* using log directory ‘/srv/hornik/tmp/CRAN_pretest/expertsurv.Rcheck’ * using R Under development (unstable) (2025-02-14 r87718) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘expertsurv/DESCRIPTION’ ... OK * this is package ‘expertsurv’ version ‘1.4.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Philip Cooney ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: Cooney (15:316) Unknown, possibly misspelled, fields in DESCRIPTION: ‘Logo’ CRAN repository db overrides: X-CRAN-Comment: Archived on 2024-05-07 as issues were not corrected in time. Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/packages/flexsurv/vignettes/standsurv.html From: inst/doc/Expertsurv-Vignette.html README.md Status: 200 Message: OK CRAN URL not in canonical form The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname The Date field is over a month old. Size of tarball: 6909262 bytes * 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 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 ‘expertsurv’ can be installed ... [37s/36s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (1+b1)’ * checking package directory ... OK * checking for future file timestamps ... 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NOTE Mismatches for apparent methods not registered: gamma: function(x) gamma.error_mod: function(parameters, values, probabilities, weights, mode, trunc) gamma: function(x) gamma.error: function(parameters, values, probabilities, weights) See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [23s/23s] OK * checking Rd files ... [2s/2s] 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 ... [3s/3s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... 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[16s/16s] ERROR Running examples in ‘expertsurv-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fit.models.expert > ### Title: Fitting Parametric Survival models with Expert Opinion > ### Aliases: fit.models.expert > ### Keywords: models > > ### ** Examples > > require("dplyr") Loading required package: dplyr Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > #Expert Opinion as a normal distribution centered on 0.1 with sd 0.005 > param_expert_example1 <- list() > param_expert_example1[[1]] <- data.frame(dist = c("norm"), + wi = c(1), # Ensure Weights sum to 1 + param1 = c(0.1), + param2 = c(0.05), + param3 = c(NA)) > timepoint_expert <- 14 # Expert opinion at t = 14 > > data2 <- data %>% rename(status = censored) %>% mutate(time2 = ifelse(time > 10, 10, time), + status2 = ifelse(time> 10, 0, status)) > > example1 <- fit.models.expert(formula=Surv(time2,status2)~1,data=data2, + distr=c("wei", "gomp"), + method="mle", + opinion_type = "survival", + times_expert = timepoint_expert, + param_expert = param_expert_example1) > > plot(example1, add.km = TRUE, t = seq(0:20)) #Plot Survival > model.fit.plot(example1, type = "aic") #Plot AIC > > # Running Bayesian approach - `iter` should be much higher, only for illustration > example1_bayes <- fit.models.expert(formula=Surv(time2,status2)~1,data=data2, + distr=c("wei", "gomp"), + method="bayes", + opinion_type = "survival", + times_expert = timepoint_expert, + param_expert = param_expert_example1, + iter = 50, + compile_mods = expertsurv::compiled_models_saved) Error in prep_call_sampler(object) : the compiled object from C++ code for this model is invalid, possible reasons: - compiled with save_dso=FALSE; - compiled on a different platform; - does not exist (created from reading csv files). Calls: fit.models.expert ... -> .local -> -> prep_call_sampler Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed cred_int 10.071 0.284 10.359 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] OK * checking PDF version of manual ... [3s/2s] OK * checking HTML version of manual ... [0s/0s] 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