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nlmixrdevelopment / nlmixr

nlmixr: an R package for population PKPD modeling
https://nlmixrdevelopment.github.io/nlmixr/
GNU General Public License v2.0
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nlmixr not working, trying to install on secondary internal drive #194

Closed JSC67 closed 5 years ago

JSC67 commented 5 years ago

Hi nlmixr development team,

I've upgraded my computer, and removed my old HD and it now serves as my hard disk drive in my new laptop. R is installed on this drive as well as my R libraries, and this is where I want nlmixr to be. (It's my F:/ drive.) Unfortunately I'm now having trouble getting nlmixr to work properly. The output is below and is fairly self-explanatory with the comments. The problem arises in compiling the model. I believe there is a conflict somehow with my RTools installations but I'm not sure what is the problem. Note that after I tried to install the latest from Github, when it didn't work I tried the latest released (in the installer for Windows) and that still isn't working.

I'd sure appreciate some help getting this to work for me as it used to on my old laptop that stopped working.

Thanks,

James

``` R version 3.6.0 (2019-04-26) -- "Planting of a Tree" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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. > getwd() [1] "F:/Users/James/Documents/R" > version _ platform x86_64-w64-mingw32 arch x86_64 os mingw32 system x86_64, mingw32 status major 3 minor 6.0 year 2019 month 04 day 26 svn rev 76424 language R version.string R version 3.6.0 (2019-04-26) nickname Planting of a Tree > .libPaths() [1] "F:/Users/James/Documents/R/win-library/3.6" [2] "F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library" > # The above output is what I want and expect. > > # Before running the test script, note that everything's working fine: RStudio gives expected output. > 2+2 [1] 4 > # Now run script. > # Copied from > # https://raw.githubusercontent.com/nlmixrdevelopment/nlmixr/master/build/test_install.R > # Below is result of sourced script. > > source('F:/Users/James/Documents/R/nlmixr test script.R') Correct R version: Yes, R version 3.6.0 (2019-04-26) RxODE installed: Yes Python installed: Yes, Python 3.7.3 sympy installed: Yes devtools package installed: Yes RxODE package installed: Yes Rtools installed or not needed: Yes SnakeCharmR package installed: Yes units package installed: Yes nlmixr package installed: Yes xpose.nlmixr package installed: Yes shinyMixR package installed: Yes Running nlme Error : Error building model > # There is an open connection that should be closed in the script. Observe: > 2+2 > # No output! > .libPaths() > # Again no output! > closeAllConnections() > # Now there's output: > 2+2 [1] 4 > .libPaths() [1] "F:/Users/James/Documents/R/win-library/3.6" [2] "F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library" > > Sys.getenv("R_LIBS_USER") [1] "F:\\Users\\James\\Documents\\R\\win-library\\3.6" > R.home() [1] "F:/Users/James/DOCUME~1/R/WIN-LI~1/3.6/NLMIXR~1.0-9/R" > # NOT RUN { > ## These result quite platform dependently : > rbind(home = R.home(), + bin = R.home("bin")) # often a sub directory of 'home' [,1] home "F:/Users/James/DOCUME~1/R/WIN-LI~1/3.6/NLMIXR~1.0-9/R" bin "F:/Users/James/DOCUME~1/R/WIN-LI~1/3.6/NLMIXR~1.0-9/R/bin/x64" > list.files(R.home("bin")) [1] "open.exe" "R.dll" "R.exe" "Rblas.dll" "Rcmd.exe" "Rfe.exe" [7] "Rgraphapp.dll" "Rgui.exe" "Riconv.dll" "Rlapack.dll" "Rscript.exe" "RSetReg.exe" [13] "Rterm.exe" > # } > # I am using the default R installation (RStudio, then Tools, Global Options...). > # Apparently this is the R installation residing within nlmixr_1.1.0-9, the latest stable released version. > # So why does the model building fail as seen with output of above testing script? > > # Will the results change if I swap the .libPaths output? > .libPaths(c(.libPaths()[2], .libPaths()[1])) > .libPaths() [1] "F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library" [2] "F:/Users/James/Documents/R/win-library/3.6" > source('F:/Users/James/Documents/R/nlmixr test script.R') Correct R version: Yes, R version 3.6.0 (2019-04-26) RxODE installed: Yes Python installed: Yes, Python 3.7.3 sympy installed: Yes devtools package installed: Yes RxODE package installed: Yes Rtools installed or not needed: Yes SnakeCharmR package installed: Yes units package installed: Yes nlmixr package installed: Yes xpose.nlmixr package installed: Yes shinyMixR package installed: Yes Running nlme Error : Error building model > # So switching the .libPaths results didn't help. > closeAllConnections() # so that RStudio's R actually returns values at the prompt > # Test 11: nlme test for theophylline > library(nlmixr) > testmod <- function() { + ini({ + tka <- .5 + tcl <- -3.2 + tv <- -1 + eta.ka ~ 1 + eta.cl ~ 2 + eta.v ~ 1 + add.err <- 0.1 + }) + model({ + ka <- exp(tka + eta.ka) + cl <- exp(tcl + eta.cl) + v <- exp(tv + eta.v) + linCmt() ~ add(add.err) + }) + } > if(Sys.info()['sysname']%in%c('Darwin','Linux')){ + message("Running nlme") + {sink("/dev/null"); fit1 <- suppressWarnings(suppressMessages(nlmixr(testmod,theo_sd,est="nlme"))); sink(); } + message("Running saem") + {sink("/dev/null"); fit2 <- suppressWarnings(suppressMessages(nlmixr(testmod,theo_sd,est="saem"))); sink(); } + message("Running focei") + {sink("/dev/null"); fit3 <- suppressWarnings(suppressMessages(nlmixr(testmod,theo_sd,est="focei"))); sink(); } + }else{ + message("Running nlme") + {sink("NUL"); fit1 <- suppressWarnings(suppressMessages(nlmixr(testmod,theo_sd,est="nlme"))); sink(); } + message("Running saem") + {sink("NUL"); fit2 <- suppressWarnings(suppressMessages(nlmixr(testmod,theo_sd,est="saem"))); sink(); } + message("Running focei") + {sink("NUL"); fit3 <- suppressWarnings(suppressMessages(nlmixr(testmod,theo_sd,est="focei"))); sink(); } + } Running nlme Error: Error building model > # This is what fails: > nlmixr(testmod,theo_sd,est="nlme") Error building model -- stdout output --------------------------------------------------------------- -- stderr output --------------------------------------------------------------- Warning message: In system(cmd) : 'make' not found -- c source -------------------------------------------------------------------- #include #define __MAX_PROD__ 0 #define _CMT CMT extern void rx_4371c56bdcc29f6e680875741a011782_x64_ode_solver_solvedata (rx_solve *solve){ _solveData = solve; } extern rx_solve *rx_4371c56bdcc29f6e680875741a011782_x64_ode_solver_get_solvedata(){ return _solveData; } SEXP rx_4371c56bdcc29f6e680875741a011782_x64_model_vars(); double _theta[3]; extern double* rx_4371c56bdcc29f6e680875741a011782_x64_theta(double *theta){ _theta[0] = theta[0]; _theta[1] = theta[1]; _theta[2] = theta[2]; return _theta; } // prj-specific differential eqns void rx_4371c56bdcc29f6e680875741a011782_x64_dydt(int *_neq, double t, double *__zzStateVar__, double *__DDtStateVar__) { int _cSub = _neq[1]; double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(t, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; ka=nlmixr_lincmt_ka; cl=nlmixr_lincmt_cl; v=nlmixr_lincmt_v; rx_ka =ka; rx_rate =0; rx_dur =0; rx_tlag =0; rx_tlag2 =0; rx_F =1; rx_F2 =1; rx_v =v; rx_k =cl/safe_zero(v); rx_alpha =rx_k; rx_A =rx_ka/safe_zero((rx_ka-rx_alpha))/safe_zero(rx_v); rx_A2 =1.0/safe_zero(rx_v); rx_beta =0; rx_B =0; rx_B2 =0; rx_gamma =0; rx_C =0; rx_C2 =0; nlmixr_lincmt_pred=solveLinB(_solveData, _cSub,t,0,rx_A,rx_A2,rx_alpha,rx_B,rx_B2,rx_beta,rx_C,rx_C2,rx_gamma,rx_ka,rx_tlag,rx_tlag2,rx_F,rx_F2,rx_rate,rx_dur); nlmixr_pred =nlmixr_lincmt_pred; (&_solveData->subjects[_cSub])->dadt_counter[0]++; } // Jacobian derived vars void rx_4371c56bdcc29f6e680875741a011782_x64_calc_jac(int *_neq, double t, double *__zzStateVar__, double *__PDStateVar__, unsigned int __NROWPD__) { int _cSub=_neq[1]; (&_solveData->subjects[_cSub])->jac_counter[0]++; } // Functional based initial conditions. void rx_4371c56bdcc29f6e680875741a011782_x64_inis(int _cSub, double *__zzStateVar__){ } // prj-specific derived vars void rx_4371c56bdcc29f6e680875741a011782_x64_calc_lhs(int _cSub, double t, double *__zzStateVar__, double *_lhs) { double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(t, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; ka=nlmixr_lincmt_ka; cl=nlmixr_lincmt_cl; v=nlmixr_lincmt_v; rx_ka =ka; rx_rate =0; rx_dur =0; rx_tlag =0; rx_tlag2 =0; rx_F =1; rx_F2 =1; rx_v =v; rx_k =cl/safe_zero(v); rx_alpha =rx_k; rx_A =rx_ka/safe_zero((rx_ka-rx_alpha))/safe_zero(rx_v); rx_A2 =1.0/safe_zero(rx_v); rx_beta =0; rx_B =0; rx_B2 =0; rx_gamma =0; rx_C =0; rx_C2 =0; nlmixr_lincmt_pred=solveLinB(_solveData, _cSub,t,0,rx_A,rx_A2,rx_alpha,rx_B,rx_B2,rx_beta,rx_C,rx_C2,rx_gamma,rx_ka,rx_tlag,rx_tlag2,rx_F,rx_F2,rx_rate,rx_dur); nlmixr_pred =nlmixr_lincmt_pred; _lhs[0]=ka; _lhs[1]=cl; _lhs[2]=v; _lhs[3]=nlmixr_lincmt_pred; _lhs[4]=nlmixr_pred; } // Functional based bioavailability double rx_4371c56bdcc29f6e680875741a011782_x64_F(int _cSub, int _cmt, double _amt, double t){ return _amt; } // Functional based absorption lag double rx_4371c56bdcc29f6e680875741a011782_x64_Lag(int _cSub, int _cmt, double t){ return t; double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(NA_REAL, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; } // Modeled zero-order rate double rx_4371c56bdcc29f6e680875741a011782_x64_Rate(int _cSub, int _cmt, double _amt, double t){ return 0.0; double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(NA_REAL, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; } // Modeled zero-order duration double rx_4371c56bdcc29f6e680875741a011782_x64_Dur(int _cSub, int _cmt, double _amt, double t){ return 0.0; } // Model Times void rx_4371c56bdcc29f6e680875741a011782_x64_mtime(int _cSub, double *_mtime){ } extern SEXP rx_4371c56bdcc29f6e680875741a011782_x64_model_vars(){ int pro=0; SEXP _mv = PROTECT(_rxGetModelLib("rx_4371c56bdcc29f6e680875741a011782_x64_model_vars"));pro++; if (!_rxIsCurrentC(_mv)){ SEXP lst = PROTECT(allocVector(VECSXP, 20));pro++; SEXP names = PROTECT(allocVector(STRSXP, 20));pro++; SEXP sNeedSort = PROTECT(allocVector(INTSXP,1));pro++; int *iNeedSort = INTEGER(sNeedSort); iNeedSort[0] = 0; SEXP sMtime = PROTECT(allocVector(INTSXP,1));pro++; int *iMtime = INTEGER(sMtime); iMtime[0] = 0; SEXP sExtraCmt = PROTECT(allocVector(INTSXP,1));pro++; int *iExtraCmt = INTEGER(sExtraCmt); iExtraCmt[0] = 2; SEXP params = PROTECT(allocVector(STRSXP, 3));pro++; SEXP lhs = PROTECT(allocVector(STRSXP, 5));pro++; SEXP state = PROTECT(allocVector(STRSXP, 0));pro++; SEXP extraState = PROTECT(allocVector(STRSXP, 0));pro++; SEXP stateRmS = PROTECT(allocVector(INTSXP, 0));pro++; SEXP timeInt = PROTECT(allocVector(INTSXP, 1));pro++; INTEGER(timeInt)[0] = 1562357352; SEXP sens = PROTECT(allocVector(STRSXP, 0));pro++; SEXP normState= PROTECT(allocVector(STRSXP, 0));pro++; SEXP fn_ini = PROTECT(allocVector(STRSXP, 0));pro++; SEXP dfdy = PROTECT(allocVector(STRSXP, 0));pro++; SEXP tran = PROTECT(allocVector(STRSXP, 20));pro++; SEXP trann = PROTECT(allocVector(STRSXP, 20));pro++; SEXP mmd5 Error: Error building model > > > > # Just trying > # https://github.com/rstudio/rstudio/issues/3563 > pkgbuild::find_rtools(debug = TRUE) > # Oops, first should test if I get output returned > 2+2 > ## Okay, fix this first. > closeAllConnections() > 2+2 [1] 4 > pkgbuild::find_rtools(debug = TRUE) Scanning R CMD config CC... cc_path: '.exe' does not exist Scanning path... Scanning registry... Found F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/Rtools for 3.5 VERSION.txt Rtools version 3.5.0.4 [1] TRUE > .Call("rs_canBuildCpp") # returns FALSE for the Github RStudio issue # 3563 [1] TRUE > pkgbuild::has_build_tools() [1] TRUE > pkgbuild::find_rtools function (debug = FALSE) { if (!debug && rtools_path_is_set()) return(!identical(rtools_path(), "")) if (!is_windows()) return(FALSE) from_config <- scan_config_for_rtools(debug) if (is_compatible(from_config)) { if (debug) cat("Found compatible gcc from R CMD config CC\n") rtools_path_set(from_config) return(TRUE) } from_path <- scan_path_for_rtools(debug) if (is_compatible(from_path)) { if (debug) cat("Found compatible gcc on path\n") rtools_path_set(from_path) return(TRUE) } if (!is.null(from_path)) { if (is.null(from_path$version)) { if (debug) cat("gcc and ls on path, assuming set up is correct\n") return(TRUE) } else { message("WARNING: Rtools ", from_path$version, " found on the path", " at ", from_path$path, " is not compatible with R ", getRversion(), ".\n\n", "Please download and install ", rtools_needed(), " from ", rtools_url, ", remove the incompatible version from your PATH.") return(invisible(FALSE)) } } registry_candidates <- scan_registry_for_rtools(debug) if (length(registry_candidates) == 0) { message("WARNING: Rtools is required to build R packages, but is not ", "currently installed.\n\n", "Please download and install ", rtools_needed(), " from ", rtools_url, ".") return(invisible(FALSE)) } from_registry <- Find(is_compatible, registry_candidates, right = TRUE) if (is.null(from_registry)) { versions <- vapply(registry_candidates, function(x) x$version, character(1)) message("WARNING: Rtools is required to build R packages, but no version ", "of Rtools compatible with R ", getRversion(), " was found. ", "(Only the following incompatible version(s) of Rtools were found:", paste(versions, collapse = ","), ")\n\n", "Please download and install ", rtools_needed(), " from ", rtools_url, ".") return(invisible(FALSE)) } installed_ver <- installed_version(from_registry$path, debug = debug) if (is.null(installed_ver)) { message("WARNING: Rtools is required to build R packages, but the ", "version of Rtools previously installed in ", from_registry$path, " has been deleted.\n\n", "Please download and install ", rtools_needed(), " from ", rtools_url, ".") return(invisible(FALSE)) } if (installed_ver != from_registry$version) { message("WARNING: Rtools is required to build R packages, but no version ", "of Rtools compatible with R ", getRversion(), " was found. ", "Rtools ", from_registry$version, " was previously installed in ", from_registry$path, " but now that directory contains Rtools ", installed_ver, ".\n\n", "Please download and install ", rtools_needed(), " from ", rtools_url, ".") return(invisible(FALSE)) } rtools_path_set(from_registry) TRUE } > pkgbuild::find_rtools(debug = TRUE) Scanning R CMD config CC... cc_path: '.exe' does not exist Scanning path... Scanning registry... Found F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/Rtools for 3.5 VERSION.txt Rtools version 3.5.0.4 [1] TRUE > # same as before > > > devtools::session_info() - Session info --------------------------------------------------------------------------------------------- setting value version R version 3.6.0 (2019-04-26) os Windows 10 x64 system x86_64, mingw32 ui RStudio language (EN) collate English_United States.1252 ctype English_United States.1252 tz America/New_York date 2019-07-05 - Packages ------------------------------------------------------------------------------------------------- ! package * version date lib source P assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.0) backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0) P brew 1.0-6 2011-04-13 [2] CRAN (R 3.6.0) callr 3.2.0 2019-03-15 [1] CRAN (R 3.6.0) P cli 1.1.0 2019-03-19 [2] CRAN (R 3.6.0) P colorspace 1.4-1 2019-03-18 [2] CRAN (R 3.6.0) P crayon 1.3.4 2017-09-16 [2] CRAN (R 3.6.0) desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) devtools 2.0.2 2019-04-08 [1] CRAN (R 3.6.0) VP digest 0.6.20 2019-05-20 [2] CRAN (R 3.6.0) P dparser 0.1.8 2017-11-13 [2] CRAN (R 3.6.0) VP dplyr 0.8.3 2019-05-14 [2] CRAN (R 3.6.0) P farver 1.1.0 2018-11-20 [2] CRAN (R 3.6.0) fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0) P generics 0.0.2 2018-11-29 [2] CRAN (R 3.6.0) P ggforce 0.2.2 2019-04-23 [2] CRAN (R 3.6.0) VP ggplot2 3.2.0 2019-04-07 [2] CRAN (R 3.6.0) P glue 1.3.1 2019-03-12 [2] CRAN (R 3.6.0) P gtable 0.3.0 2019-03-25 [2] CRAN (R 3.6.0) VP huxtable 4.6.0 2019-03-19 [2] CRAN (R 3.6.0) P knitr 1.23 2019-05-18 [2] CRAN (R 3.6.0) lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.0) P lazyeval 0.2.2 2019-03-15 [2] CRAN (R 3.6.0) P lbfgs 1.2.1 2014-08-31 [2] CRAN (R 3.6.0) P lotri 0.1.1 2019-05-14 [2] CRAN (R 3.6.0) P magrittr 1.5 2014-11-22 [2] CRAN (R 3.6.0) MASS 7.3-51.4 2019-03-31 [1] CRAN (R 3.6.0) P memoise 1.1.0 2017-04-21 [2] CRAN (R 3.6.0) P munsell 0.5.0 2018-06-12 [2] CRAN (R 3.6.0) P mvnfast 0.2.5 2018-01-31 [2] CRAN (R 3.6.0) P n1qn1 6.0.1-3 2018-09-17 [2] CRAN (R 3.6.0) nlme 3.1-139 2019-04-09 [1] CRAN (R 3.6.0) nlmixr * 1.1.0-9 2019-05-31 [1] CRAN (R 3.6.0) VP pillar 1.4.2 2019-05-28 [2] CRAN (R 3.6.0) pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.6.0) P pkgconfig 2.0.2 2018-08-16 [2] CRAN (R 3.6.0) pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0) P polyclip 1.10-0 2019-03-14 [2] CRAN (R 3.6.0) P PreciseSums 0.3 2018-04-12 [2] CRAN (R 3.6.0) prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0) processx 3.3.1 2019-05-08 [1] CRAN (R 3.6.0) ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0) P purrr 0.3.2 2019-03-15 [2] CRAN (R 3.6.0) P R6 2.4.0 2019-02-14 [2] CRAN (R 3.6.0) P Rcpp 1.0.1 2019-03-17 [2] CRAN (R 3.6.0) VP RcppArmadillo 0.9.500.2.0 2019-05-11 [2] CRAN (R 3.6.0) remotes 2.0.4 2019-04-10 [1] CRAN (R 3.6.0) P rex 1.1.2 2017-10-19 [2] CRAN (R 3.6.0) VP rlang 0.4.0 2019-04-07 [2] CRAN (R 3.6.0) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) rsconnect 0.8.13 2019-01-10 [1] CRAN (R 3.6.0) P rstudioapi 0.10 2019-03-19 [2] CRAN (R 3.6.0) VP RxODE * 0.9.0-9 2019-05-30 [2] CRAN (R 3.6.0) P scales 1.0.0 2018-08-09 [2] CRAN (R 3.6.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) P sys 3.2 2019-04-23 [2] CRAN (R 3.6.0) testthat 2.1.1 2019-04-23 [1] CRAN (R 3.6.0) VP tibble 2.1.3 2019-03-16 [2] CRAN (R 3.6.0) P tidyselect 0.2.5 2018-10-11 [2] CRAN (R 3.6.0) P tweenr 1.0.1 2018-12-14 [2] CRAN (R 3.6.0) P units 0.6-3 2019-05-03 [2] CRAN (R 3.6.0) usethis 1.5.0 2019-04-07 [1] CRAN (R 3.6.0) P vpc 1.1.0 2018-08-27 [2] CRAN (R 3.6.0) withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) VP xfun 0.8 2019-05-14 [2] CRAN (R 3.6.0) [1] F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library [2] F:/Users/James/Documents/R/win-library/3.6 V -- Loaded and on-disk version mismatch. P -- Loaded and on-disk path mismatch. > > > # What would I get if I didn't switch the .libPaths() results? > .libPaths(c(.libPaths()[2], .libPaths()[1])) > devtools::session_info() - Session info --------------------------------------------------------------------------------------------- setting value version R version 3.6.0 (2019-04-26) os Windows 10 x64 system x86_64, mingw32 ui RStudio language (EN) collate English_United States.1252 ctype English_United States.1252 tz America/New_York date 2019-07-05 - Packages ------------------------------------------------------------------------------------------------- ! package * version date lib source assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) P backports 1.1.4 2019-04-10 [2] CRAN (R 3.6.0) brew 1.0-6 2011-04-13 [1] CRAN (R 3.5.0) VP callr 3.2.0 2019-07-04 [2] CRAN (R 3.6.0) cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0) colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0) crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1) P desc 1.2.0 2018-05-01 [2] CRAN (R 3.6.0) P devtools 2.0.2 2019-04-08 [2] CRAN (R 3.6.0) digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0) dparser 0.1.8 2017-11-13 [1] CRAN (R 3.5.1) dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.0) farver 1.1.0 2018-11-20 [1] CRAN (R 3.6.0) P fs 1.3.1 2019-05-06 [2] CRAN (R 3.6.0) generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.0) ggforce 0.2.2 2019-04-23 [1] CRAN (R 3.6.0) ggplot2 3.2.0 2019-06-16 [1] CRAN (R 3.6.0) glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) huxtable 4.6.0 2019-06-24 [1] CRAN (R 3.6.0) knitr 1.23 2019-05-18 [1] CRAN (R 3.6.0) lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.0) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0) lbfgs 1.2.1 2014-08-31 [1] CRAN (R 3.5.1) lotri 0.1.1 2019-05-14 [1] CRAN (R 3.6.0) magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.1) MASS 7.3-51.4 2019-03-31 [2] CRAN (R 3.6.0) memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.1) munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.1) mvnfast 0.2.5 2018-01-31 [1] CRAN (R 3.5.1) n1qn1 6.0.1-3 2018-09-17 [1] CRAN (R 3.5.1) nlme 3.1-139 2019-04-09 [2] CRAN (R 3.6.0) nlmixr * 1.1.0-9 2019-05-31 [2] CRAN (R 3.6.0) pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0) P pkgbuild 1.0.3 2019-03-20 [2] CRAN (R 3.6.0) pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.1) P pkgload 1.0.2 2018-10-29 [2] CRAN (R 3.6.0) polyclip 1.10-0 2019-03-14 [1] CRAN (R 3.6.0) PreciseSums 0.3 2018-04-12 [1] CRAN (R 3.5.1) P prettyunits 1.0.2 2015-07-13 [2] CRAN (R 3.5.1) VP processx 3.3.1 2019-07-03 [2] CRAN (R 3.6.0) P ps 1.3.0 2018-12-21 [2] CRAN (R 3.6.0) purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.0) R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0) Rcpp 1.0.1 2019-03-17 [1] CRAN (R 3.6.0) RcppArmadillo 0.9.500.2.0 2019-06-12 [1] CRAN (R 3.6.0) VP remotes 2.0.4 2019-06-24 [2] CRAN (R 3.6.0) rex 1.1.2 2017-10-19 [1] CRAN (R 3.5.1) rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0) P rprojroot 1.3-2 2018-01-03 [2] CRAN (R 3.5.1) rsconnect 0.8.13 2019-01-10 [2] CRAN (R 3.6.0) rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.0) RxODE * 0.9.0-9 2019-07-04 [1] Github (nlmixrdevelopment/RxODE@72cf4a8) scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.1) P sessioninfo 1.1.1 2018-11-05 [2] CRAN (R 3.6.0) sys 3.2 2019-04-23 [1] CRAN (R 3.6.0) P testthat 2.1.1 2019-04-23 [2] CRAN (R 3.6.0) tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.1) tweenr 1.0.1 2018-12-14 [1] CRAN (R 3.6.0) units 0.6-3 2019-05-03 [1] CRAN (R 3.6.0) VP usethis 1.5.0 2019-07-04 [2] CRAN (R 3.6.0) vpc 1.1.0 2018-08-27 [1] CRAN (R 3.5.1) P withr 2.1.2 2018-03-15 [2] CRAN (R 3.5.1) xfun 0.8 2019-06-25 [1] CRAN (R 3.6.0) [1] F:/Users/James/Documents/R/win-library/3.6 [2] F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library V -- Loaded and on-disk version mismatch. P -- Loaded and on-disk path mismatch. > > > # Following a suggestion in nlmixr Readme: > .libPaths(.libPaths()[regexpr("nlmixr",.libPaths())!=-1]) > .libPaths() # testing it [1] "F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library" > > devtools::session_info() - Session info --------------------------------------------------------------------------------------------- setting value version R version 3.6.0 (2019-04-26) os Windows 10 x64 system x86_64, mingw32 ui RStudio language (EN) collate English_United States.1252 ctype English_United States.1252 tz America/New_York date 2019-07-05 - Packages ------------------------------------------------------------------------------------------------- ! package * version date lib source P assertthat 0.2.1 2019-03-21 [?] CRAN (R 3.6.0) backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0) P brew 1.0-6 2011-04-13 [?] CRAN (R 3.6.0) callr 3.2.0 2019-03-15 [1] CRAN (R 3.6.0) P cli 1.1.0 2019-03-19 [?] CRAN (R 3.6.0) P colorspace 1.4-1 2019-03-18 [?] CRAN (R 3.6.0) P crayon 1.3.4 2017-09-16 [?] CRAN (R 3.6.0) desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0) devtools 2.0.2 2019-04-08 [1] CRAN (R 3.6.0) VP digest 0.6.20 2019-05-20 [?] CRAN (R 3.6.0) P dparser 0.1.8 2017-11-13 [?] CRAN (R 3.6.0) VP dplyr 0.8.3 2019-05-14 [?] CRAN (R 3.6.0) P farver 1.1.0 2018-11-20 [?] CRAN (R 3.6.0) fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0) P generics 0.0.2 2018-11-29 [?] CRAN (R 3.6.0) P ggforce 0.2.2 2019-04-23 [?] CRAN (R 3.6.0) VP ggplot2 3.2.0 2019-04-07 [?] CRAN (R 3.6.0) P glue 1.3.1 2019-03-12 [?] CRAN (R 3.6.0) P gtable 0.3.0 2019-03-25 [?] CRAN (R 3.6.0) VP huxtable 4.6.0 2019-03-19 [?] CRAN (R 3.6.0) P knitr 1.23 2019-05-18 [?] CRAN (R 3.6.0) lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.0) P lazyeval 0.2.2 2019-03-15 [?] CRAN (R 3.6.0) P lbfgs 1.2.1 2014-08-31 [?] CRAN (R 3.6.0) P lotri 0.1.1 2019-05-14 [?] CRAN (R 3.6.0) P magrittr 1.5 2014-11-22 [?] CRAN (R 3.6.0) MASS 7.3-51.4 2019-03-31 [1] CRAN (R 3.6.0) P memoise 1.1.0 2017-04-21 [?] CRAN (R 3.6.0) P munsell 0.5.0 2018-06-12 [?] CRAN (R 3.6.0) P mvnfast 0.2.5 2018-01-31 [?] CRAN (R 3.6.0) P n1qn1 6.0.1-3 2018-09-17 [?] CRAN (R 3.6.0) nlme 3.1-139 2019-04-09 [1] CRAN (R 3.6.0) nlmixr * 1.1.0-9 2019-05-31 [1] CRAN (R 3.6.0) VP pillar 1.4.2 2019-05-28 [?] CRAN (R 3.6.0) pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.6.0) P pkgconfig 2.0.2 2018-08-16 [?] CRAN (R 3.6.0) pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0) P polyclip 1.10-0 2019-03-14 [?] CRAN (R 3.6.0) P PreciseSums 0.3 2018-04-12 [?] CRAN (R 3.6.0) prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0) processx 3.3.1 2019-05-08 [1] CRAN (R 3.6.0) ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0) P purrr 0.3.2 2019-03-15 [?] CRAN (R 3.6.0) P R6 2.4.0 2019-02-14 [?] CRAN (R 3.6.0) P Rcpp 1.0.1 2019-03-17 [?] CRAN (R 3.6.0) VP RcppArmadillo 0.9.500.2.0 2019-05-11 [?] CRAN (R 3.6.0) remotes 2.0.4 2019-04-10 [1] CRAN (R 3.6.0) P rex 1.1.2 2017-10-19 [?] CRAN (R 3.6.0) VP rlang 0.4.0 2019-04-07 [?] CRAN (R 3.6.0) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0) rsconnect 0.8.13 2019-01-10 [1] CRAN (R 3.6.0) P rstudioapi 0.10 2019-03-19 [?] CRAN (R 3.6.0) VP RxODE * 0.9.0-9 2019-05-30 [?] CRAN (R 3.6.0) P scales 1.0.0 2018-08-09 [?] CRAN (R 3.6.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) P sys 3.2 2019-04-23 [?] CRAN (R 3.6.0) testthat 2.1.1 2019-04-23 [1] CRAN (R 3.6.0) VP tibble 2.1.3 2019-03-16 [?] CRAN (R 3.6.0) P tidyselect 0.2.5 2018-10-11 [?] CRAN (R 3.6.0) P tweenr 1.0.1 2018-12-14 [?] CRAN (R 3.6.0) P units 0.6-3 2019-05-03 [?] CRAN (R 3.6.0) usethis 1.5.0 2019-04-07 [1] CRAN (R 3.6.0) P vpc 1.1.0 2018-08-27 [?] CRAN (R 3.6.0) withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) VP xfun 0.8 2019-05-14 [?] CRAN (R 3.6.0) [1] F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library V -- Loaded and on-disk version mismatch. P -- Loaded and on-disk path mismatch. > > # Really not sure what to do next. > > > # Now many of the rows in the lib column have [?] as an entry; not an improvement I reckon. > > # Back to https://github.com/rstudio/rstudio/issues/3563 > nzchar(Sys.which("ls.exe")) && nzchar(Sys.which("gcc.exe")) [1] FALSE > writeLines(strsplit(Sys.getenv("PATH"), ";")[[1]]) F:\Users\James\DOCUME~1\R\WIN-LI~1\3.6\NLMIXR~1.0-9\R\rxPython F:\RTools\mingw_64\bin F:\RTools\mingw_64\opt\bin F:\Users\James\DOCUME~1\R\WIN-LI~1\3.6\NLMIXR~1.0-9\R\bin\x64 F:\PROGRA~3\ANACON~3 F:\PROGRA~3\ANACON~3\Library\MINGW-~1\bin F:\PROGRA~3\ANACON~3\Library\bin F:\PROGRA~3\ANACON~3\Scripts C:\Windows\System32 C:\Windows C:\Windows\System32\wbem C:\PROGRA~2\Intel\INTEL(~1\DAL C:\PROGRA~1\Intel\INTEL(~2\DAL C:\PROGRA~2\Intel\INTEL(~1\IPT C:\PROGRA~1\Intel\INTEL(~2\IPT F:\PROGRA~1\MATLAB\R2019a\bin C:\Users\User\AppData\Local\MICROS~1\WINDOW~1 > # Just trying again... > detach("package:nlmixr", unload = TRUE) > library(nlmixr) Registered S3 method overwritten by 'nlmixr': method from augPred.nlmixrFitData > nlmixr(testmod,theo_sd,est="nlme") # this is the line where things fail Error building model -- stdout output --------------------------------------------------------------- -- stderr output --------------------------------------------------------------- Warning message: In system(cmd) : 'make' not found -- c source -------------------------------------------------------------------- #include #define __MAX_PROD__ 0 #define _CMT CMT extern void rx_4371c56bdcc29f6e680875741a011782_x64_ode_solver_solvedata (rx_solve *solve){ _solveData = solve; } extern rx_solve *rx_4371c56bdcc29f6e680875741a011782_x64_ode_solver_get_solvedata(){ return _solveData; } SEXP rx_4371c56bdcc29f6e680875741a011782_x64_model_vars(); double _theta[3]; extern double* rx_4371c56bdcc29f6e680875741a011782_x64_theta(double *theta){ _theta[0] = theta[0]; _theta[1] = theta[1]; _theta[2] = theta[2]; return _theta; } // prj-specific differential eqns void rx_4371c56bdcc29f6e680875741a011782_x64_dydt(int *_neq, double t, double *__zzStateVar__, double *__DDtStateVar__) { int _cSub = _neq[1]; double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(t, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; ka=nlmixr_lincmt_ka; cl=nlmixr_lincmt_cl; v=nlmixr_lincmt_v; rx_ka =ka; rx_rate =0; rx_dur =0; rx_tlag =0; rx_tlag2 =0; rx_F =1; rx_F2 =1; rx_v =v; rx_k =cl/safe_zero(v); rx_alpha =rx_k; rx_A =rx_ka/safe_zero((rx_ka-rx_alpha))/safe_zero(rx_v); rx_A2 =1.0/safe_zero(rx_v); rx_beta =0; rx_B =0; rx_B2 =0; rx_gamma =0; rx_C =0; rx_C2 =0; nlmixr_lincmt_pred=solveLinB(_solveData, _cSub,t,0,rx_A,rx_A2,rx_alpha,rx_B,rx_B2,rx_beta,rx_C,rx_C2,rx_gamma,rx_ka,rx_tlag,rx_tlag2,rx_F,rx_F2,rx_rate,rx_dur); nlmixr_pred =nlmixr_lincmt_pred; (&_solveData->subjects[_cSub])->dadt_counter[0]++; } // Jacobian derived vars void rx_4371c56bdcc29f6e680875741a011782_x64_calc_jac(int *_neq, double t, double *__zzStateVar__, double *__PDStateVar__, unsigned int __NROWPD__) { int _cSub=_neq[1]; (&_solveData->subjects[_cSub])->jac_counter[0]++; } // Functional based initial conditions. void rx_4371c56bdcc29f6e680875741a011782_x64_inis(int _cSub, double *__zzStateVar__){ } // prj-specific derived vars void rx_4371c56bdcc29f6e680875741a011782_x64_calc_lhs(int _cSub, double t, double *__zzStateVar__, double *_lhs) { double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(t, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; ka=nlmixr_lincmt_ka; cl=nlmixr_lincmt_cl; v=nlmixr_lincmt_v; rx_ka =ka; rx_rate =0; rx_dur =0; rx_tlag =0; rx_tlag2 =0; rx_F =1; rx_F2 =1; rx_v =v; rx_k =cl/safe_zero(v); rx_alpha =rx_k; rx_A =rx_ka/safe_zero((rx_ka-rx_alpha))/safe_zero(rx_v); rx_A2 =1.0/safe_zero(rx_v); rx_beta =0; rx_B =0; rx_B2 =0; rx_gamma =0; rx_C =0; rx_C2 =0; nlmixr_lincmt_pred=solveLinB(_solveData, _cSub,t,0,rx_A,rx_A2,rx_alpha,rx_B,rx_B2,rx_beta,rx_C,rx_C2,rx_gamma,rx_ka,rx_tlag,rx_tlag2,rx_F,rx_F2,rx_rate,rx_dur); nlmixr_pred =nlmixr_lincmt_pred; _lhs[0]=ka; _lhs[1]=cl; _lhs[2]=v; _lhs[3]=nlmixr_lincmt_pred; _lhs[4]=nlmixr_pred; } // Functional based bioavailability double rx_4371c56bdcc29f6e680875741a011782_x64_F(int _cSub, int _cmt, double _amt, double t){ return _amt; } // Functional based absorption lag double rx_4371c56bdcc29f6e680875741a011782_x64_Lag(int _cSub, int _cmt, double t){ return t; double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(NA_REAL, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; } // Modeled zero-order rate double rx_4371c56bdcc29f6e680875741a011782_x64_Rate(int _cSub, int _cmt, double _amt, double t){ return 0.0; double ka, nlmixr_lincmt_ka, cl, nlmixr_lincmt_cl, v, nlmixr_lincmt_v, rx_ka, rx_rate, rx_dur, rx_tlag, rx_tlag2, rx_F, rx_F2, rx_v, rx_k, rx_alpha, rx_A, rx_A2, rx_beta, rx_B, rx_B2, rx_gamma, rx_C, rx_C2, nlmixr_lincmt_pred, nlmixr_pred; (void)t; (void)ka; (void)nlmixr_lincmt_ka; (void)cl; (void)nlmixr_lincmt_cl; (void)v; (void)nlmixr_lincmt_v; (void)rx_ka; (void)rx_rate; (void)rx_dur; (void)rx_tlag; (void)rx_tlag2; (void)rx_F; (void)rx_F2; (void)rx_v; (void)rx_k; (void)rx_alpha; (void)rx_A; (void)rx_A2; (void)rx_beta; (void)rx_B; (void)rx_B2; (void)rx_gamma; (void)rx_C; (void)rx_C2; (void)nlmixr_lincmt_pred; (void)nlmixr_pred; _update_par_ptr(NA_REAL, _cSub, _solveData, _idx); nlmixr_lincmt_ka = _PP[0]; nlmixr_lincmt_cl = _PP[1]; nlmixr_lincmt_v = _PP[2]; } // Modeled zero-order duration double rx_4371c56bdcc29f6e680875741a011782_x64_Dur(int _cSub, int _cmt, double _amt, double t){ return 0.0; } // Model Times void rx_4371c56bdcc29f6e680875741a011782_x64_mtime(int _cSub, double *_mtime){ } extern SEXP rx_4371c56bdcc29f6e680875741a011782_x64_model_vars(){ int pro=0; SEXP _mv = PROTECT(_rxGetModelLib("rx_4371c56bdcc29f6e680875741a011782_x64_model_vars"));pro++; if (!_rxIsCurrentC(_mv)){ SEXP lst = PROTECT(allocVector(VECSXP, 20));pro++; SEXP names = PROTECT(allocVector(STRSXP, 20));pro++; SEXP sNeedSort = PROTECT(allocVector(INTSXP,1));pro++; int *iNeedSort = INTEGER(sNeedSort); iNeedSort[0] = 0; SEXP sMtime = PROTECT(allocVector(INTSXP,1));pro++; int *iMtime = INTEGER(sMtime); iMtime[0] = 0; SEXP sExtraCmt = PROTECT(allocVector(INTSXP,1));pro++; int *iExtraCmt = INTEGER(sExtraCmt); iExtraCmt[0] = 2; SEXP params = PROTECT(allocVector(STRSXP, 3));pro++; SEXP lhs = PROTECT(allocVector(STRSXP, 5));pro++; SEXP state = PROTECT(allocVector(STRSXP, 0));pro++; SEXP extraState = PROTECT(allocVector(STRSXP, 0));pro++; SEXP stateRmS = PROTECT(allocVector(INTSXP, 0));pro++; SEXP timeInt = PROTECT(allocVector(INTSXP, 1));pro++; INTEGER(timeInt)[0] = 1562357352; SEXP sens = PROTECT(allocVector(STRSXP, 0));pro++; SEXP normState= PROTECT(allocVector(STRSXP, 0));pro++; SEXP fn_ini = PROTECT(allocVector(STRSXP, 0));pro++; SEXP dfdy = PROTECT(allocVector(STRSXP, 0));pro++; SEXP tran = PROTECT(allocVector(STRSXP, 20));pro++; SEXP trann = PROTECT(allocVector(STRSXP, 20));pro++; SEXP mmd5 Error: Error building model > ```
mattfidler commented 5 years ago

The current problem is it cannot locate make;

Since nlmixr installer includes Rtools I suggest trying to rename c:\RTools to c:\Rtools.old and see if everything runs correctly. It seems that there is some collision between the two Rtools.

mattfidler commented 5 years ago

If you are using nlmixr R as your base R and then adding components to it, you will not need another Rtools. At the same time, to setup the paths you will need to include:

library(RxODE)

To use the rtools included in nlmixr.

JSC67 commented 5 years ago

Thanks, Matt. I appreciate your timely response. I'll look more closely later exactly what the conflict was to learn something about it, but for now the nlmixr test seems to be (mostly) working. Below is the output; there are LSODA errors when running FOCEI and if you can comment on them that would be great, but certainly this is progress.


R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(RxODE)
> library(nlmixr, lib.loc = "F:/Users/James/Documents/R/win-library/3.6/nlmixr_1.1.0-9/R/library")
> source('F:/Users/James/Documents/R/nlmixr test script.R')
Correct R version: Yes, R version 3.6.0 (2019-04-26)
RxODE installed: Yes
Python installed: Yes, Python 3.7.3
sympy installed: Yes
devtools package installed: Yes
RxODE package installed: Yes
Rtools installed or not needed: Yes
SnakeCharmR package installed: Yes
units package installed: Yes
nlmixr package installed: Yes
xpose.nlmixr package installed: Yes
shinyMixR package installed: Yes
Running nlme
Running saem
Running focei
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.64791e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.70873e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.37343e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.48903e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.32952e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.05262e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.70873e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.37343e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.48903e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.32952e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.05262e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.20165e-013, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.13687e-013, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.79995e-013, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
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unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 6.75737e-013, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.51099e-012, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.77819e-012, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.13687e-013, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.79995e-013, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 6.75737e-013, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.51099e-012, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.77819e-012, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.2258e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.17982e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.87633e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 6.8932e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.4832e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.22842e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.17982e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.87633e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 6.8932e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.4832e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)¼K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.22842e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.40407e-016, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.83166e-016, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.39269e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.47659e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.53782e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)È·R±ó?Þ©ª
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.75121e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.83166e-016, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.39269e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.47659e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
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unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.53782e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.75121e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.09552e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.28297e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.29512e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.30308e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.25705e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.25705e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.28297e-009, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.29512e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.30308e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.25705e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.25705e-008, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.38746e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.24558e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.54982e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.34257e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.00199e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 9.48888e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.24558e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.54982e-011, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.34257e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 3.00199e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)Èdڐø¿-É©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 9.48888e-010, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.30722e-021, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.3246e-021, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.13379e-021, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.35104e-021, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.64374e-020, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.19797e-020, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.3246e-021, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.13379e-021, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)Èdڐø¿-É©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 7.35104e-021, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.64374e-020, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)-€—0ÚÊ¿:-½©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.19797e-020, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)Èdڐø¿-É©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.50447e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.67537e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.75756e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)Èdڐø¿-É©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.46027e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.89177e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.98231e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.67537e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.75756e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.46027e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)-€—0ÚÊ¿:-½©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.89177e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.98231e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.49853e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.6648e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.73876e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.42683e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.8843e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.95867e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.6648e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.73876e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.42683e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.8843e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.95867e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)È·R±ó?Þ©ª
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.49491e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.65837e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.72732e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.4065e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))È·R±ó?Þ©ª
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.87975e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.94429e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.65837e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.72732e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.4065e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897))
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.87975e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.94429e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.50515e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.67657e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.75969e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.46406e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)Èdڐø¿-É©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.89262e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.985e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)7)€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.67657e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)È·R±ó?Þ©ª
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.75969e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.46406e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.89262e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)Èdڐø¿-É©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.985e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)7)K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.50447e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.67537e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.75756e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.46027e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.89177e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.98231e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.67537e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.75756e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
OÙ â?à-s©97)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.46027e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.89177e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.98231e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.49777e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)K”oõ?¦-1©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.66346e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.73638e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)ªæ•âz?--¨©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.42261e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.88335e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.95568e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)dll
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 2.66346e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
‰MÔÂó?œ-'©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 4.73638e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 8.42261e-015, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)€8ï8üõ¿Ì*—©
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 1.88335e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)àiÝ‚ßæ?
unhandled error message: EE:lsoda -- at t = 0 and step size _C(h) = 5.95568e-014, the
         corrector convergence failed repeatedly or
         with fabs(_C(h)) = hmin
 @(lsoda.c:897)
nlmixr run under nlme: Yes
nlmixr run under saem: Yes
nlmixr run under focei: Yes
---- Installation test finished! ----
Begin Session Info:
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] nlmixr_1.1.0-9 RxODE_0.9.0-9 

loaded via a namespace (and not attached):
 [1] reticulate_1.12           tidyselect_0.2.5          xfun_0.8                  purrr_0.3.2              
 [5] lattice_0.20-38           colorspace_1.4-1          generics_0.0.2            vpc_1.1.0                
 [9] rlang_0.4.0               huxtable_4.6.0            pillar_1.4.2              glue_1.3.1               
[13] tweenr_1.0.1              stringr_1.4.0             munsell_0.5.0             n1qn1_6.0.1-3            
[17] gtable_0.3.0              mvnfast_0.2.5             memoise_1.1.0             knitr_1.23               
[21] RcppArmadillo_0.9.500.2.0 rex_1.1.2                 parallel_3.6.0            sys_3.2                  
[25] Rcpp_1.0.1                scales_1.0.0              jsonlite_1.6              farver_1.1.0             
[29] brew_1.0-6                ggforce_0.2.2             ggplot2_3.2.0             digest_0.6.20            
[33] lotri_0.1.1               stringi_1.4.3             dplyr_0.8.3               lbfgs_1.2.1              
[37] polyclip_1.10-0           grid_3.6.0                tools_3.6.0               magrittr_1.5             
[41] dparser_0.1.8             lazyeval_0.2.2            tibble_2.1.3              PreciseSums_0.3          
[45] crayon_1.3.4              pkgconfig_2.0.2           MASS_7.3-51.4             Matrix_1.2-17            
[49] rsconnect_0.8.13          assertthat_0.2.1          rstudioapi_0.10           R6_2.4.0                 
[53] units_0.6-3               nlme_3.1-140              compiler_3.6.0           

>
mattfidler commented 5 years ago

The LSODA errors are because we haven't updated the test script to reflect the change of doses to not be amt*weight. This should be updated.

JSC67 commented 5 years ago

Well I guess I can close this now, but it sounds as if another issue should be opened (if it's not already) regarding the test script.