CRAN Package Check Results for Package idmTPreg

Last updated on 2020-07-02 02:09:51 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 6.86 64.53 71.39 OK
r-devel-linux-x86_64-debian-gcc 1.1 7.39 49.15 56.54 OK
r-devel-linux-x86_64-fedora-clang 1.1 94.29 OK
r-devel-linux-x86_64-fedora-gcc 1.1 83.94 OK
r-devel-windows-ix86+x86_64 1.1 22.00 71.00 93.00 ERROR
r-patched-linux-x86_64 1.1 8.01 65.71 73.72 OK
r-patched-solaris-x86 1.1 126.70 OK
r-release-linux-x86_64 1.1 9.18 64.16 73.34 OK
r-release-osx-x86_64 1.1 OK
r-release-windows-ix86+x86_64 1.1 14.00 73.00 87.00 ERROR
r-oldrel-osx-x86_64 1.1 OK
r-oldrel-windows-ix86+x86_64 1.1 26.00 102.00 128.00 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 0.83056449 0.86470302 4.12051582 0.002690037
    Age -0.005980971 0.01324674 -0.03194459 0.01998264 0.651625594
    Nodes -0.074748098 0.03241398 -0.13827949 -0.01121670 0.021108102
    treatmentLev 0.039682347 0.32555862 -0.59841255 0.67777725 0.902986120
    treatmentLev.5FU 0.929566117 0.33036572 0.28204930 1.57708293 0.004896750
    
    
    [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 1.882528e+04 3.07752646 15.67122813 1.880091e+04 1.880331e+04
    2 185 7.735957e-01 0.01225240 0.04172654 3.567553e-01 3.809704e-01
    3 200 8.305645e-01 0.01324674 0.03241398 3.255586e-01 3.303657e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -37792.562743 -6.43384074 -24.4529619 -3.592750e+04 -3.591057e+04
    2 185 1.119859 -0.03119996 -0.1610267 -5.978042e-01 3.003628e-01
    3 200 0.864703 -0.03194459 -0.1382795 -5.984126e-01 2.820493e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 36002.515970 5.63006298 36.978252350 3.777206e+04 37798.411013
    2 185 4.152354 0.01682946 0.002541382 8.006764e-01 1.793767
    3 200 4.120516 0.01998264 -0.011216704 6.777772e-01 1.577083
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.962079896 0.8961010 0.68943130 0.9608755 0.959963217
    2 185 0.000655362 0.5575826 0.05755207 0.7761578 0.005988416
    3 200 0.002690037 0.6516256 0.02110810 0.9029861 0.004896750
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11588 (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 0.91210079 0.70489186 4.28032697 0.006279419
    Age -0.005980971 0.01338186 -0.03220941 0.02024747 0.654913911
    Nodes -0.074748098 0.02448471 -0.12273812 -0.02675807 0.002266804
    treatmentLev 0.039682347 0.26752483 -0.48466632 0.56403102 0.882081194
    treatmentLev.5FU 0.929566117 0.29345346 0.35439733 1.50473491 0.001536615
    
    
    [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 1.030423e+15 2.14169141 9.75010759 1.030423e+15 1.030423e+15
    2 185 6.175317e-01 0.01030461 0.04252314 3.192026e-01 3.745375e-01
    3 200 9.121008e-01 0.01338186 0.02448471 2.675248e-01 2.934535e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -2.019629e+15 -4.59960404 -12.8475657 -2.019629e+15 -2.019629e+15
    2 185 1.425745e+00 -0.02738229 -0.1625880 -5.242010e-01 3.129714e-01
    3 200 7.048919e-01 -0.03220941 -0.1227381 -4.846663e-01 3.543973e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 2.019629e+15 3.79582628 25.37285608 2.019629e+15 2.019629e+15
    2 185 3.846469e+00 0.01301179 0.00410271 7.270731e-01 1.781158e+00
    3 200 4.280327e+00 0.02024747 -0.02675807 5.640310e-01 1.504735e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.000000e+00 0.8511508 0.520668354 1.0000000 1.000000000
    2 185 1.965452e-05 0.4856245 0.062389398 0.7506521 0.005180012
    3 200 6.279419e-03 0.6549139 0.002266804 0.8820812 0.001536615
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11893 (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 0.88052693 0.7667766 4.21844221 4.642947e-03
    Age -0.005980971 0.01340925 -0.0322631 0.02030116 6.555732e-01
    Nodes -0.074748098 0.01792286 -0.1098769 -0.03961929 3.038716e-05
    treatmentLev 0.039682347 0.27555629 -0.5004080 0.57977268 8.854940e-01
    treatmentLev.5FU 0.929566117 0.35413755 0.2354565 1.62367572 8.668128e-03
    
    
    [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 1.151721e+11 4.67690195 27.95698447 1.151721e+11 1.151721e+11
    2 185 6.695144e-01 0.01053236 0.03701488 3.052173e-01 5.495899e-01
    3 200 8.805269e-01 0.01340925 0.01792286 2.755563e-01 3.541376e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -2.257373e+11 -9.56861671 -48.5330443 -2.257373e+11 -2.257373e+11
    2 185 1.323859e+00 -0.02782867 -0.1517918 -4.967899e-01 -3.013130e-02
    3 200 7.667766e-01 -0.03226310 -0.1098769 -5.004080e-01 2.354565e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 2.257373e+11 8.76483895 61.058334766 2.257373e+11 2.257373e+11
    2 185 3.948355e+00 0.01345817 -0.006693477 6.996621e-01 2.124261e+00
    3 200 4.218442e+00 0.02030116 -0.039619293 5.797727e-01 1.623676e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.000000e+00 0.9315216 8.227495e-01 1.0000000 0.999999993
    2 185 8.238926e-05 0.4951079 3.228758e-02 0.7396322 0.056757335
    3 200 4.642947e-03 0.6555732 3.038716e-05 0.8854940 0.008668128
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11932 (sockconn)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64