CRAN Package Check Results for Package idmTPreg

Last updated on 2022-01-29 13:57:25 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 6.48 79.81 86.29 OK
r-devel-linux-x86_64-debian-gcc 1.1 7.89 61.50 69.39 OK
r-devel-linux-x86_64-fedora-clang 1.1 103.07 OK
r-devel-linux-x86_64-fedora-gcc 1.1 95.75 OK
r-devel-windows-x86_64-new-UL 1.1 30.00 97.00 127.00 ERROR
r-devel-windows-x86_64-new-TK 1.1 OK
r-patched-linux-x86_64 1.1 OK
r-release-linux-x86_64 1.1 6.61 73.59 80.20 OK
r-release-macos-arm64 1.1 OK
r-release-macos-x86_64 1.1 OK
r-release-windows-ix86+x86_64 1.1 17.00 87.00 104.00 ERROR
r-oldrel-macos-x86_64 1.1 OK
r-oldrel-windows-ix86+x86_64 1.1 18.00 89.00 107.00 ERROR

Check Details

Version: 1.1
Check: examples
Result: ERROR
    Running examples in 'idmTPreg-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: TPreg
    > ### Title: Regression Modeling of Transition Probabilities in a Progressive
    > ### Illness-Death Model
    > ### Aliases: TPreg
    >
    > ### ** Examples
    >
    > data(colonTPreg)
    >
    > co11 <- TPreg( ~ Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, R = 19, t = 200,
    + trans = "11", ncores = 1)
    Warning in TPreg(~Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, :
     Nodes variable in 'data' has missing value(s),
    Warning in model.matrix.default(mt, mf, contrasts) :
     non-list contrasts argument ignored
    > co11
    Call:
    TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
     link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
    
    Transition:
    [1] "11"
    
    (s,t):
    [1] 50 200
    
    Coefficients:
     Estimate St.Err LW.L UP.L P.value
    X.Intercept. 2.492609419 1.20640325 0.12805905 4.85715979 0.03881437
    Age -0.005980971 0.01883135 -0.04289043 0.03092848 0.75078303
    Nodes -0.074748098 0.03194314 -0.13735666 -0.01213953 0.01928190
    treatmentLev 0.039682347 0.40460922 -0.75335172 0.83271642 0.92187215
    treatmentLev.5FU 0.929566117 0.39242146 0.16042006 1.69871217 0.01784613
    
    
    [1] "18 observations deleted due to missingness from 'data'"
    > summary(co11)
    Call:
    TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
     link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
    (s,t):
    [1] 50 200
    
     Transition 11 :
    
     Coefficients:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -895.023387 -0.401888881 6.26264521 922.27867219 943.9213673
    2 185 2.636107 -0.007185251 -0.07924264 0.10143607 1.0470649
    3 200 2.492609 -0.005980971 -0.07474810 0.03968235 0.9295661
    
     Standard Errors:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.887300e+11 3.23073258 156.23304967 1.887300e+11 1.887300e+11
    2 185 8.367363e-01 0.01225879 0.02797473 3.434707e-01 2.921134e-01
    3 200 1.206403e+00 0.01883135 0.03194314 4.046092e-01 3.924215e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -3.699108e+11 -6.73412474 -299.9541321 -3.699108e+11 -3.699108e+11
    2 185 9.961036e-01 -0.03121247 -0.1340731 -5.717665e-01 4.745227e-01
    3 200 1.280590e-01 -0.04289043 -0.1373567 -7.533517e-01 1.604201e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 3.699108e+11 5.93034698 312.47942257 3.699108e+11 3.699108e+11
    2 185 4.276110e+00 0.01684197 -0.02441217 7.746386e-01 1.619607e+00
    3 200 4.857160e+00 0.03092848 -0.01213953 8.327164e-01 1.698712e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.999999996 0.9010021 0.968025139 1.0000000 0.999999996
    2 185 0.001630119 0.5577876 0.004616377 0.7677443 0.000337793
    3 200 0.038814370 0.7507830 0.019281897 0.9218722 0.017846126
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANWIN2.fb05.statistik.uni-dortmund.de:11866 (sockconn)
    Execution halted
Flavor: r-devel-windows-x86_64-new-UL

Version: 1.1
Check: examples
Result: ERROR
    Running examples in 'idmTPreg-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: TPreg
    > ### Title: Regression Modeling of Transition Probabilities in a Progressive
    > ### Illness-Death Model
    > ### Aliases: TPreg
    >
    > ### ** Examples
    >
    > data(colonTPreg)
    >
    > co11 <- TPreg( ~ Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, R = 19, t = 200,
    + trans = "11", ncores = 1)
    Warning in TPreg(~Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, :
     Nodes variable in 'data' has missing value(s),
    Warning in model.matrix.default(mt, mf, contrasts) :
     non-list contrasts argument ignored
    > co11
    Call:
    TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
     link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
    
    Transition:
    [1] "11"
    
    (s,t):
    [1] 50 200
    
    Coefficients:
     Estimate St.Err LW.L UP.L P.value
    X.Intercept. 2.492609419 0.733230741 1.05547717 3.92974167 0.0006751204
    Age -0.005980971 0.009900533 -0.02538602 0.01342407 0.5457732262
    Nodes -0.074748098 0.024705813 -0.12317149 -0.02632470 0.0024820044
    treatmentLev 0.039682347 0.240192965 -0.43109586 0.51046056 0.8687784748
    treatmentLev.5FU 0.929566117 0.445855218 0.05568989 1.80344234 0.0370778547
    
    
    [1] "18 observations deleted due to missingness from 'data'"
    > summary(co11)
    Call:
    TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
     link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
    (s,t):
    [1] 50 200
    
     Transition 11 :
    
     Coefficients:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -895.023387 -0.401888881 6.26264521 922.27867219 943.9213673
    2 185 2.636107 -0.007185251 -0.07924264 0.10143607 1.0470649
    3 200 2.492609 -0.005980971 -0.07474810 0.03968235 0.9295661
    
     Standard Errors:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.424136e+11 5.981486454 34.76388106 1.424136e+11 1.424136e+11
    2 185 7.235303e-01 0.011277222 0.04188458 2.825713e-01 5.194717e-01
    3 200 7.332307e-01 0.009900533 0.02470581 2.401930e-01 4.458552e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -2.791306e+11 -12.12560233 -61.8745617 -2.791306e+11 -2.791306e+11
    2 185 1.217987e+00 -0.02928861 -0.1613364 -4.524036e-01 2.890027e-02
    3 200 1.055477e+00 -0.02538602 -0.1231715 -4.310959e-01 5.568989e-02
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 2.791306e+11 11.32182457 74.399852081 2.791306e+11 2.791306e+11
    2 185 4.054226e+00 0.01491810 0.002851131 6.552758e-01 2.065229e+00
    3 200 3.929742e+00 0.01342407 -0.026324705 5.104606e-01 1.803442e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9999999950 0.9464314 0.857036345 1.0000000 0.99999999
    2 185 0.0002690652 0.5240289 0.058500459 0.7196137 0.04383827
    3 200 0.0006751204 0.5457732 0.002482004 0.8687785 0.03707785
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11065 (sockconn)
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 1.1
Check: examples
Result: ERROR
    Running examples in 'idmTPreg-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: TPreg
    > ### Title: Regression Modeling of Transition Probabilities in a Progressive
    > ### Illness-Death Model
    > ### Aliases: TPreg
    >
    > ### ** Examples
    >
    > data(colonTPreg)
    >
    > co11 <- TPreg( ~ Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, R = 19, t = 200,
    + trans = "11", ncores = 1)
    Warning in TPreg(~Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, :
     Nodes variable in 'data' has missing value(s),
    Warning in model.matrix.default(mt, mf, contrasts) :
     non-list contrasts argument ignored
    > co11
    Call:
    TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
     link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
    
    Transition:
    [1] "11"
    
    (s,t):
    [1] 50 200
    
    Coefficients:
     Estimate St.Err LW.L UP.L P.value
    X.Intercept. 2.492609419 0.81034198 0.90433914 4.08087970 0.002098000
    Age -0.005980971 0.01282444 -0.03111688 0.01915494 0.640948730
    Nodes -0.074748098 0.02402381 -0.12183477 -0.02766142 0.001861920
    treatmentLev 0.039682347 0.27682859 -0.50290168 0.58226638 0.886016711
    treatmentLev.5FU 0.929566117 0.33618566 0.27064222 1.58849001 0.005691617
    
    
    [1] "18 observations deleted due to missingness from 'data'"
    > summary(co11)
    Call:
    TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
     link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
    (s,t):
    [1] 50 200
    
     Transition 11 :
    
     Coefficients:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -895.023387 -0.401888881 6.26264521 922.27867219 943.9213673
    2 185 2.636107 -0.007185251 -0.07924264 0.10143607 1.0470649
    3 200 2.492609 -0.005980971 -0.07474810 0.03968235 0.9295661
    
     Standard Errors:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 8.629586e+10 4.69923574 27.95518775 8.629586e+10 8.629586e+10
    2 185 7.728432e-01 0.01193137 0.04556010 2.791188e-01 4.140677e-01
    3 200 8.103420e-01 0.01282444 0.02402381 2.768286e-01 3.361857e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1.691399e+11 -9.61239094 -48.5295228 -1.691399e+11 -1.691399e+11
    2 185 1.121334e+00 -0.03057073 -0.1685404 -4.456367e-01 2.354922e-01
    3 200 9.043391e-01 -0.03111688 -0.1218348 -5.029017e-01 2.706422e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.691399e+11 8.80861317 61.05481319 1.691399e+11 1.691399e+11
    2 185 4.150880e+00 0.01620023 0.01005516 6.485088e-01 1.858638e+00
    3 200 4.080880e+00 0.01915494 -0.02766142 5.822664e-01 1.588490e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9999999917 0.9318463 0.82273829 1.0000000 0.999999991
    2 185 0.0006474399 0.5470308 0.08198217 0.7162946 0.011447651
    3 200 0.0020980003 0.6409487 0.00186192 0.8860167 0.005691617
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11084 (sockconn)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64