CRAN Package Check Results for Package idmTPreg

Last updated on 2019-07-22 13:46:58 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 6.29 57.36 63.65 OK
r-devel-linux-x86_64-debian-gcc 1.1 5.40 46.12 51.52 OK
r-devel-linux-x86_64-fedora-clang 1.1 77.07 OK
r-devel-linux-x86_64-fedora-gcc 1.1 76.17 OK
r-devel-windows-ix86+x86_64 1.1 14.00 97.00 111.00 ERROR
r-patched-linux-x86_64 1.1 6.71 56.66 63.37 OK
r-patched-solaris-x86 1.1 123.30 OK
r-release-linux-x86_64 1.1 7.33 57.25 64.58 OK
r-release-windows-ix86+x86_64 1.1 13.00 70.00 83.00 ERROR
r-release-osx-x86_64 1.1 OK
r-oldrel-windows-ix86+x86_64 1.1 12.00 71.00 83.00 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 0.68971370 1.14077056 3.844448e+00 0.0003015359
    Age -0.005980971 0.01021902 -0.02601026 1.404832e-02 0.5583607555
    Nodes -0.074748098 0.03813090 -0.14948466 -1.153043e-05 0.0499604568
    treatmentLev 0.039682347 0.29604922 -0.54057412 6.199388e-01 0.8933711858
    treatmentLev.5FU 0.929566117 0.34593823 0.25152719 1.607605e+00 0.0072078175
    
    
    [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 1334.8261937 0.32354310 8.46686825 1333.8556115 1335.4315233
    2 185 1.0236902 0.01525730 0.03350062 0.3247904 0.4014218
    3 200 0.6897137 0.01021902 0.03813090 0.2960492 0.3459382
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -3511.2827266 -1.03603336 -10.3324166 -1692.0783264 -1673.5244183
    2 185 0.6296739 -0.03708955 -0.1449039 -0.5351530 0.2602782
    3 200 1.1407706 -0.02601026 -0.1494847 -0.5405741 0.2515272
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 1721.235953 0.23225560 2.285771e+01 3536.6356707 3561.367153
    2 185 4.642540 0.02271905 -1.358143e-02 0.7380252 1.833852
    3 200 3.844448 0.01404832 -1.153043e-05 0.6199388 1.607605
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.5025284010 0.2141814 0.45950335 0.4892902 0.479672918
    2 185 0.0100210540 0.6376845 0.01801020 0.7548031 0.009096900
    3 200 0.0003015359 0.5583608 0.04996046 0.8933712 0.007207818
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11387 (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 0.92842537 0.67289570 4.312323136 0.007257953
    Age -0.005980971 0.01312379 -0.03170361 0.019741665 0.648580626
    Nodes -0.074748098 0.03367131 -0.14074387 -0.008752323 0.026423240
    treatmentLev 0.039682347 0.28963726 -0.52800668 0.607371372 0.891025221
    treatmentLev.5FU 0.929566117 0.28862789 0.36385544 1.495276789 0.001279054
    
    
    [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 1.098685e+12 5.827083914 26.51100049 1.098685e+12 1.098685e+12
    2 185 6.866621e-01 0.009568724 0.03209721 2.428640e-01 3.489702e-01
    3 200 9.284254e-01 0.013123794 0.03367131 2.896373e-01 2.886279e-01
    
     Lower limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 -2.153422e+12 -11.82297335 -45.6989157 -2.153422e+12 -2.153422e+12
    2 185 1.290249e+00 -0.02593995 -0.1421532 -3.745773e-01 3.630833e-01
    3 200 6.728957e-01 -0.03170361 -0.1407439 -5.280067e-01 3.638554e-01
    
     Upper limit:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 2.153422e+12 11.01919559 58.224206166 2.153422e+12 2.153422e+12
    2 185 3.981964e+00 0.01156945 -0.016332104 5.774494e-01 1.731046e+00
    3 200 4.312323e+00 0.01974167 -0.008752323 6.073714e-01 1.495277e+00
    
     p.value:
     time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
    1 56 0.9999999994 0.9450142 0.81325562 1.0000000 0.999999999
    2 185 0.0001235284 0.4527068 0.01355547 0.6761912 0.002695878
    3 200 0.0072579535 0.6485806 0.02642324 0.8910252 0.001279054
    
    
    [1] "18 observation(s) deleted due to missingness from 'data'"
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11023 (sockconn)
    Execution halted
Flavor: r-release-windows-ix86+x86_64