global variable
     ‘quantile’
    SimulateEpidemicQuantiles: no visible binding for global variable
     ‘median’
    SimulateManagementQuantiles: no visible binding for global variable
     ‘quantile’
    SimulateManagementQuantiles: no visible binding for global variable
     ‘median’
    TimeSeriesOfDensities: no visible global function definition for
     ‘density’
    TimeSeriesOfDensities: no visible global function definition for ‘plot’
    TimeSeriesOfDensities: no visible global function definition for
     ‘lines’
    TimeSeriesOfDensities: no visible global function definition for ‘rgb’
    TimeSeriesOfDensities: no visible global function definition for ‘axis’
    TimeSeriesOfDensities: no visible global function definition for ‘box’
    epi.gibbs.mu: no visible global function definition for ‘rbeta’
    epi.gibbs.nu: no visible global function definition for ‘rbeta’
    epi.log.post.b: no visible global function definition for ‘dbinom’
    epi.log.post.b: no visible global function definition for ‘dgamma’
    epi.log.post.k: no visible global function definition for ‘dbinom’
    epi.log.post.k: no visible global function definition for ‘dgamma’
    epistep: no visible global function definition for ‘rbinom’
    mcmc.bknumu: no visible global function definition for ‘runif’
    plot.MCepi: no visible global function definition for ‘plot’
    plot.MCepi: no visible global function definition for ‘lines’
    plot.epiman: no visible global function definition for ‘title’
    plot.optvac: no visible global function definition for ‘layout’
    plot.optvac: no visible global function definition for ‘image’
    plot.optvac: no visible global function definition for ‘heat.colors’
    plot.optvac: no visible global function definition for ‘grid’
    plot.optvac: no visible global function definition for ‘text’
    plot.optvac: no visible global function definition for ‘axis’
    plot.optvac: no visible global function definition for ‘mtext’
    propose: no visible global function definition for ‘runif’
    propose: no visible global function definition for ‘dunif’
    Undefined global functions or variables:
     axis box dbinom density dgamma dunif grid heat.colors image layout
     legend lines median mtext par plot points polygon quantile rbeta
     rbinom rgamma rgb runif text title
    Consider adding
     importFrom("grDevices", "heat.colors", "rgb")
     importFrom("graphics", "axis", "box", "grid", "image", "layout",
     "legend", "lines", "mtext", "par", "plot", "points",
     "polygon", "text", "title")
     importFrom("stats", "dbinom", "density", "dgamma", "dunif", "median",
     "quantile", "rbeta", "rbinom", "rgamma", "runif")
    to your NAMESPACE file.
Flavor: r-patched-solaris-x86