• using R version 2.10.0 Patched (2009-11-18 r50482)
• using session charset: ASCII
• checking for file 'CPE/DESCRIPTION' ... OK
• this is package 'CPE' version '1.4'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking for executable files ... OK
• checking whether package 'CPE' can be installed ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking for unstated dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $BLAS_LIBS ... OK
• checking examples ... ERROR
  Running examples in 'CPE-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * phcpe
  >
  > flush(stderr()); flush(stdout())
  >
  > ### Name: phcpe
  > ### Title: Gonen \& Heller Concordance Probability Estimate for the Cox
  > ### Proportional Harzards model
  > ### Aliases: phcpe
  > ### Keywords: survival
  >
  > ### ** Examples
  >
  >
  > ### create a simple data set for testing
  > set.seed(199)
  > nn <- 1000
  > time <- rexp(nn)
  > status <- sample(0:1, nn, replace=TRUE)
  > covar <- matrix(rnorm(3*nn), ncol=3)
  > survd <- data.frame(time, status, covar)
  > names(survd) <- c("time","status","x1","x2","x3")
  >
  > library(survival)
  Loading required package: splines
  > coxph.fit <- coxph(Surv(time,status)~x1+x2+x3,data=survd)
  >
  >
  > ### Calculate CPE only (needs much less time).
  > library(CPE)
  > phcpe(coxph.fit)
  $CPE
  [1] 0.5113818
  
  > phcpe(coxph.fit,out.ties=TRUE)
  $CPE
  [1] 0.5113818
  
  > #result is identical because the covariates are not tied #
  >
  > ### Calculate CPE and CPE.SE
  > phcpe(coxph.fit, CPE.SE=TRUE)
  
  *** caught segfault ***
  address 0x20d6000, cause 'memory not mapped'
  
  Traceback:
  1: .C("coxcpe", row, col, bandwidth, xbeta, design, varbeta, out = as.double(rep(0, 3)), PACKAGE = "CPE")
  2: phcpe(coxph.fit, CPE.SE = TRUE)
  aborting ...
• elapsed time (check, wall clock): 0:16