CRAN Package Check Results for Package superpc

Last updated on 2018-06-20 01:50:37 CEST.

Check Details

Version: 1.09
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘survival’ which was already attached by Depends.
     Please remove these calls from your code.
    Package in Depends field not imported from: ‘survival’
     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-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: 1.09
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following functions:
     ‘superpc.plot.lrtest’ ‘superpc.plotcv’ ‘superpc.plotred.lrtest’
     ‘superpc.predictionplot’ ‘superpc.rainbowplot’
    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.
    cor.func: no visible global function definition for ‘median’
    cor.func: no visible global function definition for ‘quantile’
    coxfunc: no visible global function definition for ‘median’
    coxfunc: no visible global function definition for ‘quantile’
    error.bars: no visible global function definition for ‘segments’
    gen.y.mat2: no visible global function definition for ‘survfit’
    jitter: no visible global function definition for ‘rnorm’
    my.barplot: no visible global function definition for ‘rgb’
    my.barplot: no visible global function definition for ‘palette’
    my.barplot: no visible global function definition for ‘gray’
    my.barplot: no visible global function definition for ‘quantile’
    my.barplot: no visible global function definition for ‘par’
    my.barplot: no visible global function definition for ‘plot’
    my.barplot: no visible global function definition for ‘polygon’
    my.barplot: no visible global function definition for ‘text’
    permute.rows: no visible global function definition for ‘runif’
    superpc.cv: no visible global function definition for ‘quantile’
    superpc.cv: no visible global function definition for ‘coxph’
    superpc.cv: no visible global function definition for ‘coxph.control’
    superpc.cv: no visible global function definition for ‘lm’
    superpc.cv : se.na: no visible global function definition for ‘var’
    superpc.decorrelate: no visible global function definition for ‘lm’
    superpc.fit.to.outcome: no visible global function definition for
     ‘coxph’
    superpc.fit.to.outcome: no visible global function definition for
     ‘coxph.control’
    superpc.fit.to.outcome: no visible global function definition for ‘lm’
    superpc.fit.to.outcome: no visible global function definition for ‘pf’
    superpc.listfeatures: no visible binding for global variable ‘median’
    superpc.lrtest.curv: no visible global function definition for ‘coxph’
    superpc.lrtest.curv: no visible global function definition for ‘lm’
    superpc.plot.lrtest: no visible global function definition for ‘plot’
    superpc.plot.lrtest: no visible global function definition for
     ‘dev.off’
    superpc.plotcv: no visible global function definition for
     ‘smooth.spline’
    superpc.plotcv: no visible global function definition for ‘predict’
    superpc.plotcv: no visible global function definition for ‘qchisq’
    superpc.plotcv: no visible global function definition for ‘qf’
    superpc.plotcv: no visible global function definition for ‘matplot’
    superpc.plotcv: no visible global function definition for ‘matlines’
    superpc.plotcv: no visible global function definition for ‘abline’
    superpc.plotcv: no visible global function definition for ‘dev.off’
    superpc.plotred.lrtest: no visible global function definition for ‘par’
    superpc.plotred.lrtest: no visible global function definition for
     ‘plot’
    superpc.plotred.lrtest: no visible global function definition for
     ‘abline’
    superpc.plotred.lrtest: no visible global function definition for
     ‘qchisq’
    superpc.plotred.lrtest: no visible global function definition for
     ‘axis’
    superpc.plotred.lrtest: no visible global function definition for
     ‘mtext’
    superpc.plotred.lrtest: no visible global function definition for
     ‘dev.off’
    superpc.predict: no visible global function definition for ‘quantile’
    superpc.predict.red: no visible global function definition for
     ‘quantile’
    superpc.predict.red.cv : se.na: no visible global function definition
     for ‘var’
    superpc.predictionplot: no visible binding for global variable
     ‘shrinkages’
    superpc.predictionplot: no visible global function definition for
     ‘layout’
    superpc.predictionplot: no visible global function definition for ‘par’
    superpc.predictionplot: no visible global function definition for
     ‘plot’
    superpc.predictionplot: no visible global function definition for
     ‘survfit’
    superpc.predictionplot: no visible global function definition for
     ‘legend’
    superpc.predictionplot: no visible global function definition for
     ‘title’
    superpc.predictionplot: no visible global function definition for
     ‘pchisq’
    superpc.predictionplot: no visible global function definition for
     ‘text’
    superpc.predictionplot: no visible global function definition for ‘pf’
    superpc.predictionplot: no visible global function definition for
     ‘dev.off’
    superpc.rainbowplot: no visible global function definition for ‘layout’
    superpc.rainbowplot: no visible global function definition for ‘par’
    superpc.rainbowplot: no visible global function definition for ‘plot’
    superpc.rainbowplot: no visible global function definition for ‘text’
    superpc.rainbowplot: no visible global function definition for
     ‘dev.off’
    superpc.xl.decorrelate.test: no visible global function definition for
     ‘predict’
    superpc.xl.get.threshold.range: no visible global function definition
     for ‘quantile’
    surv.to.class2: no visible global function definition for ‘survfit’
    surv.to.class2: no visible global function definition for ‘quantile’
    Undefined global functions or variables:
     abline axis coxph coxph.control dev.off gray layout legend lm
     matlines matplot median mtext palette par pchisq pf plot polygon
     predict qchisq qf quantile rgb rnorm runif segments shrinkages
     smooth.spline survfit text title var
    Consider adding
     importFrom("grDevices", "dev.off", "gray", "palette", "rgb")
     importFrom("graphics", "abline", "axis", "layout", "legend",
     "matlines", "matplot", "mtext", "par", "plot", "polygon",
     "segments", "text", "title")
     importFrom("stats", "lm", "median", "pchisq", "pf", "predict",
     "qchisq", "qf", "quantile", "rnorm", "runif",
     "smooth.spline", "var")
    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

Version: 1.09
Check: Rd line widths
Result: NOTE
    Rd file 'superpc.cv.Rd':
     \usage lines wider than 90 characters:
     superpc.cv(fit, data, n.threshold = 20, n.fold = NULL, folds = NULL, n.components = 3, min.features = 5, max.features = nrow(data$x) ... [TRUNCATED]
    
    Rd file 'superpc.fit.to.outcome.Rd':
     \usage lines wider than 90 characters:
     superpc.fit.to.outcome(fit, data.test, score, competing.predictors = NULL, print=TRUE, iter.max = 5)
     \examples lines wider than 100 characters:
     fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")
    
    Rd file 'superpc.internal.Rd':
     \usage lines wider than 90 characters:
     superpc.xl.fit.to.clin(fit, data.test,score, pamr.xl.test.sample.labels, pamr.xl.clindata,pamr.xl.clinsamplabels, pamr.xl.clinprednames ... [TRUNCATED]
     superpc.xl.listgenes.compute(data, train.obj, fit.red, fitred.cv=NULL,num.genes=NULL, component.number = 1)
     superpc.xl.decorrelate(data, pamr.xl.train.sample.labels, pamr.xl.clindata, pamr.xl.clinsamplabels, pamr.xl.clinprednames, pamr.xl.clin ... [TRUNCATED]
     superpc.xl.decorrelate.test(object.decorr, xtest, pamr.xl.train.sample.labels, pamr.xl.clindata, pamr.xl.clinsamplabels, pamr.xl.clinpr ... [TRUNCATED]
     superpc.xl.rainbowplot(data, pred, pamr.xl.test.sample.labels, pamr.xl.clindata, pamr.xl.clinsamplabels, pamr.xl.clinprednames, pamr ... [TRUNCATED]
    
    Rd file 'superpc.listfeatures.Rd':
     \examples lines wider than 100 characters:
     fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")
    
    Rd file 'superpc.lrtest.curv.Rd':
     \usage lines wider than 90 characters:
     superpc.lrtest.curv(object, data, newdata, n.components = 1, threshold = NULL, n.threshold = 20)
     \examples lines wider than 100 characters:
     fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")
    
    Rd file 'superpc.plot.lrtest.Rd':
     \examples lines wider than 100 characters:
     fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")
    
    Rd file 'superpc.plotcv.Rd':
     \usage lines wider than 90 characters:
     superpc.plotcv(object, cv.type=c("full","preval"),smooth = TRUE, smooth.df = 10, call.win.metafile=FALSE, ...)
    
    Rd file 'superpc.plotred.lrtest.Rd':
     \examples lines wider than 100 characters:
     fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")
    
    Rd file 'superpc.predict.Rd':
     \usage lines wider than 90 characters:
     superpc.predict(object, data, newdata, threshold, n.components = 3, prediction.type = c("continuous", "discrete", "nonzero"), n.class = ... [TRUNCATED]
    
    Rd file 'superpc.predict.red.Rd':
     \usage lines wider than 90 characters:
     superpc.predict.red(fit, data, data.test, threshold, n.components = 3, n.shrinkage= 20, shrinkages=NULL,compute.lrtest = TRUE, sign.wt= ... [TRUNCATED]
     \examples lines wider than 100 characters:
     fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")
    
    Rd file 'superpc.predict.red.cv.Rd':
     \examples lines wider than 100 characters:
     fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")
    
    Rd file 'superpc.rainbowplot.Rd':
     \usage lines wider than 90 characters:
     superpc.rainbowplot(data, pred, sample.labels, competing.predictors, call.win.metafile=FALSE)
    
    These lines will be truncated in the PDF 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: 1.09
Check: R code for possible problems
Result: NOTE
    cor.func: no visible global function definition for 'median'
    cor.func: no visible global function definition for 'quantile'
    coxfunc: no visible global function definition for 'median'
    coxfunc: no visible global function definition for 'quantile'
    error.bars: no visible global function definition for 'segments'
    gen.y.mat2: no visible global function definition for 'survfit'
    jitter: no visible global function definition for 'rnorm'
    my.barplot: no visible global function definition for 'rgb'
    my.barplot: no visible global function definition for 'palette'
    my.barplot: no visible global function definition for 'gray'
    my.barplot: no visible global function definition for 'quantile'
    my.barplot: no visible global function definition for 'par'
    my.barplot: no visible global function definition for 'plot'
    my.barplot: no visible global function definition for 'polygon'
    my.barplot: no visible global function definition for 'text'
    permute.rows: no visible global function definition for 'runif'
    superpc.cv: no visible global function definition for 'quantile'
    superpc.cv: no visible global function definition for 'coxph'
    superpc.cv: no visible global function definition for 'coxph.control'
    superpc.cv: no visible global function definition for 'lm'
    superpc.cv : se.na: no visible global function definition for 'var'
    superpc.decorrelate: no visible global function definition for 'lm'
    superpc.fit.to.outcome: no visible global function definition for
     'coxph'
    superpc.fit.to.outcome: no visible global function definition for
     'coxph.control'
    superpc.fit.to.outcome: no visible global function definition for 'lm'
    superpc.fit.to.outcome: no visible global function definition for 'pf'
    superpc.listfeatures: no visible binding for global variable 'median'
    superpc.lrtest.curv: no visible global function definition for 'coxph'
    superpc.lrtest.curv: no visible global function definition for 'lm'
    superpc.plot.lrtest: no visible global function definition for
     'win.metafile'
    superpc.plot.lrtest: no visible global function definition for 'plot'
    superpc.plot.lrtest: no visible global function definition for
     'dev.off'
    superpc.plotcv: no visible global function definition for
     'smooth.spline'
    superpc.plotcv: no visible global function definition for 'predict'
    superpc.plotcv: no visible global function definition for 'qchisq'
    superpc.plotcv: no visible global function definition for 'qf'
    superpc.plotcv: no visible global function definition for
     'win.metafile'
    superpc.plotcv: no visible global function definition for 'matplot'
    superpc.plotcv: no visible global function definition for 'matlines'
    superpc.plotcv: no visible global function definition for 'abline'
    superpc.plotcv: no visible global function definition for 'dev.off'
    superpc.plotred.lrtest: no visible global function definition for
     'win.metafile'
    superpc.plotred.lrtest: no visible global function definition for 'par'
    superpc.plotred.lrtest: no visible global function definition for
     'plot'
    superpc.plotred.lrtest: no visible global function definition for
     'abline'
    superpc.plotred.lrtest: no visible global function definition for
     'qchisq'
    superpc.plotred.lrtest: no visible global function definition for
     'axis'
    superpc.plotred.lrtest: no visible global function definition for
     'mtext'
    superpc.plotred.lrtest: no visible global function definition for
     'dev.off'
    superpc.predict: no visible global function definition for 'quantile'
    superpc.predict.red: no visible global function definition for
     'quantile'
    superpc.predict.red.cv : se.na: no visible global function definition
     for 'var'
    superpc.predictionplot: no visible binding for global variable
     'shrinkages'
    superpc.predictionplot: no visible global function definition for
     'win.metafile'
    superpc.predictionplot: no visible global function definition for
     'layout'
    superpc.predictionplot: no visible global function definition for 'par'
    superpc.predictionplot: no visible global function definition for
     'plot'
    superpc.predictionplot: no visible global function definition for
     'survfit'
    superpc.predictionplot: no visible global function definition for
     'legend'
    superpc.predictionplot: no visible global function definition for
     'title'
    superpc.predictionplot: no visible global function definition for
     'pchisq'
    superpc.predictionplot: no visible global function definition for
     'text'
    superpc.predictionplot: no visible global function definition for 'pf'
    superpc.predictionplot: no visible global function definition for
     'dev.off'
    superpc.rainbowplot: no visible global function definition for
     'win.metafile'
    superpc.rainbowplot: no visible global function definition for 'layout'
    superpc.rainbowplot: no visible global function definition for 'par'
    superpc.rainbowplot: no visible global function definition for 'plot'
    superpc.rainbowplot: no visible global function definition for 'text'
    superpc.rainbowplot: no visible global function definition for
     'dev.off'
    superpc.xl.decorrelate.test: no visible global function definition for
     'predict'
    superpc.xl.get.threshold.range: no visible global function definition
     for 'quantile'
    surv.to.class2: no visible global function definition for 'survfit'
    surv.to.class2: no visible global function definition for 'quantile'
    Undefined global functions or variables:
     abline axis coxph coxph.control dev.off gray layout legend lm
     matlines matplot median mtext palette par pchisq pf plot polygon
     predict qchisq qf quantile rgb rnorm runif segments shrinkages
     smooth.spline survfit text title var win.metafile
    Consider adding
     importFrom("grDevices", "dev.off", "gray", "palette", "rgb",
     "win.metafile")
     importFrom("graphics", "abline", "axis", "layout", "legend",
     "matlines", "matplot", "mtext", "par", "plot", "polygon",
     "segments", "text", "title")
     importFrom("stats", "lm", "median", "pchisq", "pf", "predict",
     "qchisq", "qf", "quantile", "rnorm", "runif",
     "smooth.spline", "var")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.09
Check: R code for possible problems
Result: NOTE
    cor.func: no visible global function definition for ‘median’
    cor.func: no visible global function definition for ‘quantile’
    coxfunc: no visible global function definition for ‘median’
    coxfunc: no visible global function definition for ‘quantile’
    error.bars: no visible global function definition for ‘segments’
    gen.y.mat2: no visible global function definition for ‘survfit’
    jitter: no visible global function definition for ‘rnorm’
    my.barplot: no visible global function definition for ‘rgb’
    my.barplot: no visible global function definition for ‘palette’
    my.barplot: no visible global function definition for ‘gray’
    my.barplot: no visible global function definition for ‘quantile’
    my.barplot: no visible global function definition for ‘par’
    my.barplot: no visible global function definition for ‘plot’
    my.barplot: no visible global function definition for ‘polygon’
    my.barplot: no visible global function definition for ‘text’
    permute.rows: no visible global function definition for ‘runif’
    superpc.cv: no visible global function definition for ‘quantile’
    superpc.cv: no visible global function definition for ‘coxph’
    superpc.cv: no visible global function definition for ‘coxph.control’
    superpc.cv: no visible global function definition for ‘lm’
    superpc.cv : se.na: no visible global function definition for ‘var’
    superpc.decorrelate: no visible global function definition for ‘lm’
    superpc.fit.to.outcome: no visible global function definition for
     ‘coxph’
    superpc.fit.to.outcome: no visible global function definition for
     ‘coxph.control’
    superpc.fit.to.outcome: no visible global function definition for ‘lm’
    superpc.fit.to.outcome: no visible global function definition for ‘pf’
    superpc.listfeatures: no visible binding for global variable ‘median’
    superpc.lrtest.curv: no visible global function definition for ‘coxph’
    superpc.lrtest.curv: no visible global function definition for ‘lm’
    superpc.plot.lrtest: no visible global function definition for ‘plot’
    superpc.plot.lrtest: no visible global function definition for
     ‘dev.off’
    superpc.plotcv: no visible global function definition for
     ‘smooth.spline’
    superpc.plotcv: no visible global function definition for ‘predict’
    superpc.plotcv: no visible global function definition for ‘qchisq’
    superpc.plotcv: no visible global function definition for ‘qf’
    superpc.plotcv: no visible global function definition for ‘matplot’
    superpc.plotcv: no visible global function definition for ‘matlines’
    superpc.plotcv: no visible global function definition for ‘abline’
    superpc.plotcv: no visible global function definition for ‘dev.off’
    superpc.plotred.lrtest: no visible global function definition for ‘par’
    superpc.plotred.lrtest: no visible global function definition for
     ‘plot’
    superpc.plotred.lrtest: no visible global function definition for
     ‘abline’
    superpc.plotred.lrtest: no visible global function definition for
     ‘qchisq’
    superpc.plotred.lrtest: no visible global function definition for
     ‘axis’
    superpc.plotred.lrtest: no visible global function definition for
     ‘mtext’
    superpc.plotred.lrtest: no visible global function definition for
     ‘dev.off’
    superpc.predict: no visible global function definition for ‘quantile’
    superpc.predict.red: no visible global function definition for
     ‘quantile’
    superpc.predict.red.cv : se.na: no visible global function definition
     for ‘var’
    superpc.predictionplot: no visible binding for global variable
     ‘shrinkages’
    superpc.predictionplot: no visible global function definition for
     ‘layout’
    superpc.predictionplot: no visible global function definition for ‘par’
    superpc.predictionplot: no visible global function definition for
     ‘plot’
    superpc.predictionplot: no visible global function definition for
     ‘survfit’
    superpc.predictionplot: no visible global function definition for
     ‘legend’
    superpc.predictionplot: no visible global function definition for
     ‘title’
    superpc.predictionplot: no visible global function definition for
     ‘pchisq’
    superpc.predictionplot: no visible global function definition for
     ‘text’
    superpc.predictionplot: no visible global function definition for ‘pf’
    superpc.predictionplot: no visible global function definition for
     ‘dev.off’
    superpc.rainbowplot: no visible global function definition for ‘layout’
    superpc.rainbowplot: no visible global function definition for ‘par’
    superpc.rainbowplot: no visible global function definition for ‘plot’
    superpc.rainbowplot: no visible global function definition for ‘text’
    superpc.rainbowplot: no visible global function definition for
     ‘dev.off’
    superpc.xl.decorrelate.test: no visible global function definition for
     ‘predict’
    superpc.xl.get.threshold.range: no visible global function definition
     for ‘quantile’
    surv.to.class2: no visible global function definition for ‘survfit’
    surv.to.class2: no visible global function definition for ‘quantile’
    Undefined global functions or variables:
     abline axis coxph coxph.control dev.off gray layout legend lm
     matlines matplot median mtext palette par pchisq pf plot polygon
     predict qchisq qf quantile rgb rnorm runif segments shrinkages
     smooth.spline survfit text title var
    Consider adding
     importFrom("grDevices", "dev.off", "gray", "palette", "rgb")
     importFrom("graphics", "abline", "axis", "layout", "legend",
     "matlines", "matplot", "mtext", "par", "plot", "polygon",
     "segments", "text", "title")
     importFrom("stats", "lm", "median", "pchisq", "pf", "predict",
     "qchisq", "qf", "quantile", "rnorm", "runif",
     "smooth.spline", "var")
    to your NAMESPACE file.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64