Running 'testthat.R' [133s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(NMproject)
  > 
  > test_check("NMproject")
  Package: localanalysis
  Title: What the Package Does (One Line, Title Case)
  Version: 0.0.0.9000
  Authors@R (parsed):
      * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
  Description: What the package does (one paragraph).
  License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
      license
  Encoding: UTF-8
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.2.3
  Package: localanalysis
  Title: What the Package Does (One Line, Title Case)
  Version: 0.0.0.9000
  Authors@R (parsed):
      * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
  Description: What the package does (one paragraph).
  License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
      license
  Encoding: UTF-8
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.2.3
  Package: localanalysis
  Title: What the Package Does (One Line, Title Case)
  Version: 0.0.0.9000
  Authors@R (parsed):
      * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
  Description: What the package does (one paragraph).
  License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
      license
  Encoding: UTF-8
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.2.3
  Error : pandoc document conversion failed with error 127
  In addition: Warning message:
  In system(command) :
    'CreateProcess' failed to run 'C:\PROGRA~1\Pandoc\pandoc.exe +RTS -K512m -RTS README.knit.md --to gfm+tex_math_dollars-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output README.md --template "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmarkdown\templates\github_document\resources\default.md"'
  Package: localanalysis
  Title: What the Package Does (One Line, Title Case)
  Version: 0.0.0.9000
  Authors@R (parsed):
      * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
  Description: What the package does (one paragraph).
  License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
      license
  Encoding: UTF-8
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.2.3
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS s01_make_data.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output s01_make_data.html --lua-filter "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\RtmpW0X8DC\rmarkdown-str2697c19444f60.html" 
  error: patch failed: Models/base-tarjinde-2021-11-17-08-52-52:66
  error: Models/base-tarjinde-2021-11-17-08-52-52: patch does not apply
  Context reduced to (1/1) to apply fragment at 68
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS s02_model_log.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output s02_model_log.html --lua-filter "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\RtmpW0X8DC\rmarkdown-str2697c65287b06.html" 
  < old_ctl                                           
  > new_ctl                                           
  @@ 25,25 / 25,23 @@                                 
    ID AMT TIME DV WT                                 
    $DATA ../DerivedData/data.csv IGNORE=@            
  < $SUB ADVAN5                                       
  > $SUB ADVAN2                                       
  < $MODEL                                            
  < COMP = (COMP1, DEFDOSE)                           
  < COMP = (COMP2, DEFOBS)                            
  >                                                   
    $PK                                               
                                                      
  < TVK1T2=EXP(THETA(1))                              
  > TVKA=EXP(THETA(1))                                
  < MU_1=LOG(TVK1T2)                                  
  > MU_1=LOG(TVKA)                                    
  < K1T2 = EXP(MU_1+ETA(1))                           
  > KA = EXP(MU_1+ETA(1))                             
                                                      
  < TVK2T0=EXP(THETA(2))                              
  > TVK=EXP(THETA(2))                                 
  < MU_2=LOG(TVK2T0)                                  
  > MU_2=LOG(TVK)                                     
  < K2T0 = EXP(MU_2+ETA(2))                           
  > K = EXP(MU_2+ETA(2))                              
                                                      
  < TVV2=EXP(THETA(3))                                
  > TVV=EXP(THETA(3))                                 
  < MU_3=LOG(TVV2)                                    
  > MU_3=LOG(TVV)                                     
  < V2 = EXP(MU_3+ETA(3))                             
  > V = EXP(MU_3+ETA(3))                              
                                                      
  < CL = K2T0*V2                                      
  > CL = K*V                                          
                                                      
  < S2 = V2                                           
  > S2 = V                                            
                                                      
    $ERROR                                            
  @@ 55,12 / 53,13 @@                                 
    Y=IPRED + IPRED*EPS(1) + EPS(2)                   
                                                      
  >                                                   
    $THETA                                            
  < 0.5   ; K1T2 ; h-1 ; LOG                          
  > 0.5   ; KA ; h-1 ; LOG                            
  < -2.5   ; K2T0 ; h-1 ; LOG                         
  > -2.5   ; K ; h-1 ; LOG                            
  < -0.5   ; V2 ; L ; LOG                             
  > -0.5   ; V ; L ; LOG                              
    $OMEGA                                            
  < 0.1                               ; IIV_K1T2 ; LOG
  > 0.1                               ; IIV_KA ; LOG  
  < 0.1                               ; IIV_K2T0 ; LOG
  > 0.1                               ; IIV_K ; LOG   
  < 0.1                               ; IIV_V2 ; LOG  
  > 0.1                               ; IIV_V ; LOG   
                                                      
    $SIGMA                                            
  < old_ctl                                           
  > new_ctl                                           
  @@ 25,25 / 25,23 @@                                 
    ID AMT TIME DV WT                                 
    $DATA ../DerivedData/data.csv IGNORE=@            
  < $SUB ADVAN5                                       
  > $SUB ADVAN2                                       
  < $MODEL                                            
  < COMP = (COMP1, DEFDOSE)                           
  < COMP = (COMP2, DEFOBS)                            
  >                                                   
    $PK                                               
                                                      
  < TVK1T2=EXP(THETA(1))                              
  > TVKA=EXP(THETA(1))                                
  < MU_1=LOG(TVK1T2)                                  
  > MU_1=LOG(TVKA)                                    
  < K1T2 = EXP(MU_1+ETA(1))                           
  > KA = EXP(MU_1+ETA(1))                             
                                                      
  < TVK2T0=EXP(THETA(2))                              
  > TVK=EXP(THETA(2))                                 
  < MU_2=LOG(TVK2T0)                                  
  > MU_2=LOG(TVK)                                     
  < K2T0 = EXP(MU_2+ETA(2))                           
  > K = EXP(MU_2+ETA(2))                              
                                                      
  < TVV2=EXP(THETA(3))                                
  > TVV=EXP(THETA(3))                                 
  < MU_3=LOG(TVV2)                                    
  > MU_3=LOG(TVV)                                     
  < V2 = EXP(MU_3+ETA(3))                             
  > V = EXP(MU_3+ETA(3))                              
                                                      
  < CL = K2T0*V2                                      
  > CL = K*V                                          
                                                      
  < S2 = V2                                           
  > S2 = V                                            
                                                      
    $ERROR                                            
  @@ 55,12 / 53,13 @@                                 
    Y=IPRED + IPRED*EPS(1) + EPS(2)                   
                                                      
  >                                                   
    $THETA                                            
  < 0.5   ; K1T2 ; h-1 ; LOG                          
  > 0.5   ; KA ; h-1 ; LOG                            
  < -2.5   ; K2T0 ; h-1 ; LOG                         
  > -2.5   ; K ; h-1 ; LOG                            
  < -0.5   ; V2 ; L ; LOG                             
  > -0.5   ; V ; L ; LOG                              
    $OMEGA                                            
  < 0.1                               ; IIV_K1T2 ; LOG
  > 0.1                               ; IIV_KA ; LOG  
  < 0.1                               ; IIV_K2T0 ; LOG
  > 0.1                               ; IIV_K ; LOG   
  < 0.1                               ; IIV_V2 ; LOG  
  > 0.1                               ; IIV_V ; LOG   
                                                      
    $SIGMA                                            
  Package: localanalysis
  Title: What the Package Does (One Line, Title Case)
  Version: 0.0.0.9000
  Authors@R (parsed):
      * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
  Description: What the package does (one paragraph).
  License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
      license
  Encoding: UTF-8
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.2.3
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS s01_make_data.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output s01_make_data.html --lua-filter "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "D:\RCompile\CRANpkg\lib\4.3\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\RtmpW0X8DC\rmarkdown-str2697cbe370c0.html" 
  Scanning files .
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    adding: test_nmproject/Models/runa4t4.cor (deflated 89%)
    adding: test_nmproject/Models/runa4t4.cov (deflated 89%)
    adding: test_nmproject/Models/runa4t4.ext (deflated 83%)
    adding: test_nmproject/Models/runa4t4.lst (deflated 82%)
    adding: test_nmproject/Models/runa4t4.mod (deflated 54%)
    adding: test_nmproject/Models/runa4t4.phi (deflated 66%)
    adding: test_nmproject/Models/runc1.coi (deflated 82%)
    adding: test_nmproject/Models/runc1.cor (deflated 82%)
    adding: test_nmproject/Models/runc1.cov (deflated 82%)
    adding: test_nmproject/Models/runc1.ext (deflated 81%)
    adding: test_nmproject/Models/runc1.lst (deflated 82%)
    adding: test_nmproject/Models/runc1.mod (deflated 53%)
    adding: test_nmproject/Models/runc1.phi (deflated 65%)
    adding: test_nmproject/Models/runm1.coi (deflated 82%)
    adding: test_nmproject/Models/runm1.cor (deflated 82%)
    adding: test_nmproject/Models/runm1.cov (deflated 82%)
    adding: test_nmproject/Models/runm1.ext (deflated 81%)
    adding: test_nmproject/Models/runm1.lst (deflated 82%)
    adding: test_nmproject/Models/runm1.mod (deflated 53%)
    adding: test_nmproject/Models/runm1.phi (deflated 65%)
    adding: test_nmproject/Models/runm1s.ext (stored 0%)
    adding: test_nmproject/Models/runm1s.lst (deflated 71%)
    adding: test_nmproject/Models/runm1s.mod (deflated 53%)
    adding: test_nmproject/Models/runm2.coi (deflated 82%)
    adding: test_nmproject/Models/runm2.cor (deflated 82%)
    adding: test_nmproject/Models/runm2.cov (deflated 82%)
    adding: test_nmproject/Models/runm2.ext (deflated 81%)
    adding: test_nmproject/Models/runm2.lst (deflated 82%)
    adding: test_nmproject/Models/runm2.mod (deflated 53%)
    adding: test_nmproject/Models/runm2.phi (deflated 65%)
    adding: test_nmproject/Models/runm2WT.coi (deflated 82%)
    adding: test_nmproject/Models/runm2WT.cor (deflated 82%)
    adding: test_nmproject/Models/runm2WT.cov (deflated 81%)
    adding: test_nmproject/Models/runm2WT.ext (deflated 81%)
    adding: test_nmproject/Models/runm2WT.lst (deflated 82%)
    adding: test_nmproject/Models/runm2WT.mod (deflated 53%)
    adding: test_nmproject/Models/runm2WT.phi (deflated 65%)
    adding: test_nmproject/Models/sdtabm1 (deflated 74%)
    adding: test_nmproject/NAMESPACE (stored 0%)
    adding: test_nmproject/R/ (stored 0%)
    adding: test_nmproject/R/AUC.R (deflated 58%)
    adding: test_nmproject/README.md (deflated 48%)
    adding: test_nmproject/README.Rmd (deflated 47%)
    adding: test_nmproject/Results/ (stored 0%)
    adding: test_nmproject/Results/Readme.txt (deflated 4%)
    adding: test_nmproject/Scripts/ (stored 0%)
    adding: test_nmproject/Scripts/basic_boot.Rmd (deflated 51%)
    adding: test_nmproject/Scripts/basic_gof.Rmd (deflated 53%)
    adding: test_nmproject/Scripts/basic_ppc.Rmd (deflated 64%)
    adding: test_nmproject/Scripts/basic_vpc.Rmd (deflated 56%)
    adding: test_nmproject/Scripts/Readme.txt (stored 0%)
    adding: test_nmproject/Scripts/s01_make_data.html (deflated 68%)
    adding: test_nmproject/Scripts/s01_make_data.Rmd (deflated 49%)
    adding: test_nmproject/Scripts/s02_model_log.Rmd (deflated 56%)
    adding: test_nmproject/Scripts/s03_cov_demo_prep.Rmd (deflated 61%)
    adding: test_nmproject/Scripts/s04_covariate_modelling.Rmd (deflated 65%)
    adding: test_nmproject/Scripts/s05_advanced_usage.Rmd (deflated 60%)
    adding: test_nmproject/SourceData/ (stored 0%)
    adding: test_nmproject/SourceData/Readme.txt (stored 0%)
    adding: test_nmproject/SourceData/THEOPP.csv (deflated 64%)
    adding: test_nmproject/staging/ (stored 0%)
    adding: test_nmproject/staging/DerivedData/ (stored 0%)
    adding: test_nmproject/staging/DerivedData/Readme.txt (stored 0%)
    adding: test_nmproject/staging/Models/ (stored 0%)
    adding: test_nmproject/staging/Models/ADVAN2.mod (deflated 54%)
    adding: test_nmproject/staging/Models/patches/ (stored 0%)
    adding: test_nmproject/staging/Models/patches/patch-tarjinde-2021-11-17-08-52-52 (deflated 54%)
    adding: test_nmproject/staging/Models/Readme.txt (stored 0%)
    adding: test_nmproject/staging/R/ (stored 0%)
    adding: test_nmproject/staging/R/AUC.R (deflated 58%)
    adding: test_nmproject/staging/Results/ (stored 0%)
    adding: test_nmproject/staging/Results/Readme.txt (deflated 4%)
    adding: test_nmproject/staging/Scripts/ (stored 0%)
    adding: test_nmproject/staging/Scripts/Readme.txt (stored 0%)
    adding: test_nmproject/staging/SourceData/ (stored 0%)
    adding: test_nmproject/staging/SourceData/Readme.txt (stored 0%)
    adding: test_nmproject/test_nmproject.Rproj (deflated 32%)
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 29 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-manual_edit.R:24:3'): manual_edit ──────────────────────────────
  Error in `file.copy(file.path(testfilesloc, "."), ".", recursive = TRUE)`: could not allocate copy buffer
  Backtrace:
      ▆
   1. └─base::file.copy(file.path(testfilesloc, "."), ".", recursive = TRUE) at test-manual_edit.R:24:2
  ── Error ('test-theopp.R:36:3'): run and post ──────────────────────────────────
  Error in `(function (filename = "Rplot%03d.png", width = 480, height = 480, 
      units = "px", pointsize = 12, bg = "white", res = NA, family = "sans", 
      restoreConsole = TRUE, type = c("windows", "cairo", "cairo-png"), 
      antialias = c("default", "none", "cleartype", "gray", "subpixel"), 
      symbolfamily = "default") 
  {
      if (!checkIntFormat(filename)) 
          stop("invalid 'filename'")
      g <- .geometry(width, height, units, res)
      if (match.arg(type) == "cairo") {
          antialias <- match(match.arg(antialias), aa.cairo)
          invisible(.External(C_devCairo, filename, 2L, g$width, 
              g$height, pointsize, bg, res, antialias, 100L, if (nzchar(family)) family else "sans", 
              300, chooseSymbolFont(symbolfamily)))
      }
      else if (match.arg(type) == "cairo-png") {
          antialias <- match(match.arg(antialias), aa.cairo)
          invisible(.External(C_devCairo, filename, 5L, g$width, 
              g$height, pointsize, bg, res, antialias, 100L, if (nzchar(family)) family else "sans", 
              300, chooseSymbolFont(symbolfamily)))
      }
      else {
          new <- if (!missing(antialias)) {
              list(bitmap.aa.win = match.arg(antialias, aa.win))
          }
          else list()
          antialias <- check.options(new = new, envir = .WindowsEnv, 
              name.opt = ".Windows.Options", reset = FALSE, assign.opt = FALSE)$bitmap.aa.win
          invisible(.External(C_devga, paste0("png:", filename), 
              g$width, g$height, pointsize, FALSE, 1L, NA_real_, 
              NA_real_, bg, 1, as.integer(res), NA_integer_, FALSE, 
              .PSenv, NA, restoreConsole, "", FALSE, TRUE, family, 
              match(antialias, aa.win)))
      }
  })(filename = "D:\\temp\\RtmpW0X8DC\\file2697c7b0a6dba", width = 7, 
      height = 5, units = "in", res = 192)`: unable to start png() device
  Backtrace:
      ▆
   1. └─base::tryCatch(...) at test-theopp.R:36:2
   2.   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   3.     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   4.       └─value[[3L]](cond)
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted