CRAN Package Check Results for Package pamr

Last updated on 2017-07-16 22:47:02.

Check Details

Version: 1.55
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-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: 1.55
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     print.pamrcved print.pamrtrained
    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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.55
Check: R code for possible problems
Result: NOTE
    error.bars: no visible global function definition for ‘segments’
    error.nsc: no visible global function definition for ‘model.matrix’
    kmeans2: no visible global function definition for ‘kmeans’
    nsc: no visible global function definition for ‘model.matrix’
    nsc: no visible global function definition for ‘quantile’
    nsccv : pvalue.survival.func: no visible global function definition for
     ‘pchisq’
    nsccv: no visible global function definition for ‘model.matrix’
    order.class.survival: no visible global function definition for
     ‘approx’
    pamr.adaptthresh: no visible global function definition for ‘update’
    pamr.batchadjust: no visible global function definition for
     ‘model.matrix’
    pamr.confusion: no visible global function definition for
     ‘model.matrix’
    pamr.confusion.survival: no visible global function definition for
     ‘model.matrix’
    pamr.decorrelate: no visible global function definition for ‘lm’
    pamr.decorrelate: no visible global function definition for ‘predict’
    pamr.fdr: no visible global function definition for ‘median’
    pamr.fdr: no visible global function definition for ‘quantile’
    pamr.geneplot: no visible global function definition for ‘par’
    pamr.geneplot: no visible global function definition for ‘plot’
    pamr.geneplot: no visible global function definition for ‘box’
    pamr.geneplot: no visible global function definition for ‘axis’
    pamr.geneplot: no visible global function definition for ‘points’
    pamr.geneplot: no visible global function definition for ‘title’
    pamr.geneplot: no visible global function definition for ‘abline’
    pamr.geneplot: no visible global function definition for ‘text’
    pamr.makeclasses: no visible global function definition for ‘par’
    pamr.makeclasses: no visible global function definition for ‘dist’
    pamr.makeclasses: no visible global function definition for ‘hclust’
    pamr.makeclasses: no visible global function definition for ‘plot’
    pamr.makeclasses: no visible global function definition for ‘locator’
    pamr.menu: no visible global function definition for ‘menu’
    pamr.plotcen: no visible global function definition for ‘par’
    pamr.plotcen: no visible global function definition for ‘plot’
    pamr.plotcen: no visible global function definition for ‘box’
    pamr.plotcen: no visible global function definition for ‘abline’
    pamr.plotcen: no visible global function definition for ‘segments’
    pamr.plotcen: no visible global function definition for ‘lines’
    pamr.plotcen: no visible global function definition for ‘text’
    pamr.plotcv: no visible global function definition for ‘par’
    pamr.plotcv: no visible binding for global variable ‘var’
    pamr.plotcv: no visible global function definition for ‘plot’
    pamr.plotcv: no visible global function definition for ‘axis’
    pamr.plotcv: no visible global function definition for ‘mtext’
    pamr.plotcv: no visible global function definition for ‘lines’
    pamr.plotcv: no visible global function definition for ‘points’
    pamr.plotcv: no visible global function definition for ‘legend’
    pamr.plotcvprob: no visible global function definition for ‘par’
    pamr.plotcvprob: no visible global function definition for ‘plot’
    pamr.plotcvprob: no visible global function definition for ‘axis’
    pamr.plotcvprob: no visible global function definition for ‘points’
    pamr.plotcvprob: no visible global function definition for ‘abline’
    pamr.plotcvprob: no visible global function definition for ‘text’
    pamr.plotfdr: no visible global function definition for ‘plot’
    pamr.plotfdr: no visible global function definition for ‘segments’
    pamr.plotfdr: no visible global function definition for ‘axis’
    pamr.plotfdr: no visible global function definition for ‘mtext’
    pamr.plotfdr: no visible global function definition for ‘dev.off’
    pamr.plotstrata: no visible global function definition for ‘pchisq’
    pamr.plotstrata: no visible global function definition for ‘plot’
    pamr.plotstrata: no visible global function definition for ‘legend’
    pamr.plotstrata: no visible global function definition for ‘text’
    pamr.plotsurvival: no visible global function definition for ‘pchisq’
    pamr.plotsurvival: no visible global function definition for ‘plot’
    pamr.plotsurvival: no visible global function definition for ‘legend’
    pamr.plotsurvival: no visible global function definition for ‘text’
    pamr.pvalue.survival: no visible global function definition for
     ‘pchisq’
    pamr.surv.to.class2: no visible global function definition for
     ‘quantile’
    pamr.test.errors.surv.compute: no visible global function definition
     for ‘model.matrix’
    pamr.xl.compute.confusion: no visible global function definition for
     ‘model.matrix’
    pamr.xl.compute.offset: no visible global function definition for
     ‘model.matrix’
    pamr.xl.compute.offset: no visible global function definition for
     ‘quantile’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘par’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘plot’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘box’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘abline’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘segments’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘lines’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘text’
    pamr.xl.plotcen.compute: no visible global function definition for
     ‘dev.off’
    pamr.xl.plotcv.compute: no visible binding for global variable ‘var’
    pamr.xl.plotsurvival: no visible global function definition for ‘plot’
    pamr.xl.plotsurvival: no visible global function definition for
     ‘legend’
    pamr.xl.plotsurvival: no visible global function definition for
     ‘dev.off’
    pamr.xl.plotsurvival.strata: no visible global function definition for
     ‘pchisq’
    pamr.xl.plotsurvival.strata: no visible global function definition for
     ‘plot’
    pamr.xl.plotsurvival.strata: no visible global function definition for
     ‘legend’
    pamr.xl.plotsurvival.strata: no visible global function definition for
     ‘text’
    pamr.xl.plotsurvival.strata: no visible global function definition for
     ‘dev.off’
    pamr.xl.plotsurvival.test: no visible global function definition for
     ‘plot’
    pamr.xl.plotsurvival.test: no visible global function definition for
     ‘legend’
    pamr.xl.plotsurvival.test: no visible global function definition for
     ‘dev.off’
    permute.rows: no visible global function definition for ‘runif’
    sam.func: no visible global function definition for ‘median’
    sam.func: no visible binding for global variable ‘var’
    Undefined global functions or variables:
     abline approx axis box dev.off dist hclust kmeans legend lines lm
     locator median menu model.matrix mtext par pchisq plot points predict
     quantile runif segments text title update var
    Consider adding
     importFrom("grDevices", "dev.off")
     importFrom("graphics", "abline", "axis", "box", "legend", "lines",
     "locator", "mtext", "par", "plot", "points", "segments",
     "text", "title")
     importFrom("stats", "approx", "dist", "hclust", "kmeans", "lm",
     "median", "model.matrix", "pchisq", "predict", "quantile",
     "runif", "update", "var")
     importFrom("utils", "menu")
    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: 1.55
Check: compiled code
Result: NOTE
    File ‘pamr/libs/pamr.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ 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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.55
Check: R code for possible problems
Result: NOTE
    error.bars: no visible global function definition for 'segments'
    error.nsc: no visible global function definition for 'model.matrix'
    kmeans2: no visible global function definition for 'kmeans'
    nsc: no visible global function definition for 'model.matrix'
    nsc: no visible global function definition for 'quantile'
    nsccv : pvalue.survival.func: no visible global function definition for
     'pchisq'
    nsccv: no visible global function definition for 'model.matrix'
    order.class.survival: no visible global function definition for
     'approx'
    pamr.adaptthresh: no visible global function definition for 'update'
    pamr.batchadjust: no visible global function definition for
     'model.matrix'
    pamr.confusion: no visible global function definition for
     'model.matrix'
    pamr.confusion.survival: no visible global function definition for
     'model.matrix'
    pamr.decorrelate: no visible global function definition for 'lm'
    pamr.decorrelate: no visible global function definition for 'predict'
    pamr.fdr: no visible global function definition for 'median'
    pamr.fdr: no visible global function definition for 'quantile'
    pamr.geneplot: no visible global function definition for 'par'
    pamr.geneplot: no visible global function definition for 'plot'
    pamr.geneplot: no visible global function definition for 'box'
    pamr.geneplot: no visible global function definition for 'axis'
    pamr.geneplot: no visible global function definition for 'points'
    pamr.geneplot: no visible global function definition for 'title'
    pamr.geneplot: no visible global function definition for 'abline'
    pamr.geneplot: no visible global function definition for 'text'
    pamr.makeclasses: no visible global function definition for 'par'
    pamr.makeclasses: no visible global function definition for 'dist'
    pamr.makeclasses: no visible global function definition for 'hclust'
    pamr.makeclasses: no visible global function definition for 'plot'
    pamr.makeclasses: no visible global function definition for 'locator'
    pamr.menu: no visible global function definition for 'menu'
    pamr.plotcen: no visible global function definition for 'par'
    pamr.plotcen: no visible global function definition for 'plot'
    pamr.plotcen: no visible global function definition for 'box'
    pamr.plotcen: no visible global function definition for 'abline'
    pamr.plotcen: no visible global function definition for 'segments'
    pamr.plotcen: no visible global function definition for 'lines'
    pamr.plotcen: no visible global function definition for 'text'
    pamr.plotcv: no visible global function definition for 'par'
    pamr.plotcv: no visible binding for global variable 'var'
    pamr.plotcv: no visible global function definition for 'plot'
    pamr.plotcv: no visible global function definition for 'axis'
    pamr.plotcv: no visible global function definition for 'mtext'
    pamr.plotcv: no visible global function definition for 'lines'
    pamr.plotcv: no visible global function definition for 'points'
    pamr.plotcv: no visible global function definition for 'legend'
    pamr.plotcvprob: no visible global function definition for 'par'
    pamr.plotcvprob: no visible global function definition for 'plot'
    pamr.plotcvprob: no visible global function definition for 'axis'
    pamr.plotcvprob: no visible global function definition for 'points'
    pamr.plotcvprob: no visible global function definition for 'abline'
    pamr.plotcvprob: no visible global function definition for 'text'
    pamr.plotfdr: no visible global function definition for 'plot'
    pamr.plotfdr: no visible global function definition for 'segments'
    pamr.plotfdr: no visible global function definition for 'axis'
    pamr.plotfdr: no visible global function definition for 'mtext'
    pamr.plotfdr: no visible global function definition for 'savePlot'
    pamr.plotfdr: no visible global function definition for 'dev.off'
    pamr.plotstrata: no visible global function definition for 'pchisq'
    pamr.plotstrata: no visible global function definition for 'plot'
    pamr.plotstrata: no visible global function definition for 'legend'
    pamr.plotstrata: no visible global function definition for 'text'
    pamr.plotsurvival: no visible global function definition for 'pchisq'
    pamr.plotsurvival: no visible global function definition for 'plot'
    pamr.plotsurvival: no visible global function definition for 'legend'
    pamr.plotsurvival: no visible global function definition for 'text'
    pamr.pvalue.survival: no visible global function definition for
     'pchisq'
    pamr.surv.to.class2: no visible global function definition for
     'quantile'
    pamr.test.errors.surv.compute: no visible global function definition
     for 'model.matrix'
    pamr.xl.compute.confusion: no visible global function definition for
     'model.matrix'
    pamr.xl.compute.offset: no visible global function definition for
     'model.matrix'
    pamr.xl.compute.offset: no visible global function definition for
     'quantile'
    pamr.xl.error.trace: no visible global function definition for
     'winDialog'
    pamr.xl.plotcen.compute: no visible global function definition for
     'par'
    pamr.xl.plotcen.compute: no visible global function definition for
     'plot'
    pamr.xl.plotcen.compute: no visible global function definition for
     'box'
    pamr.xl.plotcen.compute: no visible global function definition for
     'abline'
    pamr.xl.plotcen.compute: no visible global function definition for
     'segments'
    pamr.xl.plotcen.compute: no visible global function definition for
     'lines'
    pamr.xl.plotcen.compute: no visible global function definition for
     'text'
    pamr.xl.plotcen.compute: no visible global function definition for
     'savePlot'
    pamr.xl.plotcen.compute: no visible global function definition for
     'dev.off'
    pamr.xl.plotcv.compute: no visible binding for global variable 'var'
    pamr.xl.plotsurvival: no visible global function definition for 'plot'
    pamr.xl.plotsurvival: no visible global function definition for
     'legend'
    pamr.xl.plotsurvival: no visible global function definition for
     'savePlot'
    pamr.xl.plotsurvival: no visible global function definition for
     'dev.off'
    pamr.xl.plotsurvival.strata: no visible global function definition for
     'pchisq'
    pamr.xl.plotsurvival.strata: no visible global function definition for
     'plot'
    pamr.xl.plotsurvival.strata: no visible global function definition for
     'legend'
    pamr.xl.plotsurvival.strata: no visible global function definition for
     'text'
    pamr.xl.plotsurvival.strata: no visible global function definition for
     'savePlot'
    pamr.xl.plotsurvival.strata: no visible global function definition for
     'dev.off'
    pamr.xl.plotsurvival.test: no visible global function definition for
     'plot'
    pamr.xl.plotsurvival.test: no visible global function definition for
     'legend'
    pamr.xl.plotsurvival.test: no visible global function definition for
     'savePlot'
    pamr.xl.plotsurvival.test: no visible global function definition for
     'dev.off'
    permute.rows: no visible global function definition for 'runif'
    sam.func: no visible global function definition for 'median'
    sam.func: no visible binding for global variable 'var'
    Undefined global functions or variables:
     abline approx axis box dev.off dist hclust kmeans legend lines lm
     locator median menu model.matrix mtext par pchisq plot points predict
     quantile runif savePlot segments text title update var winDialog
    Consider adding
     importFrom("grDevices", "dev.off", "savePlot")
     importFrom("graphics", "abline", "axis", "box", "legend", "lines",
     "locator", "mtext", "par", "plot", "points", "segments",
     "text", "title")
     importFrom("stats", "approx", "dist", "hclust", "kmeans", "lm",
     "median", "model.matrix", "pchisq", "predict", "quantile",
     "runif", "update", "var")
     importFrom("utils", "menu", "winDialog")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64