R Under development (unstable) (2024-09-20 r87184 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(babelmixr2) Loading required package: nlmixr2 Loading required package: nlmixr2data > > test_check("babelmixr2") i parameter labels from comments will be replaced by 'label()' i mu2 item: Rx_pow_di(WT, 2) i writing monolix files i done i run Monolix manually and rerun nlmixr() i mu2 item: Rx_pow_di(WT, 2) i leaving alone monolix files because 'monolixTest-monolix.txt' is present > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > finding duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_c7c38dbc1016e9407f0325d813e8e8ef_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 1336 > compress parHistData in nlmixr2 object, save 1624 Error : nonmem minimization not successful > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > calculate jacobian > calculate sensitivities > calculate d(f)/d(eta) > finding duplicate expressions in inner model... > optimizing duplicate expressions in inner model... > finding duplicate expressions in EBE model... > optimizing duplicate expressions in EBE model... > compiling inner model... using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_2a10b2468b49d8236b9a971bafeb64a5_x64.c:156: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition v done > finding duplicate expressions in FD model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in FD model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_bdd07d8a4ef68a791b48de68c3fe6106_x64.c:124: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition v done > compiling events FD model... using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_d0dc9398fc94cfeafe5fb57c04a215bd_x64.c:124: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition v done [====|====|====|====|====|====|====|====|====|====] 0:00:15 > compress origData in nlmixr2 object, save 27560 Updated original fit object f warning: eig_sym(): given matrix is not symmetric > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i mu2 item: Rx_pow_di(WT, 2) > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done i only exported NONMEM control stream/data i mu2 item: Rx_pow_di(WT, 2) > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i only exported NONMEM control stream/data Error in bblDatToPknca(model = env$ui, data = rawData, rxControl = rxControl) : no dosing rows (EVID = 1 or 4) detected Error : no rows in event table or input data Error in nlmixr2Est(env, ...) : Could not detect DV assignment for unit conversion using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_ae04546dcbe9f8b535daaa9564165696_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_d78944c8b410235541afdf798f9c6783_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_fe18b52362e29dd134df338aa4a6a630_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition i Ds-optimality important parameters: tcl, tv i Ds-optimality unimportant parameters: eta.cl, eta.v, add.err i Ds-optimality important parameters: tcl, tv, eta.cl i Ds-optimality unimportant parameters: eta.v, add.err i Ds-optimality important parameters: tv i Ds-optimality unimportant parameters: tcl, eta.cl, eta.v, add.err i Ds-optimality important parameters: tcl, tv i Ds-optimality unimportant parameters: eta.cl, eta.v, add.err i Ds-optimality important parameters: tcl, tv i Ds-optimality unimportant parameters: eta.cl, eta.v, add.err using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_7da82ce21f80b0ee8dc858ba397cd1fb_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_f5199c6063eea5445767b5e85257a7c0_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition i groupsize should be specified; but for now assuming 20 using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_d8ac7de274ba35b02c8fe6a3eb6b81de_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_17dcda45a7ce2b18c0d5083c9a56ce59_x64.c:119: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition i groupsize should be specified; but for now assuming 20 i assuming group size m=2 using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_0c04948eeaff4ef32380aafa8e13e821_x64.c:120: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition using C compiler: 'gcc.exe (GCC) 13.2.0' In file included from D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2_model_shared.h:3, from rx_79eda7a58bdcc2fc95dc666757038844_x64.c:120: D:\RCompile\CRANincoming\R-devel\lib\rxode2\include/rxode2.h:3: warning: "STRICT_R_HEADERS" redefined 3 | #define STRICT_R_HEADERS | : note: this is the location of the previous definition [ FAIL 0 | WARN 7 | SKIP 5 | PASS 353 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • On CRAN (5): 'test-as-nlmixr2.R:8:3', 'test-as-nlmixr2.R:66:3', 'test-bioavil-works.R:2:3', 'test-poped.R:228:7', 'test-poped.R:287:9' [ FAIL 0 | WARN 7 | SKIP 5 | PASS 353 ] > > proc.time() user system elapsed 338.26 34.65 440.10