* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BJM.Rcheck’ * using R Under development (unstable) (2026-06-26 r90194) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-16 (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22] GNU Fortran (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22] * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-06-28 20:06:04 UTC * checking for file ‘BJM/DESCRIPTION’ ... OK * this is package ‘BJM’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Wenhao Li ’ New submission Possibly misspelled words in DESCRIPTION: BJM (2:30, 10:397) The Description field should not start with the package name, 'This package' or similar. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... 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[30s/30s] ERROR Running examples in ‘BJM-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: predictPlot > ### Title: Plot of risk and future biomarker with density using dynamic > ### prediction > ### Aliases: predictPlot > > ### ** Examples > > > data(pbc3) > > data.survival.fitting = pbc3[!duplicated(pbc3$id), ] > > formMarginalSurv = Surv(years, status3) ~ age + sex > formConditionalCR = NULL > > survival_fit_all = survivalSub(data.survival.fitting, formMarginalSurv, + formConditionalCR) > > LongSubFixed = list( + "long1" = serBilir ~ year + age + sex + (years) + (years) * year, + "long2" = prothrombin ~ year + age + sex + (years) + (years) * year, + "long3" = albumin ~ year + age + age * year + sex + (years) + (years) * year, + "long4" = alkaline ~ year + age + sex + (years) + (years) * year, + "long5" = SGOT ~ year + age + sex + (years) + (years) * year, + "long6" = platelets ~ year + age + sex + (years) + (years) * year) > > LongSubRandom =list( + "long1" = ~ year| id, + "long2" = ~ year| id, + "long3" = ~ year| id, + "long4" = ~ year| id, + "long5" = ~ year| id, + "long6" = ~ year| id) > > survivalVariableAll = list( + "Tyears1", "Tyears2", "Tyears3", "Tyears4" + ) > > survivalTransFunction = list( + fun1 = function(x){abs(x - 1)}, + fun2 = function(x){abs(x - 3)}, + fun3 = function(x){abs(x - 5)}, + fun4 = function(x){abs(x - 7)} + ) > > # Complete case analysis > data.fit.all = list() > for(i in 1:length(LongSubFixed)){ + data.fit.all[[i]] = pbc3[pbc3$status3 == 1, ] + } > > # fitting longitudinal submodel > long_fit_all = longitudinalSub(data.fit.all, LongSubFixed, LongSubRandom) > > i_PID = 2 > data.raw.predict.plot = pbc3[pbc3$id == i_PID, ] > data.predict.all.pre = list(data.raw.predict.plot, data.raw.predict.plot, data.raw.predict.plot, + data.raw.predict.plot, data.raw.predict.plot, data.raw.predict.plot) > > # plot biomarker 1 history, predict future biomarker > > predictPlot(data.predict.all.pre, long_fit_all, survival_fit_all, + prediction.time = 5, bio_his = 1, bio_pred = 1, + horizon = seq(0.0, 3.0, 0.5), time_variable = "year", + survivalVariableAll, survivalTransFunction, + bandcount1 = 10, bandcount2 = 10, bandcount3 = 200) Error in f_y_D_all_predict[[1]] * S_T_all_predict : non-conformable arrays Calls: predictPlot -> dynamicPrediction -> t Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed dynamicPredictionBio 7.215 0.092 7.311 dynamicPrediction 6.722 0.048 6.774 longitudinalSub 6.446 0.008 6.457 * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs