CRAN Package Check Results for Package samr

Last updated on 2015-07-30 03:48:34.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0 1.02 37.38 38.40 NOTE
r-devel-linux-x86_64-debian-gcc 2.0 1.01 35.55 36.56 NOTE
r-devel-linux-x86_64-fedora-clang 2.0 70.55 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0 66.62 NOTE
r-devel-osx-x86_64-clang 2.0 57.33 NOTE
r-devel-windows-ix86+x86_64 2.0 8.00 91.00 99.00 NOTE
r-patched-linux-x86_64 2.0 1.04 41.38 42.42 NOTE
r-patched-solaris-sparc 2.0 591.20 NOTE
r-patched-solaris-x86 2.0 95.30 NOTE
r-release-linux-x86_64 2.0 1.06 39.02 40.08 NOTE
r-release-osx-x86_64-mavericks 2.0 NOTE
r-release-windows-ix86+x86_64 2.0 9.00 97.00 106.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0 9.00 110.00 119.00 NOTE

Check Details

Version: 2.0
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 2.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘impute’ ‘matrixStats’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘impute’ ‘matrixStats’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.SAMoutput print.SAMoutput
    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-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 2.0
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following function:
     ‘samr.assess.samplesize.plot’
    Found the platform-specific device:
     ‘win.metafile’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    est.s0: no visible global function definition for ‘quantile’
    est.s0: no visible global function definition for ‘mad’
    est.s0: no visible global function definition for ‘var’
    foldchange.seq.twoclass.paired: no visible global function definition
     for ‘rowMedians’
    foldchange.seq.twoclass.unpaired: no visible global function definition
     for ‘rowMedians’
    localfdr: no visible global function definition for ‘median’
    localfdr: no visible global function definition for ‘smooth.spline’
    paired.ttest.func: no visible global function definition for ‘var’
    patterndiscovery.func: no visible global function definition for
     ‘quantile’
    patterndiscovery.func: no visible global function definition for
     ‘median’
    permute.rows: no visible global function definition for ‘runif’
    predictlocalfdr: no visible global function definition for ‘predict’
    resample: no visible global function definition for ‘rpois’
    resample: no visible global function definition for ‘runif’
    samr: no visible global function definition for ‘impute.knn’
    samr: no visible binding for global variable ‘median’
    samr: no visible global function definition for ‘quantile’
    samr.assess.samplesize: no visible global function definition for
     ‘quantile’
    samr.assess.samplesize: no visible global function definition for
     ‘median’
    samr.assess.samplesize.plot: no visible global function definition for
     ‘par’
    samr.assess.samplesize.plot: no visible global function definition for
     ‘plot’
    samr.assess.samplesize.plot: no visible global function definition for
     ‘lines’
    samr.assess.samplesize.plot: no visible global function definition for
     ‘mtext’
    samr.assess.samplesize.plot: no visible global function definition for
     ‘abline’
    samr.assess.samplesize.plot: no visible global function definition for
     ‘title’
    samr.assess.samplesize.plot: no visible global function definition for
     ‘dev.off’
    samr.compute.delta.table.array: no visible binding for global variable
     ‘var’
    samr.compute.delta.table.array: no visible binding for global variable
     ‘median’
    samr.compute.delta.table.array: no visible binding for global variable
     ‘quantile’
    samr.compute.delta.table.seq: no visible binding for global variable
     ‘median’
    samr.compute.delta.table.seq: no visible binding for global variable
     ‘quantile’
    samr.estimate.depth: no visible global function definition for
     ‘quantile’
    samr.missrate: no visible global function definition for ‘quantile’
    samr.plot: no visible global function definition for ‘plot’
    samr.plot: no visible global function definition for ‘points’
    samr.plot: no visible global function definition for ‘abline’
    samr.tail.strength: no visible global function definition for ‘var’
    samr.xl.compute.plot.xy: no visible global function definition for
     ‘points’
    samr.xl.compute.plot.xy: no visible global function definition for
     ‘abline’
    samr.xl.impute.data: no visible global function definition for
     ‘impute.knn’
    samr.xl.impute.data: no visible binding for global variable
     ‘samr.xl.var.knn.neighbors’
    Undefined global functions or variables:
     abline dev.off impute.knn lines mad median mtext par plot points
     predict quantile rowMedians rpois runif samr.xl.var.knn.neighbors
     smooth.spline title var
    Consider adding
     importFrom("grDevices", "dev.off")
     importFrom("graphics", "abline", "lines", "mtext", "par", "plot",
     "points", "title")
     importFrom("stats", "mad", "median", "predict", "quantile", "rpois",
     "runif", "smooth.spline", "var")
    to your NAMESPACE.
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: 2.0
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'samr-internal':
     ‘plot.SAMoutput’ ‘print.SAMoutput’
    
    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.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following function:
     ‘samr.assess.samplesize.plot’
    Found the platform-specific device:
     ‘win.metafile’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    foldchange.seq.twoclass.paired: no visible global function definition
     for ‘rowMedians’
    foldchange.seq.twoclass.unpaired: no visible global function definition
     for ‘rowMedians’
    samr: no visible global function definition for ‘impute.knn’
    samr.xl.impute.data: no visible global function definition for
     ‘impute.knn’
    samr.xl.impute.data: no visible binding for global variable
     ‘samr.xl.var.knn.neighbors’
    Undefined global functions or variables:
     impute.knn rowMedians samr.xl.var.knn.neighbors
Flavor: r-devel-osx-x86_64-clang

Version: 2.0
Check: R code for possible problems
Result: NOTE
    .error.trace: no visible global function definition for 'winDialog'
    est.s0: no visible global function definition for 'quantile'
    est.s0: no visible global function definition for 'mad'
    est.s0: no visible global function definition for 'var'
    foldchange.seq.twoclass.paired: no visible global function definition
     for 'rowMedians'
    foldchange.seq.twoclass.unpaired: no visible global function definition
     for 'rowMedians'
    localfdr: no visible global function definition for 'median'
    localfdr: no visible global function definition for 'smooth.spline'
    paired.ttest.func: no visible global function definition for 'var'
    patterndiscovery.func: no visible global function definition for
     'quantile'
    patterndiscovery.func: no visible global function definition for
     'median'
    permute.rows: no visible global function definition for 'runif'
    predictlocalfdr: no visible global function definition for 'predict'
    resample: no visible global function definition for 'rpois'
    resample: no visible global function definition for 'runif'
    samr: no visible global function definition for 'impute.knn'
    samr: no visible binding for global variable 'median'
    samr: no visible global function definition for 'quantile'
    samr.assess.samplesize: no visible global function definition for
     'quantile'
    samr.assess.samplesize: no visible global function definition for
     'median'
    samr.assess.samplesize.plot: no visible global function definition for
     'win.metafile'
    samr.assess.samplesize.plot: no visible global function definition for
     'par'
    samr.assess.samplesize.plot: no visible global function definition for
     'plot'
    samr.assess.samplesize.plot: no visible global function definition for
     'lines'
    samr.assess.samplesize.plot: no visible global function definition for
     'mtext'
    samr.assess.samplesize.plot: no visible global function definition for
     'abline'
    samr.assess.samplesize.plot: no visible global function definition for
     'title'
    samr.assess.samplesize.plot: no visible global function definition for
     'dev.off'
    samr.compute.delta.table.array: no visible binding for global variable
     'var'
    samr.compute.delta.table.array: no visible binding for global variable
     'median'
    samr.compute.delta.table.array: no visible binding for global variable
     'quantile'
    samr.compute.delta.table.seq: no visible binding for global variable
     'median'
    samr.compute.delta.table.seq: no visible binding for global variable
     'quantile'
    samr.estimate.depth: no visible global function definition for
     'quantile'
    samr.missrate: no visible global function definition for 'quantile'
    samr.plot: no visible global function definition for 'plot'
    samr.plot: no visible global function definition for 'points'
    samr.plot: no visible global function definition for 'abline'
    samr.tail.strength: no visible global function definition for 'var'
    samr.xl.compute.plot.xy: no visible global function definition for
     'points'
    samr.xl.compute.plot.xy: no visible global function definition for
     'abline'
    samr.xl.error.trace: no visible global function definition for
     'winDialog'
    samr.xl.impute.data: no visible global function definition for
     'impute.knn'
    samr.xl.impute.data: no visible binding for global variable
     'samr.xl.var.knn.neighbors'
    Undefined global functions or variables:
     abline dev.off impute.knn lines mad median mtext par plot points
     predict quantile rowMedians rpois runif samr.xl.var.knn.neighbors
     smooth.spline title var win.metafile winDialog
    Consider adding
     importFrom("grDevices", "dev.off", "win.metafile")
     importFrom("graphics", "abline", "lines", "mtext", "par", "plot",
     "points", "title")
     importFrom("stats", "mad", "median", "predict", "quantile", "rpois",
     "runif", "smooth.spline", "var")
     importFrom("utils", "winDialog")
    to your NAMESPACE.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.0
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following function:
     ‘samr.assess.samplesize.plot’
    Found the platform-specific device:
     ‘win.metafile’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    foldchange.seq.twoclass.paired: no visible global function definition
     for ‘rowMedians’
    foldchange.seq.twoclass.unpaired: no visible global function definition
     for ‘rowMedians’
    samr: no visible global function definition for ‘impute.knn’
    samr.xl.impute.data: no visible global function definition for
     ‘impute.knn’
    samr.xl.impute.data: no visible binding for global variable
     ‘samr.xl.var.knn.neighbors’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 2.0
Check: R code for possible problems
Result: NOTE
    foldchange.seq.twoclass.paired: no visible global function definition
     for ‘rowMedians’
    foldchange.seq.twoclass.unpaired: no visible global function definition
     for ‘rowMedians’
    samr: no visible global function definition for ‘impute.knn’
    samr.xl.impute.data: no visible global function definition for
     ‘impute.knn’
    samr.xl.impute.data: no visible binding for global variable
     ‘samr.xl.var.knn.neighbors’
Flavors: r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64