CRAN Package Check Results for Package lcmm

Last updated on 2014-08-27 15:49:32.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.6.4 36.42 80.56 116.98 OK
r-devel-linux-x86_64-debian-gcc 1.6.4 33.98 83.50 117.47 OK
r-devel-linux-x86_64-fedora-clang 1.6.4 204.77 OK
r-devel-linux-x86_64-fedora-gcc 1.6.4 202.82 OK
r-devel-osx-x86_64-clang 1.6.4 173.81 OK
r-devel-windows-ix86+x86_64 1.6.4 77.00 207.00 284.00 OK
r-patched-linux-x86_64 1.6.4 39.15 80.06 119.20 OK
r-patched-solaris-sparc 1.6.4 1788.80 OK
r-patched-solaris-x86 1.6.4 322.20 ERROR
r-release-linux-ix86 1.6.4 53.64 106.97 160.61 OK
r-release-linux-x86_64 1.6.4 34.80 84.14 118.94 OK
r-release-osx-x86_64-mavericks 1.6.4 WARN
r-release-osx-x86_64-snowleopard 1.6.4 OK
r-release-windows-ix86+x86_64 1.6.4 102.00 190.00 292.00 OK
r-oldrel-windows-ix86+x86_64 1.6.4 61.00 149.00 210.00 OK

Check Details

Version: 1.6.4
Check: examples
Result: ERROR
    Running examples in ‘lcmm-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Diffepoce
    > ### Title: Computation of the difference of expected prognostic
    > ### cross-entropy (EPOCE) estimators and its 95% tracking interval
    > ### between two joint latent class models estimated with 'Jointlcmm'
    > ### Aliases: Diffepoce
    >
    > ### ** Examples
    >
    > #### estimation with 2 latent classes (ng=2)
    > data(data_Jointlcmm)
    > m2 <- Jointlcmm(fixed= Ydep1~Time*X1,random=~Time,mixture=~Time,subject='ID'
    + ,survival = Surv(Tevent,Event)~ X1+X2 ,hazard="Weibull"
    + ,hazardtype="PH",ng=2,data=data_Jointlcmm,
    + B=c( 0.7608, -9.4974, 1.0242, 1.4331, 0.1063 , 0.6714, 10.4679, 11.3178,
    + -2.5671, -0.5386, 1.4616, -0.0605, 0.9489, 0.1020, 0.2079, 1.5045),logscale=TRUE)
    Be patient, Jointlcmm is running ...
    The program took 1.58 seconds
    > m1 <- Jointlcmm(fixed= Ydep1~Time*X1,random=~Time,subject='ID'
    + ,survival = Surv(Tevent,Event)~ X1+X2 ,hazard="Weibull"
    + ,hazardtype="PH",ng=1,data=data_Jointlcmm,
    + B=c(-7.6634, 0.9136, 0.1002, 0.6641, 10.5675, -1.6589, 1.4767, -0.0806,
    + 0.9240,0.5643, 1.2277, 1.5004))
    Be patient, Jointlcmm is running ...
    The program took 5.26 seconds
    >
    > ## EPOCE computation for predictions times from 1 to 6 on the dataset used
    > ## for estimation of m.
    > VecTime <- c(1,3,5,7,9,11,13,15)
    > cvpol1 <- epoce(m1,var.time="Time",pred.times=VecTime)
    Be patient, epoce function is running ...
    The program took 0.91 seconds
    > cvpol1
    Expected Prognostic Observed Cross-Entropy (EPOCE) of the joint latent class model:
    
    Jointlcmm(fixed = Ydep1 ~ Time * X1, random = ~Time, subject = "ID",
     ng = 1, survival = Surv(Tevent, Event) ~ X1 + X2, hazard = "Weibull",
     hazardtype = "PH", data = data_Jointlcmm)
    
    EPOCE estimators on data used for estimation:
     Mean Prognostic Observed Log-likelihood (MPOL)
     and Cross-validated Prognostic Observed Log-likelihood (CVPOL)
     (CVPOL is the bias-corrected MPOL obtained by approximated cross-validation)
    
     pred. times N at risk N events MPOL CVPOL
     1 300 150 1.892619 Inf
     3 299 150 1.889431 Inf
     5 291 149 1.899210 Inf
     7 258 127 1.785964 Inf
     9 205 107 1.850733 Inf
     11 158 81 1.793531 Inf
     13 129 68 1.772987 Inf
     15 99 49 1.656587 Inf
    
    > cvpol2 <- epoce(m2,var.time="Time",pred.times=VecTime)
    Be patient, epoce function is running ...
    The program took 1.74 seconds
    > cvpol2
    Expected Prognostic Observed Cross-Entropy (EPOCE) of the joint latent class model:
    
    Jointlcmm(fixed = Ydep1 ~ Time * X1, mixture = ~Time, random = ~Time,
     subject = "ID", ng = 2, survival = Surv(Tevent, Event) ~
     X1 + X2, hazard = "Weibull", hazardtype = "PH", data = data_Jointlcmm,
     logscale = TRUE)
    
    EPOCE estimators on data used for estimation:
     Mean Prognostic Observed Log-likelihood (MPOL)
     and Cross-validated Prognostic Observed Log-likelihood (CVPOL)
     (CVPOL is the bias-corrected MPOL obtained by approximated cross-validation)
    
     pred. times N at risk N events MPOL CVPOL
     1 300 150 1.869272 2.092841
     3 299 150 1.840027 2.045497
     5 291 149 1.853149 2.056496
     7 258 127 1.735359 1.948203
     9 205 107 1.773111 2.084853
     11 158 81 1.672144 1.969925
     13 129 68 1.628349 1.924389
     15 99 49 1.463446 1.806864
    
    > DeltaEPOCE <- Diffepoce(cvpol1,cvpol2)
    > summary(DeltaEPOCE)
    Difference in Expected Prognostic Observed Cross-Entropy (EPOCE) estimates
     from the two following joint latent class models:
    
    Jointlcmm(fixed = Ydep1 ~ Time * X1, random = ~Time, subject = "ID",
     ng = 1, survival = Surv(Tevent, Event) ~ X1 + X2, hazard = "Weibull",
     hazardtype = "PH", data = data_Jointlcmm)
    Jointlcmm(fixed = Ydep1 ~ Time * X1, mixture = ~Time, random = ~Time,
     subject = "ID", ng = 2, survival = Surv(Tevent, Event) ~
     X1 + X2, hazard = "Weibull", hazardtype = "PH", data = data_Jointlcmm,
     logscale = TRUE)
    
    Difference in the Cross-Validated Prognostic Observed Log-likelihood (CVPOL)
     and its 95% tracking interval
    
     pred. times Diff CVPOL 95%TIinf 95%TIsup
     1 Inf Inf Inf
     3 Inf Inf Inf
     5 Inf Inf Inf
     7 Inf Inf Inf
     9 Inf Inf Inf
     11 Inf Inf Inf
     13 Inf Inf Inf
     15 Inf Inf Inf
    
    > plot(DeltaEPOCE,bty="l")
    Error in plot.window(...) : need finite 'ylim' values
    Calls: plot ... matplot -> plot -> plot.default -> localWindow -> plot.window
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.6.4
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
     Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
Flavor: r-release-osx-x86_64-mavericks