Running 'testthat.R'
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: 7.1.2
  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
  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
  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
  
  "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 "C:\r_packages\pkgcheck\lib\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\r_packages\pkgcheck\lib\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\r_packages\pkgcheck\lib\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\r_packages\pkgcheck\CRAN\NMproject\tmp\Rtmp0KpSrg\rmarkdown-str2e0d81ab254a1.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
  'git' is not recognized as an internal or external command,
  operable program or batch file.
  'git' is not recognized as an internal or external command,
  operable program or batch file.
  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: 7.1.2
     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
  
  "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 "C:\r_packages\pkgcheck\lib\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\r_packages\pkgcheck\lib\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\r_packages\pkgcheck\lib\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\r_packages\pkgcheck\CRAN\NMproject\tmp\Rtmp0KpSrg\rmarkdown-str2e0d868675a5a.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
  'git' is not recognized as an internal or external command,
  operable program or batch file.
  'git' is not recognized as an internal or external command,
  operable program or batch file.
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    adding: test_nmproject/Models/m1_simest/est/run1.mod (deflated 53%)
    adding: test_nmproject/Models/m1_simest/est/run1.phi (deflated 65%)
    adding: test_nmproject/Models/m1_simest/est/run2.coi (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run2.cor (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run2.cov (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run2.ext (deflated 81%)
    adding: test_nmproject/Models/m1_simest/est/run2.lst (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run2.mod (deflated 53%)
    adding: test_nmproject/Models/m1_simest/est/run2.phi (deflated 66%)
    adding: test_nmproject/Models/m1_simest/est/run3.coi (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run3.cor (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run3.cov (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run3.ext (deflated 81%)
    adding: test_nmproject/Models/m1_simest/est/run3.lst (deflated 82%)
    adding: test_nmproject/Models/m1_simest/est/run3.mod (deflated 53%)
    adding: test_nmproject/Models/m1_simest/est/run3.phi (deflated 66%)
    adding: test_nmproject/Models/m1_simest/run1.ext (stored 0%)
    adding: test_nmproject/Models/m1_simest/run1.lst (deflated 63%)
    adding: test_nmproject/Models/m1_simest/run1.mod (deflated 53%)
    adding: test_nmproject/Models/m1_simest/run2.ext (stored 0%)
    adding: test_nmproject/Models/m1_simest/run2.lst (deflated 63%)
    adding: test_nmproject/Models/m1_simest/run2.mod (deflated 53%)
    adding: test_nmproject/Models/m1_simest/run3.ext (stored 0%)
    adding: test_nmproject/Models/m1_simest/run3.lst (deflated 63%)
    adding: test_nmproject/Models/m1_simest/run3.mod (deflated 53%)
    adding: test_nmproject/Models/m2/ (stored 0%)
    adding: test_nmproject/Models/m2/meta.yaml (deflated 53%)
    adding: test_nmproject/Models/m2/NM_run1/ (stored 0%)
    adding: test_nmproject/Models/m2/NM_run1/psn.clt (deflated 75%)
    adding: test_nmproject/Models/m2/NM_run1/psn.cnv (deflated 62%)
    adding: test_nmproject/Models/m2/NM_run1/psn.coi (deflated 82%)
    adding: test_nmproject/Models/m2/NM_run1/psn.cor (deflated 82%)
    adding: test_nmproject/Models/m2/NM_run1/psn.cov (deflated 82%)
    adding: test_nmproject/Models/m2/NM_run1/psn.cpu (deflated 15%)
    adding: test_nmproject/Models/m2/NM_run1/psn.ext (deflated 81%)
    adding: test_nmproject/Models/m2/NM_run1/psn.lst (deflated 82%)
    adding: test_nmproject/Models/m2/NM_run1/psn.mod (deflated 54%)
    adding: test_nmproject/Models/m2/NM_run1/psn.phi (deflated 66%)
    adding: test_nmproject/Models/m2/NM_run1/psn.shk (deflated 73%)
    adding: test_nmproject/Models/m2/NM_run1/psn.shm (deflated 90%)
    adding: test_nmproject/Models/m2WT/ (stored 0%)
    adding: test_nmproject/Models/m2WT/meta.yaml (deflated 53%)
    adding: test_nmproject/Models/m2WT/NM_run1/ (stored 0%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.clt (deflated 75%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.cnv (deflated 62%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.coi (deflated 82%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.cor (deflated 82%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.cov (deflated 82%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.cpu (deflated 15%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.ext (deflated 81%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.lst (deflated 82%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.mod (deflated 55%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.phi (deflated 66%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.shk (deflated 73%)
    adding: test_nmproject/Models/m2WT/NM_run1/psn.shm (deflated 90%)
    adding: test_nmproject/Models/patabm1 (deflated 83%)
    adding: test_nmproject/Models/patches/ (stored 0%)
    adding: test_nmproject/Models/patches/patch-tarjinde-2021-08-15-16-55-38 (deflated 54%)
    adding: test_nmproject/Models/Readme.txt (stored 0%)
    adding: test_nmproject/Models/runa12t1.coi (deflated 92%)
    adding: test_nmproject/Models/runa12t1.cor (deflated 92%)
    adding: test_nmproject/Models/runa12t1.cov (deflated 92%)
    adding: test_nmproject/Models/runa12t1.ext (deflated 92%)
    adding: test_nmproject/Models/runa12t1.lst (deflated 85%)
    adding: test_nmproject/Models/runa12t1.mod (deflated 57%)
    adding: test_nmproject/Models/runa12t1.phi (deflated 80%)
    adding: test_nmproject/Models/runa12t4.coi (deflated 92%)
    adding: test_nmproject/Models/runa12t4.cor (deflated 92%)
    adding: test_nmproject/Models/runa12t4.cov (deflated 92%)
    adding: test_nmproject/Models/runa12t4.ext (deflated 92%)
    adding: test_nmproject/Models/runa12t4.lst (deflated 85%)
    adding: test_nmproject/Models/runa12t4.mod (deflated 56%)
    adding: test_nmproject/Models/runa12t4.phi (deflated 80%)
    adding: test_nmproject/Models/runa2t1.coi (deflated 82%)
    adding: test_nmproject/Models/runa2t1.cor (deflated 82%)
    adding: test_nmproject/Models/runa2t1.cov (deflated 82%)
    adding: test_nmproject/Models/runa2t1.ext (deflated 81%)
    adding: test_nmproject/Models/runa2t1.lst (deflated 82%)
    adding: test_nmproject/Models/runa2t1.mod (deflated 53%)
    adding: test_nmproject/Models/runa2t1.phi (deflated 65%)
    adding: test_nmproject/Models/runa2t2.coi (deflated 82%)
    adding: test_nmproject/Models/runa2t2.cor (deflated 82%)
    adding: test_nmproject/Models/runa2t2.cov (deflated 82%)
    adding: test_nmproject/Models/runa2t2.ext (deflated 81%)
    adding: test_nmproject/Models/runa2t2.lst (deflated 82%)
    adding: test_nmproject/Models/runa2t2.mod (deflated 53%)
    adding: test_nmproject/Models/runa2t2.phi (deflated 66%)
    adding: test_nmproject/Models/runa4t1.coi (deflated 89%)
    adding: test_nmproject/Models/runa4t1.cor (deflated 89%)
    adding: test_nmproject/Models/runa4t1.cov (deflated 89%)
    adding: test_nmproject/Models/runa4t1.ext (deflated 82%)
    adding: test_nmproject/Models/runa4t1.lst (deflated 83%)
    adding: test_nmproject/Models/runa4t1.mod (deflated 55%)
    adding: test_nmproject/Models/runa4t1.phi (deflated 65%)
    adding: test_nmproject/Models/runa4t3.coi (deflated 87%)
    adding: test_nmproject/Models/runa4t3.cor (deflated 87%)
    adding: test_nmproject/Models/runa4t3.cov (deflated 87%)
    adding: test_nmproject/Models/runa4t3.ext (deflated 89%)
    adding: test_nmproject/Models/runa4t3.lst (deflated 81%)
    adding: test_nmproject/Models/runa4t3.mod (deflated 54%)
    adding: test_nmproject/Models/runa4t3.phi (deflated 79%)
    adding: test_nmproject/Models/runa4t4.coi (deflated 89%)
    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 65%)
    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 66%)
    adding: test_nmproject/Models/runm2WT.coi (deflated 82%)
    adding: test_nmproject/Models/runm2WT.cor (deflated 82%)
    adding: test_nmproject/Models/runm2WT.cov (deflated 82%)
    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 66%)
    adding: test_nmproject/Models/sdtabm1 (deflated 74%)
    adding: test_nmproject/Models/temp/ (stored 0%)
    adding: test_nmproject/Models/temp/runm1.mod (deflated 54%)
    adding: test_nmproject/Models/temp/runm1s.mod (deflated 54%)
    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/basic_gof.m1.nb.html (deflated 58%)
    adding: test_nmproject/Results/basic_ppc.m1s.nb.html (deflated 63%)
    adding: test_nmproject/Results/basic_vpc.m1s.nb.html (deflated 63%)
    adding: test_nmproject/Results/Readme.txt (deflated 4%)
    adding: test_nmproject/Scripts/ (stored 0%)
    adding: test_nmproject/Scripts/basic_boot.Rmd (deflated 53%)
    adding: test_nmproject/Scripts/basic_gof.Rmd (deflated 55%)
    adding: test_nmproject/Scripts/basic_ppc.Rmd (deflated 65%)
    adding: test_nmproject/Scripts/basic_vpc.Rmd (deflated 58%)
    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-2021-04-20-13-50-09 (deflated 52%)
    adding: test_nmproject/staging/Models/patches/patch-tarjinde-2021-04-20-13-50-09.tmp (deflated 52%)
    adding: test_nmproject/staging/Models/patches/patch-tarjinde-2021-06-04-17-07-24 (deflated 53%)
    adding: test_nmproject/staging/Models/patches/patch-tarjinde-2021-06-04-17-07-24.tmp (deflated 53%)
    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 26%)
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-manual_edit.R:41:3): manual_edit ────────────────────────────────
  Error in `(function (m, patch_id, return_merge_conf_ctl = FALSE) 
  {
      patch_id <- gsub("patch-", "", patch_id)
      patch_name <- paste0("patch-", patch_id)
      patch_path <- file.path(nm_dir("models"), "patches", patch_name)
      patch_file_exists <- file.exists(patch_path)
      if (!patch_file_exists) 
          stop("patch file doesn't exist")
      patch_contents <- readLines(patch_path)
      temp_ctl_path <- patch_contents[grepl("^---", patch_contents)]
      temp_ctl_path <- gsub("\\S+\\s.{2}(.*)", "\\1", temp_ctl_path)
      mnew <- m %>% simple_field(ctl_path = temp_ctl_path, ctl_name = basename(temp_ctl_path))
      mnew %>% text() %>% writeLines(temp_ctl_path)
      on.exit(unlink(temp_ctl_path))
      patch_cmd <- paste("git apply -C1", patch_path)
      suppressWarnings(res <- system_cmd(patch_cmd, intern = TRUE))
      if (isTRUE(attributes(res)$status > 0)) {
          patch_cmd <- paste("git apply --whitespace=fix -C1", 
              patch_path)
          suppressWarnings(res <- system_cmd(patch_cmd, intern = TRUE))
          if (isTRUE(attributes(res)$status > 0)) {
              if (!git_cmd_available) 
                  stop("need git available from system() for this to work")
              git_log <- git2r::commits()
              if (length(git_log) == 0) {
                  usethis::ui_stop("apply_manual_edit() hit an unresolvable merge conflict, \n            this is normally due to the control file having changed significantly\n            since the manual edit was performed. Right clicking the patch text and \n            selecting  Addins -> View patch will show the edits the patch is attempting \n            to apply.  This can be used to create a new patch.")
              }
              orig_commit <- git_log[[1]]
              find_commit <- paste("pre-manual edit: ", patch_id)
              found_commits <- git_log[sapply(git_log, function(commit) commit$message) %in% 
                  find_commit]
              commit_found <- length(found_commits) == 1
              if (commit_found) {
                  check_git_uservalues()
                  system("git reset", intern = TRUE)
                  git2r::add(path = temp_ctl_path)
                  on.exit(system(paste("git reset", orig_commit$sha), 
                    intern = TRUE), add = TRUE)
                  commit_diff <- git2r::diff(git2r::repository(), 
                    index = TRUE, as_char = TRUE)
                  commit_diff <- strsplit(commit_diff, "\n")[[1]]
                  empty_commit_coming <- length(commit_diff) == 
                    0
                  if (empty_commit_coming) {
                    usethis::ui_stop("apply_manual_edit() hit an unresolvable merge conflict, \n            this is normally due to the control file having changed significantly\n            since the manual edit was performed. Right clicking the patch text and \n            selecting  Addins -> View patch will show the edits the patch is attempting \n            to apply.  This can be used to create a new patch.")
                  }
                  commit_msg <- paste("temp commit: ", ctl_path(m))
                  git2r::commit(message = commit_msg)
                  patch_cmd <- paste("git am -C1 --3way <", patch_path)
                  res <- suppressWarnings(system_cmd(patch_cmd, 
                    intern = TRUE))
                  if (any(grepl("git config", res))) {
                    usethis::ui_stop("Need to set project level user.name and user.email:\n            {usethis::ui_code(\"usethis::use_git_config(scope = 'project', user.name = 'Jane', user.email = 'jane@example.com')\")}\n          retry when finished")
                  }
                  if (isTRUE(attributes(res)$status > 0)) {
                    git2r::add(path = temp_ctl_path)
                    added_stuff <- git2r::diff(git2r::repository(), 
                      index = TRUE, as_char = TRUE)
                    conflict_present <- FALSE
                    if (length(added_stuff) == 1) {
                      conflict_present <- any(grepl("\\+<<<<<<<", 
                        added_stuff))
                    }
                    if (conflict_present) {
                      warn_msg <- paste0("manual edit merge conflict detected:\n\n", 
                        "-------------------------------------------\n", 
                        added_stuff, "-------------------------------------------\n")
                      if (return_merge_conf_ctl) 
                        return(readLines(temp_ctl_path))
                      usethis::ui_info(warn_msg)
                      usethis::ui_stop("You can resolve this conflict by selecting the code\n            and ensuring the apply_manual_edit() is the last pipe highlighted\n            and then selecting Addins -> Resolve manual edit conflict")
                    }
                    patch_cmd <- paste("git am --whitespace=fix -C1 --3way <", 
                      patch_path)
                    res <- system_cmd(patch_cmd, intern = TRUE)
                    if (isTRUE(attributes(res)$status > 0)) {
                      git2r::add(path = temp_ctl_path)
                      added_stuff <- git2r::diff(git2r::repository(), 
                        index = TRUE, as_char = TRUE)
                      conflict_present <- FALSE
                      if (length(added_stuff) == 1) {
                        conflict_present <- any(grepl("\\+<<<<<<< ours", 
                          added_stuff))
                      }
                      if (conflict_present) {
                        warn_msg <- paste0("manual edit merge conflict detected:\n\n", 
                          "-------------------------------------------\n", 
                          added_stuff, "-------------------------------------------\n")
                        if (return_merge_conf_ctl) 
                          return(readLines(temp_ctl_path))
                        usethis::ui_info(warn_msg)
                        usethis::ui_stop("You can resolve this conflict by highlighting the code\n          in your script up to this apply_manual_edit() statement and selecting:\n            Addins -> Resolve manual edit conflict")
                      }
                    }
                  }
              }
              else {
                  usethis::ui_stop("apply_manual_edit() hit an unresolvable merge conflict, \n            this is normally due to the control file having changed significantly\n            since the manual edit was performed. Right clicking the patch text and \n            selecting  Addins -> View patch will show the edits the patch is attempting \n            to apply.  This can be used to create a new patch.")
              }
          }
      }
      out_file <- readLines(temp_ctl_path)
      m <- m %>% ctl_contents_simple(out_file)
      invisible(m)
  })(m = dots[[1L]][[1L]], patch_id = dots[[2L]][[1L]])`: need git available from system() for this to work
  Backtrace:
      ▆
   1. ├─m1 %>% child("m1s_temp") %>% update_parameters(m1) %>% ... at test-manual_edit.R:41:2
   2. ├─NMproject::apply_manual_edit(., "tarjinde-2021-08-15-16-55-38")
   3. └─NMproject:::apply_manual_edit.nm_list(., "tarjinde-2021-08-15-16-55-38")
   4.   ├─base::do.call(...)
   5.   └─base::mapply(...)
   6.     └─NMproject `<fn>`(m = dots[[1L]][[1L]], patch_id = dots[[2L]][[1L]])
  ── Error (test-theopp.R:36:3): run and post ────────────────────────────────────
  Error in `(function (m, patch_id, return_merge_conf_ctl = FALSE) 
  {
      patch_id <- gsub("patch-", "", patch_id)
      patch_name <- paste0("patch-", patch_id)
      patch_path <- file.path(nm_dir("models"), "patches", patch_name)
      patch_file_exists <- file.exists(patch_path)
      if (!patch_file_exists) 
          stop("patch file doesn't exist")
      patch_contents <- readLines(patch_path)
      temp_ctl_path <- patch_contents[grepl("^---", patch_contents)]
      temp_ctl_path <- gsub("\\S+\\s.{2}(.*)", "\\1", temp_ctl_path)
      mnew <- m %>% simple_field(ctl_path = temp_ctl_path, ctl_name = basename(temp_ctl_path))
      mnew %>% text() %>% writeLines(temp_ctl_path)
      on.exit(unlink(temp_ctl_path))
      patch_cmd <- paste("git apply -C1", patch_path)
      suppressWarnings(res <- system_cmd(patch_cmd, intern = TRUE))
      if (isTRUE(attributes(res)$status > 0)) {
          patch_cmd <- paste("git apply --whitespace=fix -C1", 
              patch_path)
          suppressWarnings(res <- system_cmd(patch_cmd, intern = TRUE))
          if (isTRUE(attributes(res)$status > 0)) {
              if (!git_cmd_available) 
                  stop("need git available from system() for this to work")
              git_log <- git2r::commits()
              if (length(git_log) == 0) {
                  usethis::ui_stop("apply_manual_edit() hit an unresolvable merge conflict, \n            this is normally due to the control file having changed significantly\n            since the manual edit was performed. Right clicking the patch text and \n            selecting  Addins -> View patch will show the edits the patch is attempting \n            to apply.  This can be used to create a new patch.")
              }
              orig_commit <- git_log[[1]]
              find_commit <- paste("pre-manual edit: ", patch_id)
              found_commits <- git_log[sapply(git_log, function(commit) commit$message) %in% 
                  find_commit]
              commit_found <- length(found_commits) == 1
              if (commit_found) {
                  check_git_uservalues()
                  system("git reset", intern = TRUE)
                  git2r::add(path = temp_ctl_path)
                  on.exit(system(paste("git reset", orig_commit$sha), 
                    intern = TRUE), add = TRUE)
                  commit_diff <- git2r::diff(git2r::repository(), 
                    index = TRUE, as_char = TRUE)
                  commit_diff <- strsplit(commit_diff, "\n")[[1]]
                  empty_commit_coming <- length(commit_diff) == 
                    0
                  if (empty_commit_coming) {
                    usethis::ui_stop("apply_manual_edit() hit an unresolvable merge conflict, \n            this is normally due to the control file having changed significantly\n            since the manual edit was performed. Right clicking the patch text and \n            selecting  Addins -> View patch will show the edits the patch is attempting \n            to apply.  This can be used to create a new patch.")
                  }
                  commit_msg <- paste("temp commit: ", ctl_path(m))
                  git2r::commit(message = commit_msg)
                  patch_cmd <- paste("git am -C1 --3way <", patch_path)
                  res <- suppressWarnings(system_cmd(patch_cmd, 
                    intern = TRUE))
                  if (any(grepl("git config", res))) {
                    usethis::ui_stop("Need to set project level user.name and user.email:\n            {usethis::ui_code(\"usethis::use_git_config(scope = 'project', user.name = 'Jane', user.email = 'jane@example.com')\")}\n          retry when finished")
                  }
                  if (isTRUE(attributes(res)$status > 0)) {
                    git2r::add(path = temp_ctl_path)
                    added_stuff <- git2r::diff(git2r::repository(), 
                      index = TRUE, as_char = TRUE)
                    conflict_present <- FALSE
                    if (length(added_stuff) == 1) {
                      conflict_present <- any(grepl("\\+<<<<<<<", 
                        added_stuff))
                    }
                    if (conflict_present) {
                      warn_msg <- paste0("manual edit merge conflict detected:\n\n", 
                        "-------------------------------------------\n", 
                        added_stuff, "-------------------------------------------\n")
                      if (return_merge_conf_ctl) 
                        return(readLines(temp_ctl_path))
                      usethis::ui_info(warn_msg)
                      usethis::ui_stop("You can resolve this conflict by selecting the code\n            and ensuring the apply_manual_edit() is the last pipe highlighted\n            and then selecting Addins -> Resolve manual edit conflict")
                    }
                    patch_cmd <- paste("git am --whitespace=fix -C1 --3way <", 
                      patch_path)
                    res <- system_cmd(patch_cmd, intern = TRUE)
                    if (isTRUE(attributes(res)$status > 0)) {
                      git2r::add(path = temp_ctl_path)
                      added_stuff <- git2r::diff(git2r::repository(), 
                        index = TRUE, as_char = TRUE)
                      conflict_present <- FALSE
                      if (length(added_stuff) == 1) {
                        conflict_present <- any(grepl("\\+<<<<<<< ours", 
                          added_stuff))
                      }
                      if (conflict_present) {
                        warn_msg <- paste0("manual edit merge conflict detected:\n\n", 
                          "-------------------------------------------\n", 
                          added_stuff, "-------------------------------------------\n")
                        if (return_merge_conf_ctl) 
                          return(readLines(temp_ctl_path))
                        usethis::ui_info(warn_msg)
                        usethis::ui_stop("You can resolve this conflict by highlighting the code\n          in your script up to this apply_manual_edit() statement and selecting:\n            Addins -> Resolve manual edit conflict")
                      }
                    }
                  }
              }
              else {
                  usethis::ui_stop("apply_manual_edit() hit an unresolvable merge conflict, \n            this is normally due to the control file having changed significantly\n            since the manual edit was performed. Right clicking the patch text and \n            selecting  Addins -> View patch will show the edits the patch is attempting \n            to apply.  This can be used to create a new patch.")
              }
          }
      }
      out_file <- readLines(temp_ctl_path)
      m <- m %>% ctl_contents_simple(out_file)
      invisible(m)
  })(m = dots[[1L]][[1L]], patch_id = dots[[2L]][[1L]])`: need git available from system() for this to work
  Backtrace:
      ▆
   1. └─base::tryCatch(...) at test-theopp.R:36:2
   2.   └─base tryCatchList(expr, classes, parentenv, handlers)
   3.     └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   4.       └─value[[3L]](cond)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted