CRAN Package Check Results for Package idmTPreg

Last updated on 2023-02-04 08:01:18 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 8.65 74.39 83.04 OK
r-devel-linux-x86_64-debian-gcc 1.1 7.15 58.00 65.15 OK
r-devel-linux-x86_64-fedora-clang 1.1 104.68 OK
r-devel-linux-x86_64-fedora-gcc 1.1 101.78 OK
r-devel-windows-x86_64 1.1 14.00 97.00 111.00 ERROR
r-patched-linux-x86_64 1.1 8.51 77.05 85.56 OK
r-release-linux-x86_64 1.1 7.96 73.37 81.33 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 16.00 108.00 124.00 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 20.00 97.00 117.00 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 1.00518121 0.52245424 4.46276459 0.013147038
    Age -0.005980971 0.01622514 -0.03778225 0.02582031 0.712408284
    Nodes -0.074748098 0.02748884 -0.12862622 -0.02086998 0.006543679
    treatmentLev 0.039682347 0.26116899 -0.47220887 0.55157356 0.879233260
    treatmentLev.5FU 0.929566117 0.37367672 0.19715975 1.66197249 0.012860064
    
    
    [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 2.245524e+07 2.94623869 21.41680730 2.245523e+07 2.245524e+07
    2 185 1.006691e+00 0.01434188 0.02690013 3.535027e-01 2.848759e-01
    3 200 1.005181e+00 0.01622514 0.02748884 2.611690e-01 3.736767e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -4.401223e+07 -6.17651672 -35.7142971 -4.401228e+07 -4.401226e+07
    2 185 6.629920e-01 -0.03529533 -0.1319669 -5.914292e-01 4.887081e-01
    3 200 5.224542e-01 -0.03778225 -0.1286262 -4.722089e-01 1.971597e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 4.401232e+07 5.37273896 48.23958752 4.401224e+07 4.401226e+07
    2 185 4.609222e+00 0.02092483 -0.02651839 7.943014e-01 1.605422e+00
    3 200 4.462765e+00 0.02582031 -0.02086998 5.515736e-01 1.661972e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.999998373 0.8914992 0.769967574 0.9999993 0.9999998897
    2 185 0.008829521 0.6163726 0.003221114 0.7741539 0.0002373724
    3 200 0.013147038 0.7124083 0.006543679 0.8792333 0.0128600639
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANWIN2.fb05.statistik.uni-dortmund.de:11258 (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 0.78688714 0.95031063 4.03490821 0.001536587
    Age -0.005980971 0.01225368 -0.02999818 0.01803624 0.625481932
    Nodes -0.074748098 0.02396554 -0.12172056 -0.02777564 0.001814769
    treatmentLev 0.039682347 0.29182765 -0.53229985 0.61166454 0.891838113
    treatmentLev.5FU 0.929566117 0.29011027 0.36094998 1.49818225 0.001354468
    
    
    [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 7703.1475663 5.73420480 23.70901904 7641.7808147 7641.2087059
    2 185 0.8166113 0.01218941 0.03870429 0.2288178 0.3126899
    3 200 0.7868871 0.01225368 0.02396554 0.2918277 0.2901103
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1.599319e+04 -11.64093029 -40.2070321 -1.405561e+04 -1.403285e+04
    2 185 1.035549e+00 -0.03107650 -0.1551030 -3.470468e-01 4.341927e-01
    3 200 9.503106e-01 -0.02999818 -0.1217206 -5.322998e-01 3.609500e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 14203.145843 10.83715253 52.732322533 1.590017e+04 15920.690431
    2 185 4.236665 0.01670600 -0.003382242 5.499189e-01 1.659937
    3 200 4.034908 0.01803624 -0.027775638 6.116645e-01 1.498182
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.907502510 0.9441250 0.791667333 0.9039374 0.9016871237
    2 185 0.001246134 0.5555484 0.040620126 0.6575451 0.0008122885
    3 200 0.001536587 0.6254819 0.001814769 0.8918381 0.0013544682
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANWIN2.fb05.statistik.uni-dortmund.de:11257 (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 0.649082036 1.22040863 3.76481021 0.0001229306
    Age -0.005980971 0.009918899 -0.02542201 0.01346007 0.5465171063
    Nodes -0.074748098 0.028394817 -0.13040194 -0.01909426 0.0084770085
    treatmentLev 0.039682347 0.287234716 -0.52329770 0.60266239 0.8901194744
    treatmentLev.5FU 0.929566117 0.357972164 0.22794067 1.63119156 0.0094108940
    
    
    [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 1.393827e+10 2.938951093 14.79794157 1.393827e+10 1.393827e+10
    2 185 6.884345e-01 0.010561894 0.02744450 2.683727e-01 4.329235e-01
    3 200 6.490820e-01 0.009918899 0.02839482 2.872347e-01 3.579722e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -2.731900e+10 -6.16223302 -22.7413203 -2.731900e+10 -2.731900e+10
    2 185 1.286775e+00 -0.02788656 -0.1330339 -4.245744e-01 1.985349e-01
    3 200 1.220409e+00 -0.02542201 -0.1304019 -5.232977e-01 2.279407e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 2.731900e+10 5.35845526 35.26661068 2.731900e+10 2.731900e+10
    2 185 3.985438e+00 0.01351606 -0.02545142 6.274465e-01 1.895595e+00
    3 200 3.764810e+00 0.01346007 -0.01909426 6.026624e-01 1.631192e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9999999488 0.8912318 0.672141639 0.9999999 0.999999946
    2 185 0.0001285957 0.4963148 0.003884677 0.7054550 0.015580738
    3 200 0.0001229306 0.5465171 0.008477008 0.8901195 0.009410894
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11229 (sockconn)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64