* using log directory 'd:/Rcompile/CRANpkg/local/4.1/idmTPreg.Rcheck' * using R version 4.1.3 (2022-03-10) * 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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[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 1.15873013 0.22149836 4.76372048 0.03146388 Age -0.005980971 0.01797629 -0.04121451 0.02925257 0.73934992 Nodes -0.074748098 0.03116910 -0.13583954 -0.01365665 0.01647824 treatmentLev 0.039682347 0.31630633 -0.58027807 0.65964276 0.90016301 treatmentLev.5FU 0.929566117 0.44703766 0.05337230 1.80575993 0.03758142 [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 6.546042e+10 3.60350755 18.50221540 6.546042e+10 6.546042e+10 2 185 9.470586e-01 0.01465992 0.03050941 2.677623e-01 4.317283e-01 3 200 1.158730e+00 0.01797629 0.03116910 3.163063e-01 4.470377e-01 Lower limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 -1.283024e+11 -7.46476369 -30.0016970 -1.283024e+11 -1.283024e+11 2 185 7.798720e-01 -0.03591870 -0.1390411 -4.233781e-01 2.008774e-01 3 200 2.214984e-01 -0.04121451 -0.1358395 -5.802781e-01 5.337230e-02 Upper limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 1.283024e+11 6.66098592 42.52698740 1.283024e+11 1.283024e+11 2 185 4.492342e+00 0.02154820 -0.01944420 6.262503e-01 1.893252e+00 3 200 4.763720e+00 0.02925257 -0.01365665 6.596428e-01 1.805760e+00 p.value: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 0.999999989 0.9111983 0.735000872 1.000000 0.99999999 2 185 0.005378124 0.6240427 0.009395489 0.704815 0.01529630 3 200 0.031463879 0.7393499 0.016478243 0.900163 0.03758142 [1] "18 observation(s) deleted due to missingness from 'data'" > > > > cleanEx() Error: connections left open: <-CRANwin.fb05.statistik.uni-dortmund.de:11046 (sockconn) Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR