Running 'testthat.R' [89s]
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
  LazyData: true
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.1.2
  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
  LazyData: true
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.1.2
  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
  LazyData: true
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.1.2
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ echo   : logi FALSE
   $ message: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-2
    ordinary text without R code
  
  label: unnamed-chunk-3
    ordinary text without R code
  
  label: unnamed-chunk-4
    ordinary text without R code
  
  label: unnamed-chunk-5
    ordinary text without R code
  
  "D:/compiler/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 --self-contained --variable bs3=TRUE --standalone --section-divs --template "D:\temp\Rtmpcbosxu\RLIBS_ee5815e4c7f\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "D:\temp\RtmpUH8VeH\rmarkdown-str9c0453497d0e.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
  error: patch failed: Models/base-tarjinde-2021-08-15-16-55-38:53
  error: Models/base-tarjinde-2021-08-15-16-55-38: patch does not apply
  error: patch failed: Models/base-tarjinde-2021-08-15-16-55-38:53
  error: Models/base-tarjinde-2021-08-15-16-55-38: patch does not apply
  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
  LazyData: true
  Roxygen: list(markdown = TRUE)
  RoxygenNote: 7.1.2
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ echo   : logi FALSE
   $ message: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-2
    ordinary text without R code
  
  label: unnamed-chunk-3
    ordinary text without R code
  
  label: unnamed-chunk-4
    ordinary text without R code
  
  label: unnamed-chunk-5
    ordinary text without R code
  
  "D:/compiler/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 --self-contained --variable bs3=TRUE --standalone --section-divs --template "D:\temp\Rtmpcbosxu\RLIBS_ee5815e4c7f\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "D:\temp\RtmpUH8VeH\rmarkdown-str9c04bb41238.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ echo   : logi FALSE
   $ message: logi FALSE
  
    ordinary text without R code
  
  label: parent_ob
    ordinary text without R code
  
  label: basic_gof
    ordinary text without R code
  
  label: sim
    ordinary text without R code
  
  label: sim_diags
    ordinary text without R code
  
  label: manual_edit
    ordinary text without R code
  
  label: child_obs
    ordinary text without R code
  
  label: summary_rr
    ordinary text without R code
  
  label: decision1
    ordinary text without R code
  
  label: boot
    ordinary text without R code
  
  label: run_boot
    ordinary text without R code
  
  label: make_xv
    ordinary text without R code
  
  label: run_xv (with options) 
  List of 1
   $ eval: logi FALSE
  
    ordinary text without R code
  
  "D:/compiler/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 --self-contained --variable bs3=TRUE --standalone --section-divs --template "D:\temp\Rtmpcbosxu\RLIBS_ee5815e4c7f\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "D:\temp\RtmpUH8VeH\rmarkdown-str9c04291d2cb8.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ echo   : logi FALSE
   $ message: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-2
    ordinary text without R code
  
  label: unnamed-chunk-3
    ordinary text without R code
  
  label: unnamed-chunk-4
    ordinary text without R code
  
  "D:/compiler/pandoc/pandoc" +RTS -K512m -RTS s03_cov_demo_prep.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output s03_cov_demo_prep.html --self-contained --variable bs3=TRUE --standalone --section-divs --template "D:\temp\Rtmpcbosxu\RLIBS_ee5815e4c7f\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "D:\temp\RtmpUH8VeH\rmarkdown-str9c04704b58ae.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ echo   : logi FALSE
   $ message: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-2 (with options) 
  List of 2
   $ message: logi FALSE
   $ results: chr "hide"
  
    ordinary text without R code
  
  label: unnamed-chunk-3
    ordinary text without R code
  
  label: unnamed-chunk-4 (with options) 
  List of 2
   $ message: logi FALSE
   $ results: chr "hide"
  
    ordinary text without R code
  
  label: unnamed-chunk-5
    ordinary text without R code
  
  label: unnamed-chunk-6 (with options) 
  List of 2
   $ message: logi FALSE
   $ results: chr "hide"
  
    ordinary text without R code
  
  label: unnamed-chunk-7
    ordinary text without R code
  
  label: unnamed-chunk-8 (with options) 
  List of 2
   $ message: logi FALSE
   $ results: chr "hide"
  
    ordinary text without R code
  
  label: unnamed-chunk-9
    ordinary text without R code
  
  label: unnamed-chunk-10
    ordinary text without R code
  
  label: unnamed-chunk-11
    ordinary text without R code
  
  label: unnamed-chunk-12
    ordinary text without R code
  
  label: unnamed-chunk-13 (with options) 
  List of 2
   $ message: logi FALSE
   $ results: chr "hide"
  
    ordinary text without R code
  
  label: unnamed-chunk-14
    ordinary text without R code
  
  label: unnamed-chunk-15
    ordinary text without R code
  
  label: unnamed-chunk-16
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  label: unnamed-chunk-17
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  "D:/compiler/pandoc/pandoc" +RTS -K512m -RTS s04_covariate_modelling.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output s04_covariate_modelling.html --self-contained --variable bs3=TRUE --standalone --section-divs --template "D:\temp\Rtmpcbosxu\RLIBS_ee5815e4c7f\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "D:\temp\RtmpUH8VeH\rmarkdown-str9c0475e6448.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
     inline R code fragments
  
  label: setup (with options) 
  List of 1
   $ include: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-1 (with options) 
  List of 2
   $ echo   : logi FALSE
   $ message: logi FALSE
  
    ordinary text without R code
  
  label: unnamed-chunk-2
    ordinary text without R code
  
  label: unnamed-chunk-3
    ordinary text without R code
  
  label: unnamed-chunk-4
    ordinary text without R code
  
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  label: unnamed-chunk-6
    ordinary text without R code
  
  label: unnamed-chunk-7
    ordinary text without R code
  
  label: unnamed-chunk-8
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  label: advan_test
    ordinary text without R code
  
  label: core_test
    ordinary text without R code
  
  label: sim_reest
    ordinary text without R code
  
  "D:/compiler/pandoc/pandoc" +RTS -K512m -RTS s05_advanced_usage.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output s05_advanced_usage.html --self-contained --variable bs3=TRUE --standalone --section-divs --template "D:\temp\Rtmpcbosxu\RLIBS_ee5815e4c7f\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "D:\temp\RtmpUH8VeH\rmarkdown-str9c04740558.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
  List of 15
   $ type        : chr "execute"
   $ run_id      : chr "m1"
   $ run_in      : chr "Models"
   $ executed    : logi FALSE
   $ ctl_contents: chr collapsed - view with ctl_contents()
   $ ctl_orig    : chr collapsed - view with ctl_orig()
   $ data_path   : chr "DerivedData/data.csv"
   $ cmd         : chr "execute runm1.mod -dir=m1"
   $ cores       : int 1
   $ parafile    : chr "path/to/parafile.pnm"
   $ run_dir     : chr "m1"
   $ ctl_name    : chr "runm1.mod"
   $ results_dir : chr "Results"
   $ unique_id   : chr "execute.Models/m1"
   $ lst_path    : chr "m1/NM_run1/psn.lst"
   - attr(*, "class")= chr [1:3] "nm_execute" "nm_generic" "list"
  < old_ctl                               
  > new_ctl                               
  @@ 25,8 / 25,6 @@                       
    ID AMT TIME DV WT                     
    $DATA ../DerivedData/data.csv IGNORE=@
  < $SUB ADVAN5                           
  > $SUB ADVAN2                           
  < $MODEL                                
  < COMP = (COMP1)                        
  < COMP = (COMP2)                        
  >                                       
    $PK                                   
                                          
  @@ 47,7 / 45,4 @@                       
    S2 = V                                
                                          
  < K1T2 = KA                             
  < K2T0 = K                              
  < V2 = V                                
    $ERROR                                
                                          
  < old_ctl                               
  > new_ctl                               
  @@ 25,8 / 25,6 @@                       
    ID AMT TIME DV WT                     
    $DATA ../DerivedData/data.csv IGNORE=@
  < $SUB ADVAN5                           
  > $SUB ADVAN2                           
  < $MODEL                                
  < COMP = (COMP1)                        
  < COMP = (COMP2)                        
  >                                       
    $PK                                   
                                          
  @@ 47,7 / 45,4 @@                       
    S2 = V                                
                                          
  < K1T2 = KA                             
  < K2T0 = K                              
  < V2 = V                                
    $ERROR                                
                                          
  == Failed tests ================================================================
  -- Failure (test-basic.R:81:3): set up -----------------------------------------
  stime["elapsed"] >= 1 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ]
  Error: Test failures
  Execution halted