CRAN Package Check Results for Package idmTPreg

Last updated on 2020-01-28 05:50:15 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 8.25 63.04 71.29 OK
r-devel-linux-x86_64-debian-gcc 1.1 7.27 49.65 56.92 OK
r-devel-linux-x86_64-fedora-clang 1.1 84.78 OK
r-devel-linux-x86_64-fedora-gcc 1.1 84.74 OK
r-devel-windows-ix86+x86_64 1.1 16.00 96.00 112.00 ERROR
r-devel-windows-ix86+x86_64-gcc8 1.1 25.00 117.00 142.00 ERROR
r-patched-linux-x86_64 1.1 OK
r-patched-solaris-x86 1.1 117.00 OK
r-release-linux-x86_64 1.1 7.75 56.57 64.32 OK
r-release-windows-ix86+x86_64 1.1 14.00 70.00 84.00 ERROR
r-release-osx-x86_64 1.1 OK
r-oldrel-windows-ix86+x86_64 1.1 12.00 74.00 86.00 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 1.10074300 0.33515314 4.65006569 0.023544669
    Age -0.005980971 0.01589271 -0.03713068 0.02516874 0.706668409
    Nodes -0.074748098 0.02538127 -0.12449539 -0.02500080 0.003229445
    treatmentLev 0.039682347 0.32007019 -0.58765523 0.66701992 0.901331000
    treatmentLev.5FU 0.929566117 0.33816420 0.26676429 1.59236794 0.005980288
    
    
    [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 7.093661e+10 2.14769917 9.79334082 7.093661e+10 7.093661e+10
    2 185 8.030855e-01 0.01265034 0.01802432 3.483500e-01 3.019442e-01
    3 200 1.100743e+00 0.01589271 0.02538127 3.200702e-01 3.381642e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1.390358e+11 -4.61137926 -12.9323028 -1.390358e+11 -1.390358e+11
    2 185 1.062059e+00 -0.03197991 -0.1145703 -5.813300e-01 4.552543e-01
    3 200 3.351531e-01 -0.03713068 -0.1244954 -5.876552e-01 2.667643e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.390358e+11 3.80760150 25.45759322 1.390358e+11 1.390358e+11
    2 185 4.210154e+00 0.01760941 -0.04391498 7.842021e-01 1.638875e+00
    3 200 4.650066e+00 0.02516874 -0.02500080 6.670199e-01 1.592368e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.999999990 0.8515624 5.225107e-01 1.0000000 0.9999999894
    2 185 0.001029007 0.5700425 1.100463e-05 0.7709059 0.0005248484
    3 200 0.023544669 0.7066684 3.229445e-03 0.9013310 0.0059802878
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11286 (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 1.08081043 0.37422098 4.61099786 0.02109716
    Age -0.005980971 0.01631643 -0.03796117 0.02599922 0.71394626
    Nodes -0.074748098 0.02911936 -0.13182205 -0.01767415 0.01025959
    treatmentLev 0.039682347 0.37348348 -0.69234528 0.77170998 0.91538458
    treatmentLev.5FU 0.929566117 0.42129332 0.10383121 1.75530102 0.02735193
    
    
    [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 1.009169e+12 5.83915184 27.63503254 1.009169e+12 1.009169e+12
    2 185 9.391456e-01 0.01453072 0.03153360 3.259830e-01 4.063552e-01
    3 200 1.080810e+00 0.01631643 0.02911936 3.734835e-01 4.212933e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1.977972e+12 -11.84662649 -47.9020186 -1.977972e+12 -1.977972e+12
    2 185 7.953814e-01 -0.03566546 -0.1410485 -5.374907e-01 2.506087e-01
    3 200 3.742210e-01 -0.03796117 -0.1318220 -6.923453e-01 1.038312e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.977972e+12 11.04284872 60.42730899 1.977972e+12 1.977972e+12
    2 185 4.476832e+00 0.02129496 -0.01743679 7.403628e-01 1.843521e+00
    3 200 4.610998e+00 0.02599922 -0.01767415 7.717100e-01 1.755301e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.999999999 0.9451277 0.82071940 1.0000000 0.999999999
    2 185 0.005001764 0.6209623 0.01197232 0.7556716 0.009974179
    3 200 0.021097165 0.7139463 0.01025959 0.9153846 0.027351931
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11092 (sockconn)
    Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8

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 0.82614994 0.87335555 4.11186329 0.002551725
    Age -0.005980971 0.01172680 -0.02896551 0.01700357 0.610033523
    Nodes -0.074748098 0.02682615 -0.12732734 -0.02216885 0.005329875
    treatmentLev 0.039682347 0.25926097 -0.46846915 0.54783385 0.878351376
    treatmentLev.5FU 0.929566117 0.34823689 0.24702181 1.61211042 0.007599823
    
    
    [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 1.905602e+10 3.50594505 20.90056199 1.905602e+10 1.905602e+10
    2 185 7.999562e-01 0.01340923 0.02696628 2.283956e-01 3.553179e-01
    3 200 8.261499e-01 0.01172680 0.02682615 2.592610e-01 3.482369e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -3.734981e+10 -7.27354117 -34.7024563 -3.734980e+10 -3.734980e+10
    2 185 1.068193e+00 -0.03346735 -0.1320966 -3.462193e-01 3.506417e-01
    3 200 8.733555e-01 -0.02896551 -0.1273273 -4.684692e-01 2.470218e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 3.734981e+10 6.46976341 47.22774671 3.734981e+10 3.734981e+10
    2 185 4.204021e+00 0.01909685 -0.02638873 5.490914e-01 1.743488e+00
    3 200 4.111863e+00 0.01700357 -0.02216885 5.478338e-01 1.612110e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9999999625 0.9087379 0.764451740 1.0000000 0.999999960
    2 185 0.0009831185 0.5920667 0.003297170 0.6569526 0.003210401
    3 200 0.0025517254 0.6100335 0.005329875 0.8783514 0.007599823
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11625 (sockconn)
    Execution halted
Flavor: r-release-windows-ix86+x86_64