* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/SuperSurv.Rcheck’ * using R Under development (unstable) (2026-05-26 r90080) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-05-27 14:51:57 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘SuperSurv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SuperSurv’ version ‘0.1.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘fastshap’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SuperSurv’ can be installed ... [24s/76s] OK * checking package directory ... OK * checking ‘build’ 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [5s/13s] OK * checking whether the package can be loaded with stated dependencies ... [4s/13s] OK * checking whether the package can be unloaded cleanly ... [4s/11s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/11s] OK * checking whether the namespace can be unloaded cleanly ... [4s/12s] 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 ... [37s/52s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [7s/11s] ERROR Running examples in ‘SuperSurv-Ex.R’ failed The error most likely occurred in: > ### Name: plot_marginal_rmst_curve > ### Title: Plot Adjusted Marginal RMST Contrast Over Time > ### Aliases: plot_marginal_rmst_curve > > ### ** Examples > > data("metabric", package = "SuperSurv") > dat <- metabric[1:80, ] > x_cols <- grep("^x", names(dat), value = TRUE)[1:5] > X <- dat[, x_cols, drop = FALSE] > new.times <- seq(20, 120, by = 20) > > fit <- SuperSurv( + time = dat$duration, + event = dat$event, + X = X, + newdata = X, + new.times = new.times, + event.library = c("surv.coxph", "surv.glmnet"), + cens.library = c("surv.coxph"), + control = list(saveFitLibrary = TRUE) + ) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet The Algorithm will be removed from the Super Learner (i.e. given weight 0) Error in loadNamespace(x) : there is no package called ‘glmnet’ Warning in FUN(X[[i]], ...) : Error in algorithm surv.glmnet on full data The Algorithm will be removed from the Super Learner (i.e. given weight 0) > > tau_grid <- seq(40, 120, by = 20) > plot_marginal_rmst_curve( + fit = fit, + data = dat, + trt_col = "x4", + times = new.times, + tau_seq = tau_grid, + inference = TRUE, + B = 100, + seed = 123 + ) Error in UseMethod("predict") : no applicable method for 'predict' applied to an object of class "NULL" Calls: plot_marginal_rmst_curve ... estimate_marginal_rmst -> predict -> predict.SuperSurv -> do.call -> predict Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-SuperSurv-methods.R’ Running ‘test-library-validation.R’ [9s/16s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [12s/24s] OK * checking PDF version of manual ... [11s/21s] OK * checking HTML version of manual ... [10s/18s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/gannet/ripley/R/packages/tests-Suggests/SuperSurv.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:50.23, 185.28 + 18.28