* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/depmixS4.Rcheck’
* using R Under development (unstable) (2026-06-03 r90098)
* 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: 2026-06-03 14:34:02 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘depmixS4/DESCRIPTION’ ... OK
* this is package ‘depmixS4’ version ‘1.5-2’
* 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 ‘depmixS4’ can be installed ... [19s/50s] OK
* used C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [26s/57s] 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 data for ASCII and uncompressed saves ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/119s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test1speed.R’ [5s/14s]
  Comparing ‘test1speed.Rout’ to ‘test1speed.Rout.save’ ... OK
  Running ‘test2getsetpars.R’
  Comparing ‘test2getsetpars.Rout’ to ‘test2getsetpars.Rout.save’ ... OK
  Running ‘test3responses.R’
  Running ‘test4examples.R’ [54s/143s]
 [64s/171s] ERROR
Running the tests in ‘tests/test4examples.R’ failed.
Complete output:
  > #
  > # Example regression tests for refactoring preparation.
  > #
  > # Suggested next unit-test targets:
  > # - parameter round trips: getpars(), setpars(), freepars(), fixed/equal/conrows
  > # - likelihood engines: fb(), forwardbackward(), viterbi(), posterior()
  > # - optimizers: fit() with EM, fixed parameters, equality constraints, and hard EM
  > # - response classes: GLMresponse and MVNresponse dens(), fit(), predict(), getpars()
  > # - data-shape handling: ntimes, multivariate responses, missing values, and weights
  > #
  > # The checks below intentionally exercise the examples and selected former
  > # \dontrun{} blocks against numeric baselines from the current implementation.
  > 
  > require(depmixS4)
  Loading required package: depmixS4
  Loading required package: nnet
  Loading required package: MASS
  Loading required package: Rsolnp
  Loading required package: nlme
  > 
  > check_equal <- function(value, expected, tolerance = 1e-6, label = NULL) {
  + 	if(!isTRUE(all.equal(value, expected, tolerance = tolerance,
  + 		check.attributes = FALSE))) {
  + 		stop(paste("unexpected value", label), call. = FALSE)
  + 	}
  + }
  > 
  > loglik <- function(object) {
  + 	suppressWarnings(unname(as.numeric(logLik(object))))
  + }
  > 
  > quiet <- function(expr) {
  + 	value <- NULL
  + 	capture.output(value <- force(expr))
  + 	value
  + }
  > 
  > run_example <- function(topic) {
  + 	env <- new.env(parent = globalenv())
  + 	quiet(suppressWarnings(utils::example(topic, package = "depmixS4", ask = FALSE,
  + 		echo = FALSE, local = env, run.dontrun = FALSE,
  + 		character.only = TRUE)))
  + 	env
  + }
  > 
  > cat("Running Rd examples for regression coverage\n")
  Running Rd examples for regression coverage
  > 
  > example_topics <- c(
  + 	"balance", "depmix-methods", "fit", "depmix", "depmixS4-package",
  + 	"em.control", "forwardbackward", "makeDepmix", "mix-class",
  + 	"mix.fitted-class", "mix", "multistart", "posterior", "responses",
  + 	"simulate", "sp500", "speed", "vcov", "viterbi"
  + )
  > 
  > example_envs <- lapply(example_topics, run_example)
  > names(example_envs) <- example_topics
  > 
  > check_equal(loglik(example_envs$depmix$fm), -296.107777497663,
  + 	label = "depmix fm logLik")
  > check_equal(loglik(example_envs$depmix$fmsp), 1334.635143365299,
  + 	label = "depmix fmsp logLik")
  > check_equal(loglik(example_envs$fit$fmod1), -248.972219690931,
  + 	label = "fit fmod1 logLik")
  > check_equal(loglik(example_envs$fit$fmod2), -249.212895124180,
  + 	label = "fit fmod2 logLik")
  > check_equal(loglik(example_envs$fit$fmod4), -1083.036278731958,
  + 	label = "fit fmod4 logLik")
  > check_equal(example_envs$fit$pst_new, c(2, 1, 1),
  + 	label = "fit new-data Viterbi states")
  > check_equal(dim(example_envs$fit$pst_prob), c(439, 2),
  + 	label = "fit smoothing dimensions")
  > check_equal(loglik(example_envs$makeDepmix$fm1), -248.972219690931,
  + 	label = "makeDepmix fm1 logLik")
  > check_equal(loglik(example_envs$makeDepmix$fm2), -297.952933433641,
  + 	label = "makeDepmix fm2 logLik")
  > check_equal(loglik(example_envs$multistart$fmod2), -248.972216998551,
  + 	label = "multistart fmod2 logLik")
  > check_equal(loglik(example_envs$posterior$fmod), -248.972216763550,
  + 	label = "posterior fmod logLik")
  > check_equal(dim(example_envs$posterior$pst_prob), c(439, 2),
  + 	label = "posterior smoothing dimensions")
  > check_equal(loglik(example_envs$vcov$fmod1), -248.972219690931,
  + 	label = "vcov fmod1 logLik")
  > check_equal(loglik(example_envs$viterbi$fmod), -248.972218212895,
  + 	label = "viterbi fmod logLik")
  > 
  > cat("Running fast local dontrun regression examples\n")
  Running fast local dontrun regression examples
  > 
  > set.seed(3)
  > y1 <- rpois(50, 1)
  > y2 <- rpois(50, 2)
  > ydf <- data.frame(y = c(y1, y2))
  > m1 <- depmix(y ~ 1, ns = 1, family = poisson(), data = ydf)
  > set.seed(1)
  > fm1 <- quiet(fit(m1, verbose = FALSE))
  > m2 <- depmix(y ~ 1, ns = 2, family = poisson(), data = ydf)
  > set.seed(1)
  > fm2 <- quiet(fit(m2, verbose = FALSE))
  > m3 <- depmix(y ~ 1, ns = 3, family = poisson(), data = ydf)
  > set.seed(1)
  > fm3 <- quiet(fit(m3, em = em.control(maxit = 500), verbose = FALSE))
  > check_equal(c(loglik(fm1), loglik(fm2), loglik(fm3)),
  + 	c(-159.305417842699, -145.527968416625, -145.414961863022),
  + 	label = "Poisson change-point logLik")
  > check_equal(c(BIC(fm1), BIC(fm2), BIC(fm3)),
  + 	c(323.216005871386, 314.081787763190, 341.486795771914),
  + 	label = "Poisson change-point BIC")
  > 
  > dt <- data.frame(y1 = c(0, 1, 1, 2, 4, 5),
  + 	y2 = c(1, 0, 1, 0, 1, 0),
  + 	y3 = c(4, 4, 3, 2, 1, 1))
  > m2 <- mix(cbind(y1, y2, y3) ~ 1, data = dt, ns = 2,
  + 	family = multinomial("identity"))
  > set.seed(1)
  > fm2 <- quiet(fit(m2, verbose = FALSE))
  > dm2 <- depmix(cbind(y1, y2, y3) ~ 1, data = dt, ns = 2,
  + 	family = multinomial("identity"))
  > set.seed(1)
  > fdm2 <- quiet(fit(dm2, verbose = FALSE))
  > check_equal(c(loglik(fm2), loglik(fdm2)),
  + 	c(-15.522894709188, -13.547386015719),
  + 	label = "multicolumn multinomial logLik")
  > 
  > data(speed)
  > speed[2, 1] <- NA
  > speed[3, 2] <- NA
  > mod1ms <- depmix(list(rt ~ 1, corr ~ 1), data = speed, transition = ~Pacc,
  + 	nstates = 2, family = list(gaussian(), multinomial("identity")),
  + 	ntimes = c(168, 134, 137))
  > set.seed(3)
  > fmod1ms <- suppressWarnings(quiet(fit(mod1ms, verbose = FALSE)))
  > check_equal(loglik(fmod1ms), -247.430638392413,
  + 	label = "missing-data fit logLik")
  > 
  > data(speed)
  > mod1 <- depmix(list(rt ~ 1, corr ~ 1), data = speed, transition = ~Pacc,
  + 	nstates = 2, family = list(gaussian(), multinomial("identity")),
  + 	ntimes = c(168, 134, 137))
  > set.seed(3)
  > fmod1 <- quiet(fit(mod1, verbose = FALSE))
  > pars <- c(unlist(getpars(fmod1)))
  > pars[1] <- 0
  > pars[2] <- 1
  > pars[13] <- 0.5
  > pars[14] <- 0.5
  > mod2 <- setpars(mod1, pars)
  > free <- c(0, 0, rep(c(0, 1), 4), 1, 1, 0, 0, 1, 1, 1, 1)
  > fmod2 <- quiet(fit(mod2, fixed = !free, verbose = FALSE))
  Warning message:
  In p0 * vscale[(neq + 2):(nc + np + 1)] :
    longer object length is not a multiple of shorter object length
  > pars <- c(unlist(getpars(fmod2)))
  > pars[4] <- pars[8] <- -4
  > pars[6] <- pars[10] <- 10
  > mod3 <- setpars(mod2, pars)
  > conpat <- c(0, 0, rep(c(0, 1), 4), 1, 1, 0, 0, 1, 1, 1, 1)
  > conpat[4] <- conpat[8] <- 2
  > conpat[6] <- conpat[10] <- 3
  > fmod3 <- suppressWarnings(quiet(fit(mod3, equal = conpat, verbose = FALSE)))
  > conr <- matrix(0, 2, 18)
  > conr[1, 4] <- 1
  > conr[1, 8] <- -1
  > conr[2, 6] <- 1
  > conr[2, 10] <- -1
  > fmod3b <- suppressWarnings(quiet(fit(mod3, conrows = conr,
  + 	fixed = !free, verbose = FALSE)))
  > check_equal(c(loglik(fmod1), loglik(fmod2), loglik(fmod3), loglik(fmod3b)),
  + 	c(-248.972219690931, -249.212895124180,
  + 		-277.106880997915, -277.106880997915),
  + 	label = "linear-constraint fit logLik")
  Error: unexpected value linear-constraint fit logLik
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [64s/167s] OK
* checking PDF version of manual ... [11s/25s] OK
* checking HTML version of manual ... [9s/27s] 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-noLD/depmixS4.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 12:29.92, 273.76 + 15.66