* using log directory 'd:/Rcompile/CRANpkg/local/4.0/idmTPreg.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'idmTPreg/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'idmTPreg' version '1.1' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'idmTPreg' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... 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OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [8s] 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 0.50655020 1.49977103 3.485447804 8.621099e-07 Age -0.005980971 0.00864528 -0.02292572 0.010963778 4.890509e-01 Nodes -0.074748098 0.03465894 -0.14267963 -0.006816567 3.103095e-02 treatmentLev 0.039682347 0.24305203 -0.43669963 0.516064319 8.703083e-01 treatmentLev.5FU 0.929566117 0.41512834 0.11591456 1.743217670 2.514122e-02 [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 3.268937e+11 5.142773396 21.30475596 3.268937e+11 3.268937e+11 2 185 4.682973e-01 0.008201646 0.03592604 2.889209e-01 4.719593e-01 3 200 5.065502e-01 0.008645280 0.03465894 2.430520e-01 4.151283e-01 Lower limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 -6.407117e+11 -10.48172474 -35.4946765 -6.407117e+11 -6.407117e+11 2 185 1.718244e+00 -0.02326048 -0.1496577 -4.648489e-01 1.220246e-01 3 200 1.499771e+00 -0.02292572 -0.1426796 -4.366996e-01 1.159146e-01 Upper limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 6.407117e+11 9.677946974 48.019966892 6.407117e+11 6.407117e+11 2 185 3.553969e+00 0.008889974 -0.008827610 6.677210e-01 1.972105e+00 3 200 3.485448e+00 0.010963778 -0.006816567 5.160643e-01 1.743218e+00 p.value: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 1.000000e+00 0.9377117 0.76879209 1.0000000 1.00000000 2 185 1.811194e-08 0.3809896 0.02740387 0.7255239 0.02651742 3 200 8.621099e-07 0.4890509 0.03103095 0.8703083 0.02514122 [1] "18 observation(s) deleted due to missingness from 'data'" > > > > cleanEx() Error: connections left open: <-CRANwin.fb05.statistik.uni-dortmund.de:11615 (sockconn) Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR