R Under development (unstable) (2024-01-29 r85841 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(rxode2) rxode2 2.1.2 using 2 threads (see ?getRxThreads) no cache: create with `rxCreateCache()` > library(nlmixr2est) Loading required package: nlmixr2data > verbose_minimization <- FALSE > test_check("nlmixr2est") R Under development (unstable) (2024-01-29 r85841 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(nlmixr2est) Loading required package: nlmixr2data > rxode2::rxClean() > one.cmt <- function() { + ini({ + tka <- 0.45 + tcl <- log(c(0, 2.7, 100)) + tv <- 3.45 + eta.ka ~ 0.6 + eta.cl ~ 0.3 + eta.v ~ 0.1 + add.sd <- 0.7 + }) + model({ + ka <- exp(tka + eta.ka) + cl <- exp(tcl + eta.cl) + v <- exp(tv + eta.v) + linCmt() ~ add(add.sd) + }) + } > fit <- nlmixr(one.cmt, theo_sd, est = "saem", control = saemControl(print = 0, + nBurn = 1, nEm = 1)) ℹ parameter labels from comments are typically ignored in non-interactive mode ℹ Need to run with the source intact to parse comments → loading into symengine environment... → pruning branches (`if`/`else`) of saem model... ✔ done → finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 ✔ done using C compiler: 'gcc.exe (GCC) 12.3.0' rxode2 2.1.2 using 2 threads (see ?getRxThreads) no cache: create with `rxCreateCache()` Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 → loading into symengine environment... → pruning branches (`if`/`else`) of saem model... ✔ done → finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 → finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 → finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 ✔ done using C compiler: 'gcc.exe (GCC) 12.3.0' → Calculating residuals/tables ✔ done → compress origData in nlmixr2 object, save 5952 → compress phiM in nlmixr2 object, save 280 → compress parHistData in nlmixr2 object, save 1864 → compress saem0 in nlmixr2 object, save 27512 > saveRDS(fit, "fit.rds") > > proc.time() user system elapsed 6.06 1.26 11.92 Calculating -2LL by Gaussian quadrature (nnodes=3,nsd=1.6) [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 12.3.0' Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 > compress phiM in nlmixr2 object, save 280 > compress parHistData in nlmixr2 object, save 1640 > compress saem0 in nlmixr2 object, save 12288 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 12.3.0' Calculating covariance matrix [====|====|====|====|====|====|====|====|====|====] 0:00:00 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem predOnly model 0... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 > compress phiM in nlmixr2 object, save 280 > compress parHistData in nlmixr2 object, save 1640 > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > calculate jacobian > calculate d(f)/d(eta) [====|====|====|====|====|====|====|====|====|====] 0:00:00 > calculate d(R^2)/d(eta) [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in inner model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in inner model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling inner model... using C compiler: 'gcc.exe (GCC) 12.3.0' v done > finding duplicate expressions in FD model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: 'gcc.exe (GCC) 12.3.0' v done > compiling events FD model... using C compiler: 'gcc.exe (GCC) 12.3.0' v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 5952 i parameter labels from comments will be replaced by 'label()' using C compiler: 'gcc.exe (GCC) 12.3.0' [ FAIL 0 | WARN 0 | SKIP 0 | PASS 183 ] > ## test_check("nlmixr2est", stop_on_failure = FALSE, wrap=TRUE, > ## reporter = testthat::LocationReporter) > > proc.time() user system elapsed 26.70 6.43 64.28