* using log directory 'd:/Rcompile/CRANpkg/local/4.3/idmTPreg.Rcheck' * using R Under development (unstable) (2022-08-11 r82713 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * 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 0.473944860 1.56367749 3.421541344 1.446194e-07 Age -0.005980971 0.006589688 -0.01889676 0.006934818 3.640760e-01 Nodes -0.074748098 0.028546134 -0.13069852 -0.018797675 8.831687e-03 treatmentLev 0.039682347 0.249967705 -0.45025436 0.529619049 8.738659e-01 treatmentLev.5FU 0.929566117 0.297014755 0.34741720 1.511715037 1.749868e-03 [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 2.695167e+11 3.612147607 14.89612245 2.695167e+11 2.695167e+11 2 185 8.314327e-01 0.014520568 0.02565680 1.971479e-01 4.103197e-01 3 200 4.739449e-01 0.006589688 0.02854613 2.499677e-01 2.970148e-01 Lower limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 -5.282528e+11 -7.48169819 -22.9337548 -5.282528e+11 -5.282528e+11 2 185 1.006499e+00 -0.03564556 -0.1295300 -2.849738e-01 2.428383e-01 3 200 1.563677e+00 -0.01889676 -0.1306985 -4.502544e-01 3.474172e-01 Upper limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 5.282528e+11 6.677920428 35.45904522 5.282528e+11 5.282528e+11 2 185 4.265715e+00 0.021275061 -0.02895532 4.878459e-01 1.851291e+00 3 200 3.421541e+00 0.006934818 -0.01879768 5.296190e-01 1.511715e+00 p.value: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 1.000000e+00 0.9114099 0.674177807 1.0000000 1.000000000 2 185 1.521458e-03 0.6207182 0.002011268 0.6068901 0.010715966 3 200 1.446194e-07 0.3640760 0.008831687 0.8738659 0.001749868 [1] "18 observation(s) deleted due to missingness from 'data'" > > > > cleanEx() Error: connections left open: <-CRANWIN2.fb05.statistik.uni-dortmund.de:11816 (sockconn) Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR