* using log directory 'd:/Rcompile/CRANpkg/local/4.2/idmTPreg.Rcheck' * using R version 4.2.1 (2022-06-23 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 1.01960264 0.49418825 4.49103058 0.01449779 Age -0.005980971 0.01517786 -0.03572957 0.02376763 0.69353752 Nodes -0.074748098 0.02932947 -0.13223387 -0.01726233 0.01081669 treatmentLev 0.039682347 0.25191654 -0.45407407 0.53343877 0.87483363 treatmentLev.5FU 0.929566117 0.37673239 0.19117063 1.66796160 0.01360815 [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 1.251236e+11 6.26149943 36.04430022 1.251236e+11 1.251236e+11 2 185 7.543116e-01 0.01195671 0.03251933 2.405429e-01 3.363748e-01 3 200 1.019603e+00 0.01517786 0.02932947 2.519165e-01 3.767324e-01 Lower limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 -2.452423e+11 -12.67442776 -64.3841832 -2.452423e+11 -2.452423e+11 2 185 1.157656e+00 -0.03062039 -0.1429805 -3.700280e-01 3.877703e-01 3 200 4.941883e-01 -0.03572957 -0.1322339 -4.540741e-01 1.911706e-01 Upper limit: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 2.452423e+11 11.87065000 76.90947364 2.452423e+11 2.452423e+11 2 185 4.114558e+00 0.01624989 -0.01550476 5.729001e-01 1.706359e+00 3 200 4.491031e+00 0.02376763 -0.01726233 5.334388e-01 1.667962e+00 p.value: time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU 1 56 0.9999999943 0.9488236 0.86206307 1.0000000 0.999999994 2 185 0.0004745618 0.5478806 0.01481845 0.6732466 0.001853263 3 200 0.0144977857 0.6935375 0.01081669 0.8748336 0.013608147 [1] "18 observation(s) deleted due to missingness from 'data'" > > > > cleanEx() Error: connections left open: <-CRANWIN2.fb05.statistik.uni-dortmund.de:11152 (sockconn) Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR