CRAN Package Check Results for Package flexsurv

Last updated on 2016-12-08 18:46:59.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 2.93 143.10 146.03 OK
r-devel-linux-x86_64-debian-gcc 1.0.0 3.16 132.11 135.27 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 287.06 OK --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.0.0 144.43 OK --no-stop-on-test-error
r-devel-macos-x86_64-clang 1.0.0 99.79 OK --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.0.0 8.00 277.00 285.00 OK
r-patched-linux-x86_64 1.0.0 2.75 129.47 132.22 OK
r-patched-solaris-sparc 1.0.0 1484.90 OK
r-patched-solaris-x86 1.0.0 268.10 OK
r-release-linux-x86_64 1.0.0 2.70 127.81 130.51 OK
r-release-osx-x86_64-mavericks 1.0.0 OK
r-release-windows-ix86+x86_64 1.0.0 8.00 207.00 215.00 ERROR
r-oldrel-windows-ix86+x86_64 1.0.0 13.00 333.00 346.00 OK

Check Details

Version: 1.0.0
Check: examples
Result: 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
Flavor: r-release-windows-ix86+x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    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
Flavor: r-release-windows-ix86+x86_64