* using log directory ‘/data/localhost/ripley/R/packages/tests-OpenBLAS/mlt.Rcheck’
* using R Under development (unstable) (2026-07-19 r90278)
* 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: 2026-07-20 01:46:40 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘mlt/DESCRIPTION’ ... OK
* this is package ‘mlt’ version ‘1.8-1’
* 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 ‘mlt’ can be installed ... [9s/12s] OK
* used C compiler: ‘gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s/21s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘2sample.R’
  Comparing ‘2sample.Rout’ to ‘2sample.Rout.save’ ... OK
  Running ‘Cox-Ex.R’
  Comparing ‘Cox-Ex.Rout’ to ‘Cox-Ex.Rout.save’ ... OK
  Running ‘bugfixes.R’
  Running ‘distr-Ex.R’
  Running ‘dpq-Ex.R’
  Comparing ‘dpq-Ex.Rout’ to ‘dpq-Ex.Rout.save’ ... OK
  Running ‘glm-Ex.R’
  Comparing ‘glm-Ex.Rout’ to ‘glm-Ex.Rout.save’ ... OK
  Running ‘lm-Ex.R’
  Comparing ‘lm-Ex.Rout’ to ‘lm-Ex.Rout.save’ ... OK
  Running ‘missing-responses.R’
  Running ‘mmlt_ll_sc.R’ [35s/37s]
  Running ‘polr-Ex.R’
  Comparing ‘polr-Ex.Rout’ to ‘polr-Ex.Rout.save’ ... OK
  Running ‘predict-Ex.R’
  Comparing ‘predict-Ex.Rout’ to ‘predict-Ex.Rout.save’ ... OK
  Running ‘subset.R’
  Comparing ‘subset.Rout’ to ‘subset.Rout.save’ ... OK
  Running ‘surv-Ex.R’
  Comparing ‘surv-Ex.Rout’ to ‘surv-Ex.Rout.save’ ... OK
 [65s/73s] ERROR
Running the tests in ‘tests/bugfixes.R’ failed.
Complete output:
  > 
  > library("mlt")
  Loading required package: basefun
  Loading required package: variables
  > library("sandwich")
  > set.seed(29)
  > options(digits = 5)
  > 
  > ### Nadja Klein
  > dat <- data.frame(matrix(rnorm(900),ncol=3))
  > names(dat) <- c("y","x1","x2")
  > sup <- qnorm(c(.1, .9))
  > ### set-up conditional transformation model for conditional
  > y <- numeric_var("y", support = sup, bounds = c(-Inf, Inf))
  > x1 <- numeric_var("x1", support = sup, bounds = c(-Inf, Inf)) 
  > x2 <- numeric_var("x2", support = sup, bounds = c(-Inf, Inf)) 
  > ctmm2 <- ctm(response = Bernstein_basis(y, order = 4, ui = "increasing"),
  +               interacting = c(x1=Bernstein_basis(x1, order = 3),
  +                               x2=Bernstein_basis(x2, order = 3)))
  > ### fit model
  > mltm2 <- mlt(ctmm2, data = dat, scale = TRUE)
  > p <- predict(mltm2, newdata = data.frame(x1=0, x2 = 0), q = mkgrid(mltm2, n = 10)[["y"]])
  > ### plot data
  > plot(mltm2,newdata=expand.grid(x1=0:1, x2 = 0:1))
  > 
  > ### check update
  > dist <- numeric_var("dist", support = c(2.0, 100), bounds = c(0, Inf))
  > speed <- numeric_var("speed", support = c(5.0, 23), bounds = c(0, Inf)) 
  > ctmm <- ctm(response = Bernstein_basis(dist, order = 4, ui = "increasing"),
  +             interacting = Bernstein_basis(speed, order = 3))
  > 
  > m <- mlt(ctmm, data = cars)
  > e <- estfun(m)
  > w <- runif(nrow(cars)) < .8
  > m1 <- update(m, weights = w, theta = coef(m))
  > e1 <- estfun(m1, parm = coef(m))
  > stopifnot(max(abs(e * w - e1)) < .Machine$double.eps)
  > e1 <- estfun(m1)
  > m2 <- mlt(ctmm, data = cars[w > 0,], theta = coef(m))
  > stopifnot(isTRUE(all.equal(logLik(m1), logLik(m2))))
  Error: isTRUE(all.equal(logLik(m1), logLik(m2))) is not TRUE
  Execution halted
* 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/localhost/ripley/R/packages/tests-OpenBLAS/mlt.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:33.01, 123.51 + 8.83