Last updated on 2014-10-02 01:48:29.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.09 | 0.74 | 29.44 | 30.18 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.09 | 0.73 | 28.22 | 28.96 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.09 | 61.37 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.09 | 59.35 | NOTE | |||
| r-devel-osx-x86_64-clang | 1.09 | 50.96 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.09 | 3.00 | 40.00 | 43.00 | NOTE | |
| r-patched-linux-x86_64 | 1.09 | 0.77 | 30.34 | 31.12 | NOTE | |
| r-patched-solaris-sparc | 1.09 | 344.20 | NOTE | |||
| r-patched-solaris-x86 | 1.09 | 80.60 | NOTE | |||
| r-release-linux-ix86 | 1.09 | 1.08 | 38.99 | 40.07 | NOTE | |
| r-release-linux-x86_64 | 1.09 | 0.74 | 30.22 | 30.96 | 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 |
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
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-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: 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