Package: monolix2rx Check: tests New result: ERROR Running ‘testthat.R’ [11s/11s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(monolix2rx) > > test_check("monolix2rx") i integrated model file 'oral1_1cpt_kaVCl.txt' into mlxtran object i updating model values to final parameter estimates i done i reading run info (# obs, doses, Monolix Version, etc) from summary.txt i done i reading covariance from FisherInformation/covarianceEstimatesLin.txt i done i imported monolix and translated to rxode2 compatible data ($monolixData) i imported monolix ETAS (_SAEM) imported to rxode2 compatible data ($etaData) i imported monolix pred/ipred data to compare ($predIpredData) using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ i solving ipred problem i done i solving pred problem i done NULL i integrated model file 'oral1_noFPE_2cptP1cptM_uni_kaVkk12k21kmKpm.txt' into mlxtran object i updating model values to final parameter estimates i done i reading run info (# obs, doses, Monolix Version, etc) from summary.txt i done i reading covariance from FisherInformation/covarianceEstimatesSA.txt i done i imported monolix and translated to rxode2 compatible data ($monolixData) i imported monolix ETAS (_SAEM) imported to rxode2 compatible data ($etaData) i imported monolix pred/ipred data to compare ($predIpredData) using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ i filtering out censored observations for validation i done i solving ipred problem i done i solving pred problem i monolix and rxode2 solves have different number of rows ($monolixNotMatched) i done NULL [LONGITUDINAL] EQUATION: syntax error error: ================================================================================ :ERR: 'inftDose' Monolix declaration not supported in translation: :001: a=inftDose ================================================================================ :ERR: delay() not supported in translation: :001: ddt_x = ka*x-k*delay(x,tau) ================================================================================ :ERR: rem() not supported in translation: :001: ddt_x = ka*x-k*rem(tau) ================================================================================ :ERR: wsmm() not supported in translation: :001: f = wsmm(f1, p, f2, 1-p) ================================================================================ :ERR: bsmm() not supported in translation: :001: f = bsmm(f1, p, f2, 1-p) ================================================================================ :ERR: bsmm() not supported in translation: :001: M = bsmm(M1,p1,M2,1-p1) ================================================================================ mlxtran [INDIVIDUAL] DEFINITION syntax error: :001: F = {distribution=normal, typical=F_pop, sd=omega_F, min=0, max=1} ^ ================================================================================ mlxtran [INDIVIDUAL] DEFINITION syntax error: :001: F = {distribution=normal, mean=F_pop_2, sd=omega_F, min=0, max=1} ^ ================================================================================ mlxtran [INDIVIDUAL] DEFINITION syntax error: :001: f = {distribution=logitnormal, typical=F_pop,sd=omega_F, min=min0, max=1} ^ ================================================================================ mlxtran [INDIVIDUAL] DEFINITION syntax error: :001: f = {distribution=logitnormal, typical=F_pop,sd=omega_F, min=0, max=max1} ^ ================================================================================ i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object i updating model values to final parameter estimates i done i reading covariance from FisherInformation/covarianceEstimatesLin.txt i done i reading covariance from FisherInformation/covarianceEstimatesSA.txt i done i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object i updating model values to final parameter estimates i done i reading run info (# obs, doses, Monolix Version, etc) from summary.txt i done i reading covariance from FisherInformation/covarianceEstimatesLin.txt i done i reading covariance from FisherInformation/covarianceEstimatesSA.txt i done i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object i updating model values to final parameter estimates i done i reading run info (# obs, doses, Monolix Version, etc) from summary.txt i done i reading covariance from FisherInformation/covarianceEstimatesLin.txt i done i reading covariance from FisherInformation/covarianceEstimatesSA.txt i done i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object i updating model values to final parameter estimates i done i reading run info (# obs, doses, Monolix Version, etc) from summary.txt i done i reading covariance from FisherInformation/covarianceEstimatesLin.txt i done i reading covariance from FisherInformation/covarianceEstimatesSA.txt i done i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object i updating model values to final parameter estimates i done i reading run info (# obs, doses, Monolix Version, etc) from summary.txt i done i reading covariance from FisherInformation/covarianceEstimatesLin.txt i done i reading covariance from FisherInformation/covarianceEstimatesSA.txt i done i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object i updating model values to final parameter estimates i done i reading run info (# obs, doses, Monolix Version, etc) from summary.txt i done i reading covariance from FisherInformation/covarianceEstimatesLin.txt i done i reading covariance from FisherInformation/covarianceEstimatesSA.txt i done i integrated model file 'pk.turnover.emax3-monolix.txt' into mlxtran object [LONGITUDINAL] EQUATION: syntax error: :001: Cc = pkmodel(Tlag, ka, p, V, Vm, Km, k12, k21, k13, k31, ke0) ^ ================================================================================ [ FAIL 1 | WARN 1 | SKIP 17 | PASS 346 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • On CRAN (16): 'test-content.R:31:3', 'test-data-import.R:9:5', 'test-data-import.R:23:5', 'test-dataSettings.R:20:3', 'test-fileinfo.R:7:3', 'test-fit.R:11:3', 'test-ind-def.R:60:3', 'test-ind.R:10:3', 'test-longDef.R:45:3', 'test-longOut.R:5:3', 'test-longitudinal.R:10:3', 'test-mlxtran.R:337:5', 'test-mlxtranOp.R:15:3', 'test-parameter.R:22:3', 'test-rxsolve.R:10:3', 'test-task.R:43:3' • lixoftConnectors not available (1): 'test-lixoft.R:3:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-def2ini.R:117:3'): (code run outside of `test_that()`) ───────── Error in `vapply(seq_len(dim(.mat)[1]), function(.i) { x$label[x$neta1 == .i & x$neta2 == .i] }, character(1), USE.NAMES = FALSE)`: values must be type 'character', but FUN(X[[1]]) result is type 'integer' Backtrace: ▆ 1. └─monolix2rx:::.def2ini(indDef, pars, longDef) at test-def2ini.R:117:3 2. └─monolix2rx:::.def2iniFixOmega(.omega, .env$extraFixed) 3. ├─lotri::as.lotri(.env$df) 4. └─lotri:::as.lotri.data.frame(.env$df) 5. └─lotri:::.as.lotri.data.frame.mat(.lotriMatDf) 6. └─base::vapply(...) [ FAIL 1 | WARN 1 | SKIP 17 | PASS 346 ] Deleting unused snapshots: • data-import/multiple-endpoint-theo-p1.svg • data-import/multiple-endpoint-theo-pall.svg • data-import/single-endpoint-theo-p1.svg • data-import/single-endpoint-theo-pall.svg Error: Test failures Execution halted