Last updated on 2020-08-07 01:50:35 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| clusterRepro | 12 | ||
| pamr | 2 | 10 | |
| PMA | 12 | ||
| samr | 12 | ||
| selectiveInference | 12 | ||
| superpc | 5 | 7 |
Current CRAN status: OK: 12
Current CRAN status: NOTE: 2, OK: 10
Version: 1.56.1
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: ERROR: 5, NOTE: 7
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-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.
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 '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
'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
'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
'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 '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 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", "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: examples
Result: ERROR
Running examples in 'superpc-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: superpc.cv
> ### Title: Cross-validation for supervised principal components
> ### Aliases: superpc.cv
> ### Keywords: regression survival
>
> ### ** Examples
>
> set.seed(332)
> x<-matrix(rnorm(1000*40),ncol=40)
> y<-10+svd(x[1:60,])$v[,1]+ .1*rnorm(40)
> censoring.status<- sample(c(rep(1,30),rep(0,10)))
>
> featurenames <- paste("feature",as.character(1:1000),sep="")
> data<-list(x=x,y=y, censoring.status=censoring.status, featurenames=featurenames)
>
>
> a<- superpc.train(data, type="survival")
> aa<-superpc.cv(a,data)
fold= 1
12345678910111213141516Error in svd(x, LINPACK = TRUE) :
the LINPACK argument has been defunct since R 3.1.0
Calls: superpc.cv -> mysvd -> svd
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.09
Check: examples
Result: ERROR
Running examples in ‘superpc-Ex.R’ failed
The error most likely occurred in:
> ### Name: superpc.cv
> ### Title: Cross-validation for supervised principal components
> ### Aliases: superpc.cv
> ### Keywords: regression survival
>
> ### ** Examples
>
> set.seed(332)
> x<-matrix(rnorm(1000*40),ncol=40)
> y<-10+svd(x[1:60,])$v[,1]+ .1*rnorm(40)
> censoring.status<- sample(c(rep(1,30),rep(0,10)))
>
> featurenames <- paste("feature",as.character(1:1000),sep="")
> data<-list(x=x,y=y, censoring.status=censoring.status, featurenames=featurenames)
>
>
> a<- superpc.train(data, type="survival")
> aa<-superpc.cv(a,data)
fold= 1
12345678910111213141516Error in svd(x, LINPACK = TRUE) :
the LINPACK argument has been defunct since R 3.1.0
Calls: superpc.cv -> mysvd -> svd
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-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 '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
'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
'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
'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 '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 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", "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
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 ‘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
‘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
‘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
‘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 ‘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 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", "polygon",
"segments", "text", "title")
importFrom("stats", "lm", "median", "pchisq", "pf", "predict",
"qchisq", "qf", "quantile", "rnorm", "runif",
"smooth.spline", "var")
to your NAMESPACE file.
Flavor: r-release-macos-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.
Flavor: r-oldrel-macos-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.
Flavor: r-oldrel-windows-ix86+x86_64