* 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 ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [10s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... 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 0.95188829 0.62690837 4.35831047 0.008829284 Age -0.005980971 0.01496799 -0.03531823 0.02335629 0.689462826 Nodes -0.074748098 0.03120089 -0.13590184 -0.01359436 0.016588468 treatmentLev 0.039682347 0.31838124 -0.58434487 0.66370957 0.900810277 treatmentLev.5FU 0.929566117 0.36712533 0.21000047 1.64913176 0.011340978 [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 5.693555e+11 5.20356884 21.68566756 5.693555e+11 5.693555e+11 2 185 8.820049e-01 0.01324854 0.03231367 2.933664e-01 3.836232e-01 3 200 9.518883e-01 0.01496799 0.03120089 3.183812e-01 3.671253e-01 Lower limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 -1.115937e+12 -10.60088381 -36.2412632 -1.115937e+12 -1.115937e+12 2 185 9.073772e-01 -0.03315239 -0.1425774 -4.735620e-01 2.951633e-01 3 200 6.269084e-01 -0.03531823 -0.1359018 -5.843449e-01 2.100005e-01 Upper limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 1.115937e+12 9.79710605 48.76655363 1.115937e+12 1.115937e+12 2 185 4.364836e+00 0.01878189 -0.01590785 6.764341e-01 1.798966e+00 3 200 4.358310e+00 0.02335629 -0.01359436 6.637096e-01 1.649132e+00 p.value: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 0.999999999 0.9384379 0.77274063 1.0000000 0.999999999 2 185 0.002801060 0.5875824 0.01419483 0.7295187 0.006344787 3 200 0.008829284 0.6894628 0.01658847 0.9008103 0.011340978 [1] "18 observation(s) deleted due to missingness from 'data'" > > > > cleanEx() Error: connections left open: <-CRANwin.fb05.statistik.uni-dortmund.de:11245 (sockconn) Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR