* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/simode.Rcheck’
* using R Under development (unstable) (2026-08-14 r90405)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-14 17:53:22 UTC
* checking for file ‘simode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simode’ version ‘1.2.2’
* package encoding: UTF-8
* 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 ‘simode’ can be installed ... 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 ... 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 ... NOTE
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [12s/12s] 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 ... OK
* checking examples with --run-donttest ... [392s/394s] ERROR
Running examples in ‘simode-Ex.R’ failed
The error most likely occurred in:

> ### Name: simode
> ### Title: Statistical inference of ordinary differential equations using
> ###   separable integral-matching
> ### Aliases: simode
> 
> ### ** Examples
> 
> 
> ## =================================================
> ## Predator-Prey Lotka-Volterra model
> ## =================================================
> 
> ## generate model equations and parameters (X=Prey,Y=Predator)
> pars <- c('alpha','beta','gamma','delta')
> vars <- c('X','Y')
> eq_X <- 'alpha*X-beta*X*Y'
> eq_Y <- 'delta*X*Y-gamma*Y'
> equations <- c(eq_X,eq_Y)
> names(equations) <- vars
> x0 <- c(0.9,0.9)
> names(x0) <- vars
> theta <- c(2/3,4/3,1,1)
> names(theta) <- pars
> 
> ## generate observations
> n <- 50
> time <- seq(0,25,length.out=n)
> model_out <- solve_ode(equations,theta,x0,time)
> x_det <- model_out[,vars]
> set.seed(1000)
> sigma <- 0.05
> obs <- list()
> for(i in 1:length(vars)) {
+   obs[[i]] <- pmax(0, rnorm(n,x_det[,i],sigma))
+ }
> names(obs) <- vars
> 
> ## estimate model parameters with known initial conditions
> simode_fit1 <- simode(equations=equations, pars=pars, fixed=x0, time=time, obs=obs)
> plot(simode_fit1, type='fit', time=seq(0,25,length.out=100), pars_true=theta, mfrow=c(2,1))
> plot(simode_fit1, type='est', pars_true=theta)
> 
> ## No test: 
> ## estimate model parameters and initial conditions
> simode_fit2 <- simode(equations=equations, pars=c(pars,vars), time=time, obs=obs)
> plot(simode_fit2, type='fit', time=seq(0,25,length.out=100), pars_true=c(theta,x0), mfrow=c(2,1))
> plot(simode_fit2, type='est', pars_true=c(theta,x0))
> 
> profiles_fit2 <- profile(simode_fit2,step_size=0.01,max_steps=50)
> plot(profiles_fit2,mfrow=c(2,3))
> ci_fit2 <- confint(profiles_fit2)
> ci_fit2
call:
confint.profile.simode(object = profiles_fit2)
level:
0.95 
intervals:
    par   nls_est     lower     upper
1 alpha 0.6808252 0.6343605 0.7303201
2  beta 1.3371559 1.2538731 1.4266004
3 gamma 0.9741731 0.9049307 1.0488701
4 delta 0.9821350 0.9128926 1.0568320
5     X 0.8678510 0.8298712 0.9074470
6     Y 0.9114065 0.8835277 0.9398914
> plot(ci_fit2,pars_true=c(theta,x0),legend=T)
Error in plot.confint.simode(ci_fit2, pars_true = c(theta, x0), legend = T) : 
  T used instead of TRUE
Calls: plot -> plot.confint.simode
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/localhost/ripley/R/packages/tests-donttest/simode.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:54.01, 456.42 + 15.17