CRAN Package Check Results for Package idmTPreg

Last updated on 2022-06-29 02:55:13 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 7.98 74.74 82.72 OK
r-devel-linux-x86_64-debian-gcc 1.1 7.44 56.44 63.88 OK
r-devel-linux-x86_64-fedora-clang 1.1 107.63 OK
r-devel-linux-x86_64-fedora-gcc 1.1 107.24 OK
r-devel-windows-x86_64 1.1 15.00 93.00 108.00 ERROR
r-patched-linux-x86_64 1.1 7.51 71.42 78.93 OK
r-release-linux-x86_64 1.1 7.13 69.94 77.07 OK
r-release-macos-arm64 1.1 30.00 OK
r-release-macos-x86_64 1.1 44.00 OK
r-release-windows-x86_64 1.1 19.00 96.00 115.00 ERROR
r-oldrel-macos-arm64 1.1 38.00 OK
r-oldrel-macos-x86_64 1.1 65.00 OK
r-oldrel-windows-ix86+x86_64 1.1 18.00 93.00 111.00 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 0.77544658 0.97273412 4.01248472 0.001307093
    Age -0.005980971 0.01296611 -0.03139454 0.01943260 0.644599711
    Nodes -0.074748098 0.02992843 -0.13340782 -0.01608838 0.012505072
    treatmentLev 0.039682347 0.23049779 -0.41209333 0.49145802 0.863312267
    treatmentLev.5FU 0.929566117 0.35186223 0.23991614 1.61921609 0.008245534
    
    
    [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 45.793521 -0.401888881 6.26264521 -18.53823536 3.1044597
    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 1.375190e+05 4.24839702 800.34624956 1.374276e+05 1.374291e+05
    2 185 7.421247e-01 0.01236642 0.03201036 3.465436e-01 5.426030e-01
    3 200 7.754466e-01 0.01296611 0.02992843 2.304978e-01 3.518622e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -2.694914e+05 -8.72874703 -1562.4160039 -2.693766e+05 -2.693580e+05
    2 185 1.181542e+00 -0.03142343 -0.1419829 -5.777894e-01 -1.643706e-02
    3 200 9.727341e-01 -0.03139454 -0.1334078 -4.120933e-01 2.399161e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 2.695830e+05 7.92496927 1574.94129435 2.693395e+05 2.693642e+05
    2 185 4.090671e+00 0.01705293 -0.01650234 7.806615e-01 2.110567e+00
    3 200 4.012485e+00 0.01943260 -0.01608838 4.914580e-01 1.619216e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9997343062 0.9246343 0.99375668 0.9998924 0.999981976
    2 185 0.0003821586 0.5612207 0.01330381 0.7697454 0.053643150
    3 200 0.0013070926 0.6445997 0.01250507 0.8633123 0.008245534
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANWIN2.fb05.statistik.uni-dortmund.de:11408 (sockconn)
    Execution halted
Flavor: r-devel-windows-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 0.78592322 0.95219991 4.03301893 0.001516180
    Age -0.005980971 0.01285152 -0.03116995 0.01920801 0.641652043
    Nodes -0.074748098 0.02938807 -0.13234872 -0.01714748 0.010975302
    treatmentLev 0.039682347 0.23371199 -0.41839315 0.49775784 0.865173985
    treatmentLev.5FU 0.929566117 0.33091271 0.28097721 1.57815502 0.004968057
    
    
    [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 1.578767e+11 4.57751465 28.53622606 1.578767e+11 1.578767e+11
    2 185 7.245785e-01 0.01127958 0.02796492 1.668106e-01 5.209104e-01
    3 200 7.859232e-01 0.01285152 0.02938807 2.337120e-01 3.309127e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -3.094383e+11 -9.37381759 -49.6683579 -3.094383e+11 -3.094383e+11
    2 185 1.215933e+00 -0.02929323 -0.1340539 -2.255127e-01 2.608040e-02
    3 200 9.521999e-01 -0.03116995 -0.1323487 -4.183932e-01 2.809772e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 3.094383e+11 8.57003983 62.19364828 3.094383e+11 3.094383e+11
    2 185 4.056281e+00 0.01492272 -0.02443141 4.283848e-01 2.068049e+00
    3 200 4.033019e+00 0.01920801 -0.01714748 4.977578e-01 1.578155e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9999999955 0.9300386 0.826289415 1.0000000 0.999999995
    2 185 0.0002746308 0.5241156 0.004602044 0.5431269 0.044424104
    3 200 0.0015161805 0.6416520 0.010975302 0.8651740 0.004968057
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANWIN2.fb05.statistik.uni-dortmund.de:11400 (sockconn)
    Execution halted
Flavor: r-release-windows-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 0.79590070 0.93264404 4.05257480 0.001737325
    Age -0.005980971 0.01213227 -0.02976022 0.01779828 0.622026463
    Nodes -0.074748098 0.02377337 -0.12134390 -0.02815230 0.001665445
    treatmentLev 0.039682347 0.22907402 -0.40930273 0.48866742 0.862471142
    treatmentLev.5FU 0.929566117 0.39639910 0.15262387 1.70650836 0.019025764
    
    
    [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 6.013572e+06 4.47584239 27.68313577 6.013597e+06 6.013596e+06
    2 185 7.321583e-01 0.01208183 0.03436154 2.763495e-01 4.130873e-01
    3 200 7.959007e-01 0.01213227 0.02377337 2.290740e-01 3.963991e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1.178750e+07 -9.17453996 -47.9963009 -1.178573e+07 -1.178570e+07
    2 185 1.201077e+00 -0.03086564 -0.1465913 -4.402089e-01 2.374138e-01
    3 200 9.326440e-01 -0.02976022 -0.1213439 -4.093027e-01 1.526239e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.178571e+07 8.37076220 60.52159132 1.178757e+07 1.178759e+07
    2 185 4.071137e+00 0.01649514 -0.01189402 6.430810e-01 1.856716e+00
    3 200 4.052575e+00 0.01779828 -0.02815230 4.886674e-01 1.706508e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9998812477 0.9284536 0.821025646 0.9998776 0.99987476
    2 185 0.0003176544 0.5520338 0.021102628 0.7135763 0.01125339
    3 200 0.0017373254 0.6220265 0.001665445 0.8624711 0.01902576
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11227 (sockconn)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64