CRAN Package Check Results for Package quipu

Last updated on 2018-06-01 08:49:09 CEST.

Check Details

Version: 1.9.0
Check: R code for possible problems
Result: NOTE
    draw_legend: no visible global function definition for ‘legend’
    draw_legend: no visible global function definition for ‘par’
    draw_nodes: no visible global function definition for ‘lines’
    draw_nodes: no visible global function definition for ‘points’
    draw_nodes: no visible global function definition for ‘text’
    draw_vertical_lines: no visible global function definition for ‘lines’
    draw_vertical_lines: no visible global function definition for ‘abline’
    layout_large_plot: no visible global function definition for ‘par’
    layout_large_plot: no visible global function definition for ‘mtext’
    layout_large_plot: no visible global function definition for ‘axis’
    layout_large_plot: no visible global function definition for ‘lines’
    layout_small_plot: no visible global function definition for ‘par’
    rquipu: no visible global function definition for ‘colors’
    rquipu: no visible global function definition for ‘jpeg’
    rquipu: no visible global function definition for ‘png’
    rquipu: no visible global function definition for ‘dev.off’
    Undefined global functions or variables:
     abline axis colors dev.off jpeg legend lines mtext par png points
     text
    Consider adding
     importFrom("grDevices", "colors", "dev.off", "jpeg", "png")
     importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
     "par", "points", "text")
    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: 1.9.0
Check: examples
Result: ERROR
    Running examples in ‘quipu-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: rquipu
    > ### Title: Creates quipu-type charts for a set of SSR markers
    > ### Aliases: rquipu
    >
    > ### ** Examples
    >
    > library(quipu)
    >
    > data(potato.quipu)
    > dat = potato.quipu
    >
    > str(dat)
    'data.frame': 203 obs. of 4 variables:
     $ accession_id: chr "sample.1" "sample.1" "sample.1" "sample.1" ...
     $ primer_name : chr "STM1064" "STM1064" "STM1064" "STPoAc58" ...
     $ marker_size : int 207 209 214 246 248 250 187 190 102 107 ...
     $ map_location: chr "II" "II" "II" "V" ...
    >
    > rquipu(dat)
    Error in if (img.format %in% c("jpeg", "jpg")) nameclones2 = file.path(dir.print, :
     the condition has length > 1
    Calls: rquipu
    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: 1.9.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 95-96 (Quipu_tutorial.Rnw)
    Error: processing vignette ‘Quipu_tutorial.Rnw’ failed with diagnostics:
    the condition has length > 1
    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: 1.9.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning: running command 'kpsewhich framed.sty' had status 1
    Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
     unable to find LaTeX package 'framed'; will use a copy from knitr
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'Quipu_tutorial.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `sectsty.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ! Emergency stop.
    <read *>
    
    l.31 \sectionfont
     {\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-...
    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-oldrel-osx-x86_64