* using log directory ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/mlt.docreg.Rcheck’
* using R Under development (unstable) (2025-04-19 r88162)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘mlt.docreg/DESCRIPTION’ ... OK
* this is package ‘mlt.docreg’ version ‘1.1-10’
* 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 ‘mlt.docreg’ can be installed ... [17s/31s] 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 ... [5s/10s] OK
* checking loading without being on the library search path ... [5s/11s] 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 ... [21s/28s] 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 line endings in shell scripts ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AFT-Ex.R’
  Comparing ‘AFT-Ex.Rout’ to ‘AFT-Ex.Rout.save’ ... OK
  Running ‘GBSG2.R’
  Running ‘KM-Ex.R’
  Comparing ‘KM-Ex.Rout’ to ‘KM-Ex.Rout.save’ ... OK
  Running ‘faithful.R’ [9s/23s]
  Comparing ‘faithful.Rout’ to ‘faithful.Rout.save’ ... OK
  Running ‘orm-Ex.R’ [45s/83s]
  Comparing ‘orm-Ex.Rout’ to ‘orm-Ex.Rout.save’ ... OK
  Running ‘timedep_covar.R’ [11s/17s]
  Running ‘truncreg-Ex.R’ [6s/12s]
  Comparing ‘truncreg-Ex.Rout’ to ‘truncreg-Ex.Rout.save’ ... OK
 [85s/159s] ERROR
Running the tests in ‘tests/timedep_covar.R’ failed.
Complete output:
  > 
  > library("mlt")
  Loading required package: basefun
  Loading required package: variables
  > library("survival")
  > library("flexsurv")
  > 
  > chk <- function(x, y, ...) {
  + 
  +     ret <- all.equal(x, y, ...)
  +     if (isTRUE(ret)) return(ret)
  +     print(ret)
  +     return(TRUE)
  + }
  > tol <- .001
  > 
  > ### right-censored veteran data
  > ### exponential model
  > fit1 <- coxph(Surv(time, status) ~ karno + age + trt, veteran)
  > fit2 <- survreg(Surv(time, status) ~ karno + age + trt, veteran, dist = "exponential")
  > fit3 <- flexsurvreg(Surv(time, status) ~ karno + age + trt, data= veteran, dist = "exponential")
  > 
  > veteran$ytime <- with(veteran, Surv(time, status))
  > dy <- numeric_var("ytime", support = c(0.1, 1000))
  > by <- log_basis(dy, ui = "increasing")
  > m <- mlt(ctm(by, shift = ~ karno + age + trt, data = veteran, todistr = "MinExtr"),
  +          data = veteran, fixed = c("log(ytime)" = 1))
  > 
  > stopifnot(chk(fit3$logliki, m$logliki(coef(m)[-2], weights(m)), 
  +                     tol = tol, check.attributes = FALSE))
  > 
  > stopifnot(chk(logLik(fit2), logLik(m), tol = tol))
  > stopifnot(chk(logLik(fit3), logLik(m), tol = tol, 
  +               check.attributes = FALSE))
  > 
  > ### Weibull model
  > fit2 <- survreg(Surv(time, status) ~ karno + age + trt, veteran, dist = "weibull")
  > fit3 <- flexsurvreg(Surv(time, status) ~ karno + age + trt, data= veteran, dist = "weibull")
  > 
  > veteran$ytime <- with(veteran, Surv(time, status))
  > dy <- numeric_var("ytime", support = c(0.1, 1000))
  > # by <- Bernstein_basis(dy, order = 10, ui = "increasing")
  > by <- log_basis(dy, ui = "increasing")
  > m <- mlt(ctm(by, shift = ~ karno + age + trt, data = veteran, todistr = "MinExtr"),
  +          data = veteran)
  > 
  > stopifnot(chk(fit3$logliki, m$logliki(coef(m), weights(m)), 
  +               tol = tol, check.attributes = FALSE))
  > 
  > stopifnot(chk(logLik(fit2), logLik(m), tol = tol))
  > stopifnot(chk(logLik(fit3), logLik(m), tol = tol,
  +               check.attributes = FALSE))
  > 
  > ### now with time-dependent covariates
  > vet2 <- survSplit(Surv(time, status) ~., veteran,
  +                   cut=c(60, 120), episode ="timegroup")
  > vet2$timegroup <- factor(vet2$timegroup)
  > vet2$ytime <- with(vet2, Surv(tstart, time, status))
  > 
  > ## exponential model
  > suppressWarnings(fit3 <- flexsurvreg(Surv(tstart, time, status) ~ 
  +     karno + karno:timegroup + age + trt, data= vet2, dist = "exponential"))
  > m <- mlt(ctm(by, shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"),
  +          data = vet2, fixed = c("log(ytime)" = 1))
  > 
  > stopifnot(chk(fit3$logliki, m$logliki(coef(m)[-2], weights(m)), 
  +               tol = tol, check.attributes = FALSE))
  > stopifnot(chk(logLik(fit3), logLik(m), tol = tol, check.attributes = FALSE))
  > 
  > ### Weibull model
  > fit3 <- flexsurvreg(Surv(tstart, time, status) ~ karno + karno:timegroup +
  +                      age + trt, data= vet2, dist = "weibull")
  > m <- mlt(ctm(by, shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"),
  +          data = vet2, scale = TRUE)
  > 
  > stopifnot(chk(fit3$logliki, m$logliki(coef(m), weights(m)), 
  +               tol = tol, check.attributes = FALSE))
  > stopifnot(chk(logLik(fit3), logLik(m), tol = tol, check.attributes = FALSE))
  > 
  > ## Cox model, see ?survival::survSplit
  > fit1 <- coxph(Surv(tstart, time, status) ~ karno + karno:strata(timegroup) +
  +               age + trt, data= vet2)
  > 
  > ### refit this model using mlt
  > btg <- as.basis(vet2$timegroup)
  > by <- Bernstein_basis(dy, order = 3, ui = "increasing")
  > m <- mlt(ctm(by, interacting = btg, 
  +          shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"),
  +          data = vet2, scale = TRUE)
  Error in optim(par = par, fn = fun, gr = gradient, control = control.optim,  : 
    non-finite value supplied by optim
  Error in ret$convergence : $ operator is invalid for atomic vectors
  Error in ret$par : $ operator is invalid for atomic vectors
  Calls: mlt -> do.call -> .mlt_fit -> <Anonymous>
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [199s/325s] 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
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/mlt.docreg.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 11:52.33, 395.14 + 28.49