CRAN Package Check Results for Package bios2mds

Last updated on 2017-05-24 22:46:58.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.2 1.74 46.41 48.15 NOTE
r-devel-linux-x86_64-debian-gcc 1.2.2 1.88 45.47 47.35 NOTE
r-devel-linux-x86_64-fedora-clang 1.2.2 89.77 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.2.2 86.87 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.2.2 7.00 76.00 83.00 NOTE
r-patched-linux-x86_64 1.2.2 1.62 43.55 45.18 NOTE
r-patched-solaris-sparc 1.2.2 529.00 NOTE
r-patched-solaris-x86 1.2.2 121.50 NOTE
r-release-linux-x86_64 1.2.2 1.68 43.89 45.58 NOTE
r-release-windows-ix86+x86_64 1.2.2 7.00 168.00 175.00 NOTE
r-release-osx-x86_64 1.2.2 NOTE
r-oldrel-windows-ix86+x86_64 1.2.2 11.00 96.00 107.00 NOTE
r-oldrel-osx-x86_64 1.2.2 WARN

Check Details

Version: 1.2.2
Check: R code for possible problems
Result: NOTE
    col.group: no visible global function definition for ‘read.table’
    dif: no visible global function definition for ‘complete.cases’
    dis: no visible global function definition for ‘data’
    dis: no visible binding for global variable ‘sub.mat’
    dis : Sij: no visible global function definition for ‘na.omit’
    dis : Tij: no visible global function definition for ‘na.omit’
    dis: no visible global function definition for ‘complete.cases’
    mat.dis: no visible global function definition for ‘data’
    mat.dis: no visible binding for global variable ‘sub.mat’
    mmds.2D.multi: no visible global function definition for ‘dev.new’
    mmds.2D.multi: no visible global function definition for ‘pdf’
    mmds.2D.multi: no visible global function definition for ‘png’
    mmds.2D.multi: no visible global function definition for ‘tiff’
    mmds.2D.multi: no visible global function definition for ‘postscript’
    mmds.2D.multi: no visible global function definition for ‘plot’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘points’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘lines’
    mmds.2D.multi: no visible global function definition for ‘abline’
    mmds.2D.multi: no visible global function definition for ‘box’
    mmds.2D.multi: no visible global function definition for ‘dev.off’
    mmds.2D.plot: no visible global function definition for ‘dev.new’
    mmds.2D.plot: no visible global function definition for ‘pdf’
    mmds.2D.plot: no visible global function definition for ‘png’
    mmds.2D.plot: no visible global function definition for ‘tiff’
    mmds.2D.plot: no visible global function definition for ‘postscript’
    mmds.2D.plot: no visible global function definition for ‘plot’
    mmds.2D.plot: no visible global function definition for ‘text’
    mmds.2D.plot: no visible global function definition for ‘points’
    mmds.2D.plot: no visible global function definition for ‘abline’
    mmds.2D.plot: no visible global function definition for ‘box’
    mmds.2D.plot: no visible global function definition for ‘dev.off’
    mmds.3D.plot: no visible global function definition for ‘box3d’
    mmds.3D.plot: no visible global function definition for ‘axes3d’
    mmds.plot: no visible global function definition for ‘dev.new’
    mmds.plot: no visible global function definition for ‘pdf’
    mmds.plot: no visible global function definition for ‘layout’
    mmds.plot: no visible global function definition for ‘dev.off’
    scree.plot: no visible global function definition for ‘dev.new’
    scree.plot: no visible global function definition for ‘pdf’
    scree.plot: no visible global function definition for ‘barplot’
    scree.plot: no visible global function definition for ‘text’
    scree.plot: no visible global function definition for ‘dev.off’
    sil.score: no visible global function definition for ‘dist’
    write.mmds.pdb: no visible global function definition for ‘col2rgb’
    Undefined global functions or variables:
     abline axes3d barplot box box3d col2rgb complete.cases data dev.new
     dev.off dist layout lines na.omit pdf plot png points postscript
     read.table sub.mat text tiff
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "png",
     "postscript", "tiff")
     importFrom("graphics", "abline", "barplot", "box", "layout", "lines",
     "plot", "points", "text")
     importFrom("stats", "complete.cases", "dist", "na.omit")
     importFrom("utils", "data", "read.table")
    to your NAMESPACE file.
    
    Found the following calls to data() loading into the global environment:
    File ‘bios2mds/R/dis.R’:
     data("sub.mat", package = "bios2mds", verbose = FALSE)
    File ‘bios2mds/R/mat.dis.R’:
     data("sub.mat", package = "bios2mds", verbose = FALSE)
    See section ‘Good practice’ in ‘?data’.
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: 1.2.2
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    col.group: no visible global function definition for ‘read.table’
    dif: no visible global function definition for ‘complete.cases’
    dis: no visible global function definition for ‘data’
    dis: no visible binding for global variable ‘sub.mat’
    dis : Sij: no visible global function definition for ‘na.omit’
    dis : Tij: no visible global function definition for ‘na.omit’
    dis: no visible global function definition for ‘complete.cases’
    mat.dis: no visible global function definition for ‘data’
    mat.dis: no visible binding for global variable ‘sub.mat’
    mmds.2D.multi: no visible global function definition for ‘dev.new’
    mmds.2D.multi: no visible global function definition for ‘pdf’
    mmds.2D.multi: no visible global function definition for ‘png’
    mmds.2D.multi: no visible global function definition for ‘tiff’
    mmds.2D.multi: no visible global function definition for ‘postscript’
    mmds.2D.multi: no visible global function definition for ‘plot’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘points’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘lines’
    mmds.2D.multi: no visible global function definition for ‘abline’
    mmds.2D.multi: no visible global function definition for ‘box’
    mmds.2D.multi: no visible global function definition for ‘dev.off’
    mmds.2D.plot: no visible global function definition for ‘dev.new’
    mmds.2D.plot: no visible global function definition for ‘pdf’
    mmds.2D.plot: no visible global function definition for ‘png’
    mmds.2D.plot: no visible global function definition for ‘tiff’
    mmds.2D.plot: no visible global function definition for ‘postscript’
    mmds.2D.plot: no visible global function definition for ‘plot’
    mmds.2D.plot: no visible global function definition for ‘text’
    mmds.2D.plot: no visible global function definition for ‘points’
    mmds.2D.plot: no visible global function definition for ‘abline’
    mmds.2D.plot: no visible global function definition for ‘box’
    mmds.2D.plot: no visible global function definition for ‘dev.off’
    mmds.3D.plot: no visible global function definition for ‘box3d’
    mmds.3D.plot: no visible global function definition for ‘axes3d’
    mmds.plot: no visible global function definition for ‘dev.new’
    mmds.plot: no visible global function definition for ‘pdf’
    mmds.plot: no visible global function definition for ‘layout’
    mmds.plot: no visible global function definition for ‘dev.off’
    scree.plot: no visible global function definition for ‘dev.new’
    scree.plot: no visible global function definition for ‘pdf’
    scree.plot: no visible global function definition for ‘barplot’
    scree.plot: no visible global function definition for ‘text’
    scree.plot: no visible global function definition for ‘dev.off’
    sil.score: no visible global function definition for ‘dist’
    write.mmds.pdb: no visible global function definition for ‘col2rgb’
    Undefined global functions or variables:
     abline axes3d barplot box box3d col2rgb complete.cases data dev.new
     dev.off dist layout lines na.omit pdf plot png points postscript
     read.table sub.mat text tiff
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "png",
     "postscript", "tiff")
     importFrom("graphics", "abline", "barplot", "box", "layout", "lines",
     "plot", "points", "text")
     importFrom("stats", "complete.cases", "dist", "na.omit")
     importFrom("utils", "data", "read.table")
    to your NAMESPACE file.
    
    Found the following calls to data() loading into the global environment:
    File ‘bios2mds/R/dis.R’:
     data("sub.mat", package = "bios2mds", verbose = FALSE)
    File ‘bios2mds/R/mat.dis.R’:
     data("sub.mat", package = "bios2mds", verbose = FALSE)
    See section ‘Good practice’ in ‘?data’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2.2
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    col.group: no visible global function definition for ‘read.table’
    dif: no visible global function definition for ‘complete.cases’
    dis: no visible global function definition for ‘data’
    dis: no visible binding for global variable ‘sub.mat’
    dis : Sij: no visible global function definition for ‘na.omit’
    dis : Tij: no visible global function definition for ‘na.omit’
    dis: no visible global function definition for ‘complete.cases’
    mat.dis: no visible global function definition for ‘data’
    mat.dis: no visible binding for global variable ‘sub.mat’
    mmds.2D.multi: no visible global function definition for ‘dev.new’
    mmds.2D.multi: no visible global function definition for ‘pdf’
    mmds.2D.multi: no visible global function definition for ‘png’
    mmds.2D.multi: no visible global function definition for ‘tiff’
    mmds.2D.multi: no visible global function definition for ‘postscript’
    mmds.2D.multi: no visible global function definition for ‘plot’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘points’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘lines’
    mmds.2D.multi: no visible global function definition for ‘abline’
    mmds.2D.multi: no visible global function definition for ‘box’
    mmds.2D.multi: no visible global function definition for ‘dev.off’
    mmds.2D.plot: no visible global function definition for ‘dev.new’
    mmds.2D.plot: no visible global function definition for ‘pdf’
    mmds.2D.plot: no visible global function definition for ‘png’
    mmds.2D.plot: no visible global function definition for ‘tiff’
    mmds.2D.plot: no visible global function definition for ‘postscript’
    mmds.2D.plot: no visible global function definition for ‘plot’
    mmds.2D.plot: no visible global function definition for ‘text’
    mmds.2D.plot: no visible global function definition for ‘points’
    mmds.2D.plot: no visible global function definition for ‘abline’
    mmds.2D.plot: no visible global function definition for ‘box’
    mmds.2D.plot: no visible global function definition for ‘dev.off’
    mmds.3D.plot: no visible global function definition for ‘box3d’
    mmds.3D.plot: no visible global function definition for ‘axes3d’
    mmds.plot: no visible global function definition for ‘dev.new’
    mmds.plot: no visible global function definition for ‘pdf’
    mmds.plot: no visible global function definition for ‘layout’
    mmds.plot: no visible global function definition for ‘dev.off’
    scree.plot: no visible global function definition for ‘dev.new’
    scree.plot: no visible global function definition for ‘pdf’
    scree.plot: no visible global function definition for ‘barplot’
    scree.plot: no visible global function definition for ‘text’
    scree.plot: no visible global function definition for ‘dev.off’
    sil.score: no visible global function definition for ‘dist’
    write.mmds.pdb: no visible global function definition for ‘col2rgb’
    Undefined global functions or variables:
     abline axes3d barplot box box3d col2rgb complete.cases data dev.new
     dev.off dist layout lines na.omit pdf plot png points postscript
     read.table sub.mat text tiff
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "png",
     "postscript", "tiff")
     importFrom("graphics", "abline", "barplot", "box", "layout", "lines",
     "plot", "points", "text")
     importFrom("stats", "complete.cases", "dist", "na.omit")
     importFrom("utils", "data", "read.table")
    to your NAMESPACE file.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2.2
Check: R code for possible problems
Result: NOTE
    col.group: no visible global function definition for 'read.table'
    dif: no visible global function definition for 'complete.cases'
    dis: no visible global function definition for 'data'
    dis: no visible binding for global variable 'sub.mat'
    dis : Sij: no visible global function definition for 'na.omit'
    dis : Tij: no visible global function definition for 'na.omit'
    dis: no visible global function definition for 'complete.cases'
    mat.dis: no visible global function definition for 'data'
    mat.dis: no visible binding for global variable 'sub.mat'
    mmds.2D.multi: no visible global function definition for 'dev.new'
    mmds.2D.multi: no visible global function definition for 'pdf'
    mmds.2D.multi: no visible global function definition for 'png'
    mmds.2D.multi: no visible global function definition for 'tiff'
    mmds.2D.multi: no visible global function definition for 'postscript'
    mmds.2D.multi: no visible global function definition for 'plot'
    mmds.2D.multi : <anonymous>: no visible global function definition for
     'points'
    mmds.2D.multi : <anonymous>: no visible global function definition for
     'lines'
    mmds.2D.multi: no visible global function definition for 'abline'
    mmds.2D.multi: no visible global function definition for 'box'
    mmds.2D.multi: no visible global function definition for 'dev.off'
    mmds.2D.plot: no visible global function definition for 'dev.new'
    mmds.2D.plot: no visible global function definition for 'pdf'
    mmds.2D.plot: no visible global function definition for 'png'
    mmds.2D.plot: no visible global function definition for 'tiff'
    mmds.2D.plot: no visible global function definition for 'postscript'
    mmds.2D.plot: no visible global function definition for 'plot'
    mmds.2D.plot: no visible global function definition for 'text'
    mmds.2D.plot: no visible global function definition for 'points'
    mmds.2D.plot: no visible global function definition for 'abline'
    mmds.2D.plot: no visible global function definition for 'box'
    mmds.2D.plot: no visible global function definition for 'dev.off'
    mmds.3D.plot: no visible global function definition for 'box3d'
    mmds.3D.plot: no visible global function definition for 'axes3d'
    mmds.plot: no visible global function definition for 'dev.new'
    mmds.plot: no visible global function definition for 'pdf'
    mmds.plot: no visible global function definition for 'layout'
    mmds.plot: no visible global function definition for 'dev.off'
    scree.plot: no visible global function definition for 'dev.new'
    scree.plot: no visible global function definition for 'pdf'
    scree.plot: no visible global function definition for 'barplot'
    scree.plot: no visible global function definition for 'text'
    scree.plot: no visible global function definition for 'dev.off'
    sil.score: no visible global function definition for 'dist'
    write.mmds.pdb: no visible global function definition for 'col2rgb'
    Undefined global functions or variables:
     abline axes3d barplot box box3d col2rgb complete.cases data dev.new
     dev.off dist layout lines na.omit pdf plot png points postscript
     read.table sub.mat text tiff
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "png",
     "postscript", "tiff")
     importFrom("graphics", "abline", "barplot", "box", "layout", "lines",
     "plot", "points", "text")
     importFrom("stats", "complete.cases", "dist", "na.omit")
     importFrom("utils", "data", "read.table")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.2.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: dependencies in R code
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: S3 generic/method consistency
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: replacement functions
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: foreign function calls
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: R code for possible problems
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 keycol.group: no visible global function definition for ‘read.table’
    dif: no visible global function definition for ‘complete.cases’
    dis: no visible global function definition for ‘data’
    dis: no visible binding for global variable ‘sub.mat’
    dis : Sij: no visible global function definition for ‘na.omit’
    dis : Tij: no visible global function definition for ‘na.omit’
    dis: no visible global function definition for ‘complete.cases’
    mat.dis: no visible global function definition for ‘data’
    mat.dis: no visible binding for global variable ‘sub.mat’
    mmds.2D.multi: no visible global function definition for ‘dev.new’
    mmds.2D.multi: no visible global function definition for ‘pdf’
    mmds.2D.multi: no visible global function definition for ‘png’
    mmds.2D.multi: no visible global function definition for ‘tiff’
    mmds.2D.multi: no visible global function definition for ‘postscript’
    mmds.2D.multi: no visible global function definition for ‘plot’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘points’
    mmds.2D.multi : <anonymous>: no visible global function definition for
     ‘lines’
    mmds.2D.multi: no visible global function definition for ‘abline’
    mmds.2D.multi: no visible global function definition for ‘box’
    mmds.2D.multi: no visible global function definition for ‘dev.off’
    mmds.2D.plot: no visible global function definition for ‘dev.new’
    mmds.2D.plot: no visible global function definition for ‘pdf’
    mmds.2D.plot: no visible global function definition for ‘png’
    mmds.2D.plot: no visible global function definition for ‘tiff’
    mmds.2D.plot: no visible global function definition for ‘postscript’
    mmds.2D.plot: no visible global function definition for ‘plot’
    mmds.2D.plot: no visible global function definition for ‘text’
    mmds.2D.plot: no visible global function definition for ‘points’
    mmds.2D.plot: no visible global function definition for ‘abline’
    mmds.2D.plot: no visible global function definition for ‘box’
    mmds.2D.plot: no visible global function definition for ‘dev.off’
    mmds.3D.plot: no visible global function definition for ‘box3d’
    mmds.3D.plot: no visible global function definition for ‘axes3d’
    mmds.plot: no visible global function definition for ‘dev.new’
    mmds.plot: no visible global function definition for ‘pdf’
    mmds.plot: no visible global function definition for ‘layout’
    mmds.plot: no visible global function definition for ‘dev.off’
    scree.plot: no visible global function definition for ‘dev.new’
    scree.plot: no visible global function definition for ‘pdf’
    scree.plot: no visible global function definition for ‘barplot’
    scree.plot: no visible global function definition for ‘text’
    scree.plot: no visible global function definition for ‘dev.off’
    sil.score: no visible global function definition for ‘dist’
    write.mmds.pdb: no visible global function definition for ‘col2rgb’
    Undefined global functions or variables:
     abline axes3d barplot box box3d col2rgb complete.cases data dev.new
     dev.off dist layout lines na.omit pdf plot png points postscript
     read.table sub.mat text tiff
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "png",
     "postscript", "tiff")
     importFrom("graphics", "abline", "barplot", "box", "layout", "lines",
     "plot", "points", "text")
     importFrom("stats", "complete.cases", "dist", "na.omit")
     importFrom("utils", "data", "read.table")
    to your NAMESPACE file.
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: for missing documentation entries
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: for code/documentation mismatches
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
Flavor: r-oldrel-osx-x86_64

Version: 1.2.2
Check: Rd \usage sections
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64