CRAN Package Check Results for Package samr

Last updated on 2015-07-05 19:47:40.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0 0.98 38.29 39.27 NOTE
r-devel-linux-x86_64-debian-gcc 2.0 0.97 37.40 38.37 NOTE
r-devel-linux-x86_64-fedora-clang 2.0 74.25 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0 70.17 NOTE
r-devel-osx-x86_64-clang 2.0 61.68 NOTE
r-devel-windows-ix86+x86_64 2.0 7.00 97.00 104.00 NOTE
r-patched-linux-x86_64 2.0 1.00 38.71 39.71 NOTE
r-patched-solaris-sparc 2.0 583.10 NOTE
r-patched-solaris-x86 2.0 96.90 NOTE
r-release-linux-x86_64 2.0 1.00 38.36 39.36 NOTE
r-release-osx-x86_64-mavericks 2.0 NOTE
r-release-windows-ix86+x86_64 2.0 8.00 89.00 97.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0 11.00 122.00 133.00 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
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
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