CRAN Package Check Results for Package pec

Last updated on 2014-12-17 19:48:52.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.4.4 2.21 37.33 39.54 OK
r-devel-linux-x86_64-debian-gcc 2.4.4 2.78 36.60 39.38 OK
r-devel-linux-x86_64-fedora-clang 2.4.4 78.77 OK
r-devel-linux-x86_64-fedora-gcc 2.4.4 69.84 OK
r-devel-osx-x86_64-clang 2.4.4 69.79 OK
r-devel-windows-ix86+x86_64 2.4.4 14.00 73.00 87.00 NOTE
r-patched-linux-x86_64 2.4.4 2.17 38.08 40.25 OK
r-patched-solaris-sparc 2.4.4 414.80 OK
r-patched-solaris-x86 2.4.4 95.50 OK
r-release-linux-ix86 2.4.4 3.05 49.92 52.98 OK
r-release-linux-x86_64 2.4.4 2.32 38.11 40.43 OK
r-release-osx-x86_64-mavericks 2.4.4 ERROR
r-release-osx-x86_64-snowleopard 2.4.4 ERROR
r-release-windows-ix86+x86_64 2.4.4 15.00 78.00 93.00 NOTE
r-oldrel-windows-ix86+x86_64 2.4.4 12.00 85.00 97.00 NOTE

Check Details

Version: 2.4.4
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: 2.4.4
Check: examples
Result: ERROR
    Running examples in ‘pec-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: predictEventProb
    > ### Title: Predicting event probabilities (cumulative incidences) in
    > ### competing risk models.
    > ### Aliases: predictEventProb predictEventProb.CauseSpecificCox
    > ### predictEventProb.FGR predictEventProb.prodlim predictEventProb.rfsrc
    > ### predictEventProb.riskRegression
    > ### Keywords: survival
    >
    > ### ** Examples
    >
    > library(pec)
    > library(CoxBoost)
    Loading required package: survival
    Loading required package: splines
    Loading required package: Matrix
    Loading required package: prodlim
    > library(survival)
    > library(riskRegression)
    Loading required package: rms
    Loading required package: Hmisc
    Loading required package: grid
    Loading required package: lattice
    Loading required package: Formula
    
    Attaching package: ‘Hmisc’
    
    The following objects are masked from ‘package:base’:
    
     format.pval, round.POSIXt, trunc.POSIXt, units
    
    Loading required package: SparseM
    
    Attaching package: ‘SparseM’
    
    The following object is masked from ‘package:base’:
    
     backsolve
    
    > library(prodlim)
    > train <- SimCompRisk(100)
    > test <- SimCompRisk(10)
    > cox.fit <- CSC(Hist(time,cause)~X1+X2,data=train)
    > predictEventProb(cox.fit,newdata=test,times=seq(1:10),cause=1)
     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
    1 0.014686235 0.03887449 0.13204070 0.27090466 0.3679226 0.4000798 0.4369906
    2 0.015166003 0.04047676 0.13904277 0.29324037 0.4041409 0.4428386 0.4900227
    3 0.023196887 0.06151304 0.20542670 0.41223416 0.5449024 0.5875871 0.6366611
    4 0.004164974 0.01119386 0.03987075 0.08971772 0.1312250 0.1471878 0.1679950
    5 0.005295792 0.01422705 0.05050798 0.11300463 0.1643381 0.1839219 0.2093294
    6 0.013499214 0.03607390 0.12463660 0.26559070 0.3693515 0.4061495 0.4515435
    7 0.021072212 0.05597646 0.18834468 0.38293001 0.5116314 0.5539558 0.6033944
    8 0.016618440 0.04393312 0.14827659 0.30090278 0.4047889 0.4386154 0.4769737
    9 0.005711873 0.01518207 0.05297798 0.11379449 0.1613514 0.1782615 0.1985280
    10 0.039059320 0.10218250 0.32258987 0.58914467 0.7245255 0.7612597 0.7986084
     [,8] [,9] [,10]
    1 0.4595807 0.5114013 0.5378937
    2 0.5196380 0.5967385 0.6384777
    3 0.6654430 0.7307119 0.7581607
    4 0.1822155 0.2258354 0.2584063
    5 0.2265610 0.2787772 0.3165976
    6 0.4804287 0.5577594 0.6018131
    7 0.6329220 0.7023941 0.7336614
    8 0.5000932 0.5516520 0.5765021
    9 0.2117561 0.2454581 0.2676899
    10 0.8176558 0.8504869 0.8586282
    > ## cb.fit <- coxboost(Hist(time,cause)~X1+X2,cause=1,data=train,stepno=10)
    > ## predictEventProb(cb.fit,newdata=test,times=seq(1:10),cause=1)
    >
    > ## with strata
    > cox.fit2 <- CSC(list(Hist(time,cause)~strata(X1)+X2,Hist(time,cause)~X1+X2),data=train)
    Error in strata(X1) : object 'X1' not found
    Calls: CSC ... model.frame -> model.frame.default -> eval -> eval -> strata
    Execution halted
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard