CRAN Package Check Results for Package superpc

Last updated on 2014-11-01 05:49:05.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.09 0.76 28.70 29.47 NOTE
r-devel-linux-x86_64-debian-gcc 1.09 0.72 29.64 30.36 NOTE
r-devel-linux-x86_64-fedora-clang 1.09 63.00 NOTE
r-devel-linux-x86_64-fedora-gcc 1.09 59.44 NOTE
r-devel-osx-x86_64-clang 1.09 54.82 NOTE
r-devel-windows-ix86+x86_64 1.09 3.00 43.00 46.00 NOTE
r-patched-linux-x86_64 1.09 0.76 30.33 31.10 NOTE
r-patched-solaris-sparc 1.09 345.90 NOTE
r-patched-solaris-x86 1.09 80.90 NOTE
r-release-linux-ix86 1.09 1.25 39.31 40.56 NOTE
r-release-linux-x86_64 1.09 0.75 30.04 30.78 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.
    gen.y.mat2: no visible global function definition for ‘survfit’
    superpc.cv: no visible global function definition for ‘coxph’
    superpc.cv: no visible global function definition for ‘coxph.control’
    superpc.fit.to.outcome: no visible global function definition for
     ‘coxph’
    superpc.fit.to.outcome: no visible global function definition for
     ‘coxph.control’
    superpc.lrtest.curv: no visible global function definition for ‘coxph’
    superpc.predictionplot: no visible binding for global variable
     ‘shrinkages’
    superpc.predictionplot: no visible global function definition for
     ‘survfit’
    surv.to.class2: no visible global function definition for ‘survfit’
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

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
    gen.y.mat2: no visible global function definition for 'survfit'
    superpc.cv: no visible global function definition for 'coxph'
    superpc.cv: no visible global function definition for 'coxph.control'
    superpc.fit.to.outcome: no visible global function definition for
     'coxph'
    superpc.fit.to.outcome: no visible global function definition for
     'coxph.control'
    superpc.lrtest.curv: no visible global function definition for 'coxph'
    superpc.predictionplot: no visible binding for global variable
     'shrinkages'
    superpc.predictionplot: no visible global function definition for
     'survfit'
    surv.to.class2: no visible global function definition for 'survfit'
Flavor: r-devel-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-release-linux-ix86, r-release-linux-x86_64

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