CRAN Package Check Results for Package idmTPreg

Last updated on 2019-08-25 05:46:49 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 7.35 57.10 64.45 OK
r-devel-linux-x86_64-debian-gcc 1.1 6.93 45.67 52.60 OK
r-devel-linux-x86_64-fedora-clang 1.1 79.73 OK
r-devel-linux-x86_64-fedora-gcc 1.1 78.00 OK
r-devel-windows-ix86+x86_64 1.1 15.00 67.00 82.00 ERROR
r-patched-linux-x86_64 1.1 5.62 57.03 62.65 OK
r-patched-solaris-x86 1.1 124.70 OK
r-release-linux-x86_64 1.1 6.40 57.92 64.32 OK
r-release-windows-ix86+x86_64 1.1 19.00 100.00 119.00 ERROR
r-release-osx-x86_64 1.1 OK
r-oldrel-windows-ix86+x86_64 1.1 10.00 99.00 109.00 OK
r-oldrel-osx-x86_64 1.1 OK

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 0.78536379 0.95329639 4.03192245 0.001504429
    Age -0.005980971 0.01226258 -0.03001563 0.01805369 0.625732854
    Nodes -0.074748098 0.02716287 -0.12798732 -0.02150888 0.005925990
    treatmentLev 0.039682347 0.32027188 -0.58805053 0.66741523 0.901392818
    treatmentLev.5FU 0.929566117 0.42882560 0.08906794 1.77006429 0.030181366
    
    
    [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 9.976953e+14 2.14596863 13.42665460 9.976953e+14 9.976953e+14
    2 185 7.648078e-01 0.01220482 0.02778857 3.644915e-01 5.629116e-01
    3 200 7.853638e-01 0.01226258 0.02716287 3.202719e-01 4.288256e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1.955483e+15 -4.60798740 -20.0535978 -1.955483e+15 -1.955483e+15
    2 185 1.137083e+00 -0.03110671 -0.1337082 -6.129674e-01 -5.624190e-02
    3 200 9.532964e-01 -0.03001563 -0.1279873 -5.880505e-01 8.906794e-02
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.955483e+15 3.80420963 32.57888823 1.955483e+15 1.955483e+15
    2 185 4.135130e+00 0.01673620 -0.02477705 8.158395e-01 2.150372e+00
    3 200 4.031922e+00 0.01805369 -0.02150888 6.674152e-01 1.770064e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.0000000000 0.8514441 0.640905039 1.0000000 1.00000000
    2 185 0.0005673583 0.5560476 0.004349607 0.7807861 0.06287314
    3 200 0.0015044292 0.6257329 0.005925990 0.9013928 0.03018137
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11994 (sockconn)
    Execution halted
Flavor: r-devel-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 0.93215439 0.66558681 4.31963203 7.494560e-03
    Age -0.005980971 0.01479112 -0.03497157 0.02300963 6.859464e-01
    Nodes -0.074748098 0.02445508 -0.12268006 -0.02681614 2.239026e-03
    treatmentLev 0.039682347 0.42699752 -0.79723280 0.87659749 9.259564e-01
    treatmentLev.5FU 0.929566117 0.23792556 0.46323202 1.39590021 9.346384e-05
    
    
    [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 56 283.9288357 0.20824053 7.40208921 282.7139209 280.0767244
    2 185 0.7393759 0.01112083 0.02241744 0.3225535 0.3789607
    3 200 0.9321544 0.01479112 0.02445508 0.4269975 0.2379256
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1451.5239049 -0.81004032 -8.2454496 368.1593873 394.9709874
    2 185 1.1869300 -0.02898207 -0.1231808 -0.5307687 0.3043019
    3 200 0.6655868 -0.03497157 -0.1226801 -0.7972328 0.4632320
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -338.522869 0.006262557 20.77074005 1476.3979571 1492.871747
    2 185 4.085284 0.014611573 -0.03530447 0.7336409 1.789828
    3 200 4.319632 0.023009631 -0.02681614 0.8765975 1.395900
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.0016200046 0.05361597 0.3975167402 0.001105383 7.510704e-04
    2 185 0.0003634218 0.51820971 0.0004079815 0.753157790 5.727442e-03
    3 200 0.0074945602 0.68594641 0.0022390264 0.925956443 9.346384e-05
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11919 (sockconn)
    Execution halted
Flavor: r-release-windows-ix86+x86_64