CRAN Package Check Results for Package idmTPreg

Last updated on 2022-07-04 15:54:44 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 8.49 75.24 83.73 OK
r-devel-linux-x86_64-debian-gcc 1.1 5.57 56.61 62.18 OK
r-devel-linux-x86_64-fedora-clang 1.1 107.63 OK
r-devel-linux-x86_64-fedora-gcc 1.1 107.15 OK
r-devel-windows-x86_64 1.1 17.00 95.00 112.00 ERROR
r-patched-linux-x86_64 1.1 9.24 71.07 80.31 OK
r-release-linux-x86_64 1.1 9.74 71.31 81.05 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 12.00 98.00 110.00 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 21.00 92.00 113.00 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 0.711772092 1.09753612 3.887682720 0.0004618197
    Age -0.005980971 0.009385912 -0.02437736 0.012415417 0.5239760086
    Nodes -0.074748098 0.033931920 -0.14125466 -0.008241534 0.0276028980
    treatmentLev 0.039682347 0.283658456 -0.51628823 0.595652920 0.8887430989
    treatmentLev.5FU 0.929566117 0.279327858 0.38208351 1.477048719 0.0008751346
    
    
    [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 2170.8684412 5.823923418 27.33186046 2087.3568878 2087.2748134
    2 185 0.8480956 0.013979142 0.03455169 0.2748011 0.4089922
    3 200 0.7117721 0.009385912 0.03393192 0.2836585 0.2793279
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -4209.1086242 -11.81677878 -47.3078013 -4109.7577355 -4087.9541746
    2 185 0.9738395 -0.03458437 -0.1469640 -0.4371742 0.2454401
    3 200 1.0975361 -0.02437736 -0.1412547 -0.5162882 0.3820835
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 4300.695665 11.01300102 59.833091714 4072.6812648 4094.163094
    2 185 4.298374 0.02021387 -0.011521333 0.6400463 1.848690
    3 200 3.887683 0.01241542 -0.008241534 0.5956529 1.477049
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9831702222 0.9449844 0.81876515 0.9929139 0.9988132854
    2 185 0.0018818848 0.6072534 0.02182199 0.7120343 0.0104639172
    3 200 0.0004618197 0.5239760 0.02760290 0.8887431 0.0008751346
    
    
    [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 0.90611712 0.71661986 4.268598979 0.0059437424
    Age -0.005980971 0.01231906 -0.03012633 0.018164384 0.6273178007
    Nodes -0.074748098 0.03483064 -0.14301616 -0.006480038 0.0318694542
    treatmentLev 0.039682347 0.35931032 -0.66456587 0.743930565 0.9120601766
    treatmentLev.5FU 0.929566117 0.24510139 0.44916738 1.409964849 0.0001490915
    
    
    [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 2.131700e+11 2.10209048 14.33572105 2.131700e+11 2.131700e+11
    2 185 9.120496e-01 0.01514669 0.02775355 2.836770e-01 4.812496e-01
    3 200 9.061171e-01 0.01231906 0.03483064 3.593103e-01 2.451014e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -4.178132e+11 -4.52198622 -21.8353680 -4.178132e+11 -4.178132e+11
    2 185 8.484896e-01 -0.03687277 -0.1336396 -4.545708e-01 1.038156e-01
    3 200 7.166199e-01 -0.03012633 -0.1430162 -6.645659e-01 4.491674e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 4.178132e+11 3.71820846 34.360658466 4.178132e+11 4.178132e+11
    2 185 4.423724e+00 0.02250227 -0.024845684 6.574430e-01 1.990314e+00
    3 200 4.268599e+00 0.01816438 -0.006480038 7.439306e-01 1.409965e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.999999997 0.8483804 0.662215811 1.0000000 0.9999999965
    2 185 0.003848610 0.6352307 0.004300629 0.7206607 0.0295761306
    3 200 0.005943742 0.6273178 0.031869454 0.9120602 0.0001490915
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANWIN2.fb05.statistik.uni-dortmund.de:11475 (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 0.64734508 1.22381307 3.76140577 0.0001178716
    Age -0.005980971 0.01080396 -0.02715674 0.01519480 0.5798591367
    Nodes -0.074748098 0.02507379 -0.12389273 -0.02560347 0.0028719178
    treatmentLev 0.039682347 0.21168695 -0.37522408 0.45458877 0.8513017954
    treatmentLev.5FU 0.929566117 0.29122401 0.35876705 1.50036518 0.0014132650
    
    
    [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 56 171.8712090 1.94403864 13.54683325 93.5054349 88.3425643
    2 185 0.7877289 0.01281312 0.03340148 0.4097488 0.4903297
    3 200 0.6473451 0.01080396 0.02507379 0.2116870 0.2912240
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -1231.890957 -4.21220462 -20.2891480 739.0080197 770.7699413
    2 185 1.092158 -0.03229897 -0.1447095 -0.7016715 0.0860187
    3 200 1.223813 -0.02715674 -0.1238927 -0.3752241 0.3587671
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -558.155817 3.40842686 32.81443838 1105.5493247 1117.072793
    2 185 4.180055 0.01792847 -0.01377575 0.9045437 2.008111
    3 200 3.761406 0.01519480 -0.02560347 0.4545888 1.500365
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1.913774e-07 0.8362216 0.643869153 6.000122e-23 1.199257e-26
    2 185 8.184922e-04 0.5749524 0.017671549 8.044774e-01 3.272587e-02
    3 200 1.178716e-04 0.5798591 0.002871918 8.513018e-01 1.413265e-03
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11263 (sockconn)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64