* using log directory 'd:/Rcompile/CRANpkg/local/3.6/idmTPreg.Rcheck' * using R version 3.6.3 (2020-02-29) * 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 ... [9s] 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 ... 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 0.93149303 0.66688309 4.318335751 0.007452238 Age -0.005980971 0.01358688 -0.03261125 0.020649309 0.659790804 Nodes -0.074748098 0.04208097 -0.15722680 0.007730609 0.075684792 treatmentLev 0.039682347 1.39140453 -2.68747054 2.766835231 0.977247709 treatmentLev.5FU 0.929566117 0.30582953 0.33014025 1.528991986 0.002369782 [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 4.365691e+11 4.53552326 27.24835407 4.365691e+11 4.365691e+11 2 185 8.088417e-01 0.01226199 0.02844347 2.901629e-01 3.383992e-01 3 200 9.314930e-01 0.01358688 0.04208097 1.391405e+00 3.058295e-01 Lower limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 -8.556755e+11 -9.29151447 -47.1441288 -8.556755e+11 -8.556755e+11 2 185 1.050777e+00 -0.03121875 -0.1349918 -4.672832e-01 3.838025e-01 3 200 6.668831e-01 -0.03261125 -0.1572268 -2.687471e+00 3.301402e-01 Upper limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 8.556755e+11 8.48773671 59.669419190 8.556755e+11 8.556755e+11 2 185 4.221436e+00 0.01684825 -0.023493435 6.701553e-01 1.710327e+00 3 200 4.318336e+00 0.02064931 0.007730609 2.766835e+00 1.528992e+00 p.value: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 0.999999998 0.9293925 0.818219423 1.0000000 0.999999998 2 185 0.001117610 0.5578905 0.005336793 0.7266515 0.001973637 3 200 0.007452238 0.6597908 0.075684792 0.9772477 0.002369782 [1] "18 observation(s) deleted due to missingness from 'data'" > > > > cleanEx() Error: connections left open: <-CRANwin.fb05.statistik.uni-dortmund.de:11081 (sockconn) Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR