CRAN Package Check Results for Package pec

Last updated on 2014-07-26 16:48:41.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2.9 2.73 40.13 42.86 NOTE
r-devel-linux-x86_64-debian-gcc 2.2.9 2.82 40.45 43.27 NOTE
r-devel-linux-x86_64-fedora-clang 2.2.9 94.20 NOTE
r-devel-linux-x86_64-fedora-gcc 2.2.9 84.49 NOTE
r-devel-osx-x86_64-clang 2.2.9 76.57 NOTE
r-devel-windows-ix86+x86_64 2.2.9 15.00 76.00 91.00 NOTE
r-patched-linux-x86_64 2.2.9 2.77 40.64 43.41 NOTE
r-patched-solaris-sparc 2.2.9 501.70 NOTE
r-patched-solaris-x86 2.2.9 107.90 NOTE
r-release-linux-ix86 2.2.9 3.88 51.48 55.36 NOTE
r-release-linux-x86_64 2.2.9 2.80 41.06 43.86 NOTE
r-release-osx-x86_64-mavericks 2.2.9 NOTE
r-release-osx-x86_64-snowleopard 2.2.9 NOTE
r-release-windows-ix86+x86_64 2.2.9 15.00 79.00 94.00 NOTE
r-oldrel-windows-ix86+x86_64 2.2.9 15.00 78.00 93.00 NOTE

Check Details

Version: 2.2.9
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘prodlim’ which was already attached by Depends.
     Please remove these calls from your code.
    Package in Depends field not imported from: ‘rms’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    ':::' calls which should be '::':
     ‘prodlim:::SmartControl’ ‘prodlim:::jackknife.survival’
     ‘prodlim:::meanNeighbors’ ‘prodlim:::predictSurvIndividual’
     See the note in ?`:::` about the use of this operator.
    There are ::: calls to the package's namespace in its code. A package
     almost never needs to use ::: for its own objects:
     ‘predictSurvProb’
    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: 2.2.9
Check: top-level files
Result: NOTE
    Non-standard files/directories found at top level:
     ‘exa’ ‘reproducible’ ‘test’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.9
Check: Rd line widths
Result: NOTE
    Rd file 'cindex.Rd':
     \examples lines wider than 100 characters:
     Cpec <- cindex(list("Cox X1+X2"=fit12,"Cox X1"=fit1,"Cox X2"=fit2),formula=Surv(time,status)~1,data=dat,eval.times=Inf)
    
    Rd file 'ipcw.Rd':
     \examples lines wider than 100 characters:
     WKM=ipcw(Hist(time,status)~X2,data=dat,method="marginal",times=sort(unique(dat$time)),subjectTimes=dat$time)
     WCox=ipcw(Surv(time,status)~X2,data=dat,method="cox",times=sort(unique(dat$time)),subjectTimes=dat$time)
     WKM2=ipcw(Surv(time,status)~X2,data=dat,method="nonpar",times=sort(unique(dat$time)),subjectTimes=dat$time)
    
    Rd file 'plot.pec.Rd':
     \examples lines wider than 100 characters:
     plot(PredError.632plus,xlim=c(0,30), models="Cox.X1", special=TRUE, special.bench="Cox.X2", special.benchcol=2, special.addprederr="App ... [TRUNCATED]
    
    Rd file 'selectCox.Rd':
     \examples lines wider than 100 characters:
     f <- selectCox(Surv(time,cens)~horTh + age + menostat + tsize + tgrade + pnodes + progrec + estrec ,data=GBSG2)
    
    Rd file 'selectFGR.Rd':
     \examples lines wider than 100 characters:
     f <- FGR(formula = Hist(time, cause) ~ X1 + X2 + X3 + X4 + X5 + X6 + X7 + X8 + X9 + X10, cause=1, data = d)
    
    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: 2.2.9
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'doMC'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.9
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'riskRegression'
Flavor: r-release-osx-x86_64-snowleopard

Version: 2.2.9
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to 'prodlim' which was already attached by Depends.
     Please remove these calls from your code.
    Package in Depends field not imported from: 'rms'
     These packages need to be imported from for the case when
     this namespace is loaded but not attached.
    There are ::: calls to the package's namespace in its code. A package
     almost never needs to use ::: for its own objects:
     'predictSurvProb'
    See the information on DESCRIPTION files in the chapter 'Creating R
    packages' of the 'Writing R Extensions' manual.
Flavor: r-release-osx-x86_64-snowleopard

Version: 2.2.9
Check: R code for possible problems
Result: NOTE
    selectFGR: no visible global function definition for 'FGR'
Flavor: r-release-osx-x86_64-snowleopard