* 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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[7s] 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 0.84868941 0.82917818 4.15604066 0.003313932 Age -0.005980971 0.01258485 -0.03064728 0.01868534 0.634607670 Nodes -0.074748098 0.03205219 -0.13757039 -0.01192581 0.019696765 treatmentLev 0.039682347 0.25876977 -0.46750640 0.54687109 0.878122263 treatmentLev.5FU 0.929566117 0.69329626 -0.42929454 2.28842678 0.179987974 [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 7.107541e+11 2.53459941 13.04459698 7.107541e+11 7.107541e+11 2 185 1.000262e+00 0.01516174 0.03292542 4.050341e-01 4.222645e-01 3 200 8.486894e-01 0.01258485 0.03205219 2.587698e-01 6.932963e-01 Lower limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 -1.393078e+12 -5.36970373 -19.3047649 -1.393078e+12 -1.393078e+12 2 185 6.755924e-01 -0.03690227 -0.1437765 -6.924307e-01 2.194265e-01 3 200 8.291782e-01 -0.03064728 -0.1375704 -4.675064e-01 -4.292945e-01 Upper limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 1.393078e+12 4.56592597 31.83005530 1.393078e+12 1.393078e+12 2 185 4.596621e+00 0.02253177 -0.01470882 8.953029e-01 1.874703e+00 3 200 4.156041e+00 0.01868534 -0.01192581 5.468711e-01 2.288427e+00 p.value: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 0.999999999 0.8740147 0.63115987 1.0000000 1.00000000 2 185 0.008403444 0.6355665 0.01609600 0.8022484 0.01315142 3 200 0.003313932 0.6346077 0.01969677 0.8781223 0.17998797 [1] "18 observation(s) deleted due to missingness from 'data'" > > > > cleanEx() Error: connections left open: <-CRANwin.fb05.statistik.uni-dortmund.de:11949 (sockconn) Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR