CRAN Package Check Results for Package phmm

Last updated on 2014-04-24 15:50:44.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.7-5 5.11 104.68 109.79 OK
r-devel-linux-x86_64-debian-gcc 0.7-5 5.61 110.84 116.45 OK
r-devel-linux-x86_64-fedora-clang 0.7-5 239.26 OK
r-devel-linux-x86_64-fedora-gcc 0.7-5 236.09 OK
r-devel-osx-x86_64-clang 0.7-5 171.12 OK
r-devel-osx-x86_64-gcc 0.7-5 OK
r-devel-windows-ix86+x86_64 0.7-5 23.00 198.00 221.00 OK
r-patched-linux-x86_64 0.7-5 5.65 109.98 115.64 OK
r-patched-solaris-sparc 0.7-5 1632.30 OK
r-patched-solaris-x86 0.7-5 304.80 OK
r-release-linux-ix86 0.7-5 9.00 196.00 205.00 OK
r-release-linux-x86_64 0.7-5 5.53 109.01 114.54 OK
r-release-osx-x86_64-mavericks 0.7-5 ERROR
r-release-osx-x86_64-snowleopard 0.7-5 NOTE
r-release-windows-ix86+x86_64 0.7-5 22.00 209.00 231.00 OK
r-oldrel-windows-ix86+x86_64 0.7-5 22.00 192.00 214.00 OK

Check Details

Version: 0.7-5
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘lme4’
Flavor: r-release-osx-x86_64-mavericks

Version: 0.7-5
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘lme4’
Flavor: r-release-osx-x86_64-mavericks

Version: 0.7-5
Check: examples
Result: ERROR
    Running examples in ‘phmm-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: AIC.phmm
    > ### Title: Akaike Information Criterion for PHMM
    > ### Aliases: AIC.phmm
    > ### Keywords: survival
    >
    > ### ** Examples
    >
    > n <- 50 # total sample size
    > nclust <- 5 # number of clusters
    > clusters <- rep(1:nclust,each=n/nclust)
    > beta0 <- c(1,2)
    > set.seed(13)
    > #generate phmm data set
    > Z <- cbind(Z1=sample(0:1,n,replace=TRUE),
    + Z2=sample(0:1,n,replace=TRUE),
    + Z3=sample(0:1,n,replace=TRUE))
    > b <- cbind(rep(rnorm(nclust),each=n/nclust),rep(rnorm(nclust),each=n/nclust))
    > Wb <- matrix(0,n,2)
    > for( j in 1:2) Wb[,j] <- Z[,j]*b[,j]
    > Wb <- apply(Wb,1,sum)
    > T <- -log(runif(n,0,1))*exp(-Z[,c('Z1','Z2')]%*%beta0-Wb)
    > C <- runif(n,0,1)
    > time <- ifelse(T<C,T,C)
    > event <- ifelse(T<=C,1,0)
    > mean(event)
    [1] 0.62
    > phmmd <- data.frame(Z)
    > phmmd$cluster <- clusters
    > phmmd$time <- time
    > phmmd$event <- event
    >
    > fit.phmm <- phmm(Surv(time, event) ~ Z1 + Z2 + (-1 + Z1 + Z2 | cluster),
    + phmmd, Gbs = 100, Gbsvar = 1000, VARSTART = 1,
    + NINIT = 10, MAXSTEP = 100, CONVERG=90)
    >
    > # Same data can be fit with lmer,
    > # though the correlation structures are different.
    > poisphmmd <- pseudoPoisPHMM(fit.phmm)
    >
    > library(lme4)
    Error in library(lme4) : there is no package called ‘lme4’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 0.7-5
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: survival
    Loading required package: splines
    Loading required package: lattice
    Loading required package: Matrix
    Warning in lmer(m ~ -1 + t + z1 + z2 + (z1 + z2 | cluster) + offset(log(N)), :
     calling lmer with 'family' is deprecated; please use glmer() instead
    Warning in (function (fn, par, lower = rep.int(-Inf, n), upper = rep.int(Inf, :
     failure to converge in 10000 evaluations
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'phmm_poisson_df.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `utf8x.def' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: def)
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64-snowleopard