CRAN Package Check Results for Package superpc

Last updated on 2014-08-02 07:50:28.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.09 0.87 29.98 30.85 NOTE
r-devel-linux-x86_64-debian-gcc 1.09 0.72 32.54 33.26 NOTE
r-devel-linux-x86_64-fedora-clang 1.09 66.99 NOTE
r-devel-linux-x86_64-fedora-gcc 1.09 62.06 NOTE
r-devel-osx-x86_64-clang 1.09 54.27 NOTE
r-devel-windows-ix86+x86_64 1.09 2.00 45.00 47.00 NOTE
r-patched-linux-x86_64 1.09 0.78 29.52 30.30 NOTE
r-patched-solaris-sparc 1.09 344.20 NOTE
r-patched-solaris-x86 1.09 77.90 NOTE
r-release-linux-ix86 1.09 1.09 38.15 39.24 NOTE
r-release-linux-x86_64 1.09 0.75 29.59 30.34 NOTE
r-release-osx-x86_64-mavericks 1.09 NOTE
r-release-windows-ix86+x86_64 1.09 4.00 64.00 68.00 NOTE
r-oldrel-windows-ix86+x86_64 1.09 3.00 52.00 55.00 NOTE

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.
    See the information on DESCRIPTION files in the chapter Creating R
    packages of 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-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+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.
    superpc.predictionplot: no visible binding for global variable
     shrinkages
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-ix86, 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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.09
Check: R code for possible problems
Result: NOTE
    superpc.predictionplot: no visible binding for global variable
     'shrinkages'
Flavors: r-devel-windows-ix86+x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64