CRAN Package Check Results for Package idmTPreg

Last updated on 2022-01-22 20:48:38 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 7.53 76.58 84.11 OK
r-devel-linux-x86_64-debian-gcc 1.1 6.02 58.44 64.46 OK
r-devel-linux-x86_64-fedora-clang 1.1 104.06 OK
r-devel-linux-x86_64-fedora-gcc 1.1 92.17 OK
r-devel-windows-x86_64-new-UL 1.1 30.00 96.00 126.00 ERROR
r-devel-windows-x86_64-new-TK 1.1 OK
r-patched-linux-x86_64 1.1 7.46 73.97 81.43 OK
r-release-linux-x86_64 1.1 6.75 74.23 80.98 OK
r-release-macos-arm64 1.1 OK
r-release-macos-x86_64 1.1 OK
r-release-windows-ix86+x86_64 1.1 18.00 88.00 106.00 ERROR
r-oldrel-macos-x86_64 1.1 OK
r-oldrel-windows-ix86+x86_64 1.1 18.00 88.00 106.00 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 0.91124062 0.70657780 4.27864104 0.006230414
    Age -0.005980971 0.01241478 -0.03031394 0.01835200 0.629974931
    Nodes -0.074748098 0.02868508 -0.13097086 -0.01852533 0.009165526
    treatmentLev 0.039682347 0.28997179 -0.52866236 0.60802705 0.891150159
    treatmentLev.5FU 0.929566117 0.50540819 -0.06103393 1.92016617 0.065880138
    
    
    [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 8.577033e+11 2.99851784 19.64589575 8.577033e+11 8.577033e+11
    2 185 9.180109e-01 0.01408020 0.02388192 2.498254e-01 2.607368e-01
    3 200 9.112406e-01 0.01241478 0.02868508 2.899718e-01 5.054082e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1.681098e+12 -6.27898385 -32.2433105 -1.681098e+12 -1.681098e+12
    2 185 8.368054e-01 -0.03478244 -0.1260512 -3.882217e-01 5.360207e-01
    3 200 7.065778e-01 -0.03031394 -0.1309709 -5.286624e-01 -6.103393e-02
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.681098e+12 5.47520609 44.76860088 1.681098e+12 1.681098e+12
    2 185 4.435408e+00 0.02041194 -0.03243409 5.910939e-01 1.558109e+00
    3 200 4.278641e+00 0.01835200 -0.01852533 6.080271e-01 1.920166e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.999999999 0.8933795 0.7498961802 1.0000000 1.000000e+00
    2 185 0.004084746 0.6098351 0.0009063127 0.6847222 5.924647e-05
    3 200 0.006230414 0.6299749 0.0091655259 0.8911502 6.588014e-02
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANWIN2.fb05.statistik.uni-dortmund.de:11895 (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 0.552479498 1.40974960 3.575469234 6.431687e-06
    Age -0.005980971 0.008191653 -0.02203661 0.010074670 4.653108e-01
    Nodes -0.074748098 0.034502261 -0.14237253 -0.007123666 3.027533e-02
    treatmentLev 0.039682347 0.215021460 -0.38175972 0.461124409 8.535815e-01
    treatmentLev.5FU 0.929566117 0.375595000 0.19339992 1.665732318 1.332675e-02
    
    
    [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 1.030471e+15 7.907099439 38.71179132 1.030471e+15 1.030471e+15
    2 185 8.056366e-01 0.013055143 0.01751665 3.933925e-01 3.091954e-01
    3 200 5.524795e-01 0.008191653 0.03450226 2.150215e-01 3.755950e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -2.019723e+15 -15.89980378 -69.6124658 -2.019723e+15 -2.019723e+15
    2 185 1.057059e+00 -0.03277333 -0.1135753 -6.696132e-01 4.410419e-01
    3 200 1.409750e+00 -0.02203661 -0.1423725 -3.817597e-01 1.933999e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 2.019723e+15 15.09602602 82.137756202 2.019723e+15 2.019723e+15
    2 185 4.215155e+00 0.01840283 -0.044910014 8.724854e-01 1.653088e+00
    3 200 3.575469e+00 0.01007467 -0.007123666 4.611244e-01 1.665732e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.000000e+00 0.9594639 8.714821e-01 1.0000000 1.0000000000
    2 185 1.067597e-03 0.5820608 6.072544e-06 0.7965230 0.0007081148
    3 200 6.431687e-06 0.4653108 3.027533e-02 0.8535815 0.0133267476
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11113 (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 0.677744009 1.16423116 3.82098768 0.0002352509
    Age -0.005980971 0.009520532 -0.02464121 0.01267927 0.5298610499
    Nodes -0.074748098 0.029030252 -0.13164739 -0.01784880 0.0100288021
    treatmentLev 0.039682347 0.315198089 -0.57810591 0.65747060 0.8998138265
    treatmentLev.5FU 0.929566117 0.466825201 0.01458872 1.84454351 0.0464533070
    
    
    [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 1.810793e+04 0.281897583 8.82933063 1.811016e+04 1.810850e+04
    2 185 8.520582e-01 0.013038367 0.02694463 3.286197e-01 3.980463e-01
    3 200 6.777440e-01 0.009520532 0.02903025 3.151981e-01 4.668252e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -3.638658e+04 -0.95440814 -11.0428428 -3.457363e+04 -3.454873e+04
    2 185 9.660727e-01 -0.03274045 -0.1320541 -5.426586e-01 2.668941e-01
    3 200 1.164231e+00 -0.02464121 -0.1316474 -5.781059e-01 1.458872e-02
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 34596.528308 0.15063038 23.56813325 3.641819e+04 36436.574959
    2 185 4.306141 0.01836995 -0.02643116 7.455307e-01 1.827236
    3 200 3.820988 0.01267927 -0.01784880 6.574706e-01 1.844544
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9605789013 0.1539678 0.478138259 0.9593845 0.958428390
    2 185 0.0019760347 0.5815753 0.003272142 0.7575702 0.008525682
    3 200 0.0002352509 0.5298610 0.010028802 0.8998138 0.046453307
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11381 (sockconn)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64