CRAN Package Check Results for Package P2C2M

Last updated on 2019-01-19 00:46:36 CET.

Check Details

Version: 0.7.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'genealogicalSorting', 'phybase'
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: 0.7.6
Check: R code for possible problems
Result: NOTE
    ms.exec: no visible global function definition for ‘tail’
    p2c2m.readstarb: no visible global function definition for ‘head’
    p2c2m.readstarb: no visible binding for global variable ‘head’
    rmOutlrs: no visible global function definition for ‘boxplot.stats’
    rmext: no visible global function definition for ‘tail’
    rowMedians: no visible binding for global variable ‘median’
    stats.acrGenes: no visible binding for global variable ‘sd’
    stats.perGene: no visible binding for global variable ‘sd’
    statshelpers.cv: no visible binding for global variable ‘sd’
    statshelpers.qntls: no visible binding for global variable ‘quantile’
    Undefined global functions or variables:
     boxplot.stats head median quantile sd tail
    Consider adding
     importFrom("grDevices", "boxplot.stats")
     importFrom("stats", "median", "quantile", "sd")
     importFrom("utils", "head", "tail")
    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-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.7.6
Check: data for non-ASCII characters
Result: NOTE
     Note: found 490 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.7.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘genealogicalSorting’ ‘phybase’
Flavors: r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.7.6
Check: examples
Result: ERROR
    Running examples in ‘P2C2M-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: p2c2m.complete
    > ### Title: Execute the complete P2C2M pipeline via a single command
    > ### Aliases: p2c2m.complete
    >
    > ### ** Examples
    >
    > ## Example of the minimal data requirements to run P2C2M
    >
    > # The absolute path to the input directory is set
    > inPath <- system.file("extdata", "sim.E.003.small/", package="P2C2M")
    >
    > # The name of the xml-file generated by BEAUTi and located in
    > # "inPath" is set
    > inFile <- "sim.E.003.small.xml"
    >
    > # Posterior predictive simulations with a setting of 2 simulation
    > # replicates are preformed
    > sim.E.003.small <- p2c2m.complete(inPath, inFile, num.reps=2, save.metadata=TRUE)
    Error in python.exec(code, get.exception) : cannot import name izip
    Calls: p2c2m.complete -> p2c2m.readstarb -> <Anonymous> -> python.exec
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.7.6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.7.6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Warning: Removed 575 rows containing non-finite values
    (stat_density).
    Warning: Removed 2 rows containing missing values (geom_vline).
    Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
    Warning: Removed 575 rows containing non-finite values
    (stat_density).
    Warning: Removed 2 rows containing missing values (geom_vline).
    Warning: Removed 370 rows containing missing values (geom_point).
    Warning: Removed 370 rows containing missing values (geom_point).
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'P2C2M_Vignette.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `fullpage.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ! Emergency stop.
    <read *>
    
    l.5 \usepackage
     {listings}^^M
    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-oldrel-osx-x86_64