* using log directory 'd:/Rcompile/CRANpkg/local/3.3/flexsurv.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'flexsurv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flexsurv' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'flexsurv' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'flexsurv-Ex.R' failed
The error most likely occurred in:

> ### Name: msfit.flexsurvreg
> ### Title: Cumulative intensity function for parametric multi-state models
> ### Aliases: msfit.flexsurvreg
> ### Keywords: models
> 
> ### ** Examples
> 
> ## 3 state illness-death model for bronchiolitis obliterans
> ## Compare clock-reset / semi-Markov multi-state models
> 
> ## Simple exponential model (reduces to Markov)
> 
> bexp <- flexsurvreg(Surv(years, status) ~ trans,
+                     data=bosms3, dist="exp")
> tmat <- rbind(c(NA,1,2),c(NA,NA,3),c(NA,NA,NA))
> mexp <- msfit.flexsurvreg(bexp, t=seq(0,12,by=0.1),
+                           trans=tmat, tvar="trans", variance=FALSE)
> 
> ## Cox semi-parametric model within each transition
> 
> bcox <- coxph(Surv(years, status) ~ strata(trans), data=bosms3)
> 
> if (require("mstate")){
+ 
+ mcox <- mstate::msfit(bcox, trans=tmat)
+ 
+ ## Flexible parametric spline-based model 
+ 
+ bspl <- flexsurvspline(Surv(years, status) ~ trans + gamma1(trans),
+                        data=bosms3, k=3)
+ mspl <- msfit.flexsurvreg(bspl, t=seq(0,12,by=0.1),
+                          trans=tmat, tvar="trans", variance=FALSE)
+ 
+ ## Compare fit: exponential model is OK but the spline is better
+ 
+ plot(mcox, lwd=1, xlim=c(0, 12), ylim=c(0,4))
+ cols <- c("black","red","green")
+ for (i in 1:3){
+     lines(mexp$Haz$time[mexp$Haz$trans==i], mexp$Haz$Haz[mexp$Haz$trans==i],
+              col=cols[i], lwd=2, lty=2)
+     lines(mspl$Haz$time[mspl$Haz$trans==i], mspl$Haz$Haz[mspl$Haz$trans==i],
+              col=cols[i], lwd=3)
+ }
+ legend("topright", lwd=c(1,2,3), lty=c(1,2,1),
+    c("Cox", "Exponential", "Flexible parametric"), bty="n")
+ 
+ }
Loading required package: mstate
Error in mstate::msfit(bcox, trans = tmat) : 
  Could not reconstruct the y vector
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [73s] OK
  Running 'test_base.R' [73s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Quitting from lines 1393-1397 (flexsurv.Rnw) 
Error: processing vignette 'flexsurv.Rnw' failed with diagnostics:
Could not reconstruct the y vector
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING