R Under development (unstable) (2024-05-27 r86634 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 2.1.3 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) (2024-05-27 r86634 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) 13.2.0' ℹ calculate uninformed etas ℹ done rxode2 2.1.3 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) 13.2.0' → 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 27856 > saveRDS(fit, "fit.rds") > > proc.time() user system elapsed 4.93 0.82 9.28 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 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.2.0' i calculate uninformed etas i done 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 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.2.0' > compress origData in nlmixr2 object, save 7056 > compress phiM in nlmixr2 object, save 272 > compress parHistData in nlmixr2 object, save 1856 > compress saem0 in nlmixr2 object, save 20952 i change initial estimate of `covwt` to `100` > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.2.0' i calculate uninformed etas i done 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 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.2.0' > compress origData in nlmixr2 object, save 7056 > compress phiM in nlmixr2 object, save 272 > compress parHistData in nlmixr2 object, save 1856 > 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) 13.2.0' i calculate uninformed etas i done 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 using C compiler: 'gcc.exe (GCC) 13.2.0' > 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 12728 > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done i calculate uninformed etas i done 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) 13.2.0' v done > finding duplicate expressions in FD model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: 'gcc.exe (GCC) 13.2.0' v done > compiling events FD model... using C compiler: 'gcc.exe (GCC) 13.2.0' 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) 13.2.0' i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done i calculate uninformed etas i done 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 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.2.0' > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 48976 > compress parHistData in nlmixr2 object, save 14800 > compress saem0 in nlmixr2 object, save 10384 i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done 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 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 42976 > compress parHistData in nlmixr2 object, save 14344 i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.2.0' i calculate uninformed etas i done 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 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done using C compiler: 'gcc.exe (GCC) 13.2.0' > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 50168 > compress parHistData in nlmixr2 object, save 14688 i parameter labels from comments will be replaced by 'label()' > loading into symengine environment... > pruning branches (`if`/`else`) of saem model... v done > finding duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done 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 > optimizing duplicate expressions in saem predOnly model 1... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > finding duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in saem predOnly model 2... [====|====|====|====|====|====|====|====|====|====] 0:00:00 v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 3696 > compress phiM in nlmixr2 object, save 48968 > compress parHistData in nlmixr2 object, save 14664 [ FAIL 0 | WARN 1 | SKIP 0 | PASS 190 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 190 ] > ## test_check("nlmixr2est", stop_on_failure = FALSE, wrap=TRUE, > ## reporter = testthat::LocationReporter) > > proc.time() user system elapsed 113.18 7.70 156.78