Running ‘ggplot_extraction.R’ [11s/12s]
  Running ‘trackr-tests.R’ [11s/13s]
Running the tests in ‘tests/trackr-tests.R’ failed.
Complete output:
  > library(trackr)
  Loading required package: histry
  > library(knitr)
  > be = JSONBackend(tempfile())
  > tdb = TrackrDB(backend=be, img_dir = tempdir())
  > defaultTDB(tdb)
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "/tmp/RtmpBPRw1b/working_dir/Rtmp4MBUAJ"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (0x0)
  Field ".file":
  [1] "/tmp/RtmpBPRw1b/working_dir/Rtmp4MBUAJ/file329eeb3c108d45"
  Field "file":
  [1] "/tmp/RtmpBPRw1b/working_dir/Rtmp4MBUAJ/file329eeb3c108d45"
  
  > recs = 0
  > sysfil = system.file("test_docs/knitr_test.Rmd", package = "trackr")
  > rmdfil = file.path(tempdir(), "knitr_test.Rmd")
  > file.copy(sysfil, rmdfil)
  [1] TRUE
  > if(rmarkdown::pandoc_available()) {
  +     knit_and_record(rmdfil, verbose = TRUE)
  +     stopifnot(length(findRecords("mtcars")) == 2) ## recvars is 'fit' so that plus report
  +     recs = recs + 2
  + } else {
  +     message("Pandoc not available. Skipping knit_and_record test")
  + }
  
  
  processing file: /tmp/RtmpBPRw1b/working_dir/Rtmp4MBUAJ/knitr_test.Rmd
  
  
  processing file: knitr_test.Rmd
    ordinary text without R code
  
  label: plot
    ordinary text without R code
  
  label: lm
    ordinary text without R code
  
  output file: knitr_test.knit.md
  
  /usr/bin/pandoc +RTS -K512m -RTS knitr_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output knitr_test.html --lua-filter /data/gannet/ripley/R/test-clang/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /data/gannet/ripley/R/test-clang/rmarkdown/rmarkdown/lua/latex-div.lua --email-obfuscation none --standalone --section-divs --template /data/gannet/ripley/R/test-clang/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/RtmpBPRw1b/working_dir/Rtmp4MBUAJ/rmarkdown-str329eeb4e6a90b4.html 
  
  Output created: knitr_test.html
  Note: method with signature 'FeatureSet#TrackrDB' chosen for function 'prep_for_backend',
   target signature 'ObjFeatureSet#TrackrDB'.
   "ObjFeatureSet#ANY" would also be valid
  
  
  processing file: /tmp/RtmpBPRw1b/working_dir/Rtmp4MBUAJ/knitr_test.Rmd
  No existing record found for id SpkyV2:89849a1afc4a1f1c3f70168731cdb824
  Adding RmdFeatureSet object with ID SpkyV2:89849a1afc4a1f1c3f70168731cdb824...
  ID  SpkyV2:89849a1afc4a1f1c3f70168731cdb824 
  No existing record found for id SpkyV2:f938f3de0677a93ceb849e273a181e9b
  Adding ObjFeatureSet object with ID SpkyV2:f938f3de0677a93ceb849e273a181e9b...
  ID  SpkyV2:f938f3de0677a93ceb849e273a181e9b 
  > 
  > f = function(paths) readLines(paths)
  > fil = system.file("test_docs", "knitr_test.Rmd", package = "trackr")
  > recordFiles(fil, ingestfun = f, verbose = TRUE)
    adding: data/gannet/ripley/R/packages/tests-clang/trackr.Rcheck/trackr/test_docs/knitr_test.Rmd (deflated 35%)
  Error in nchar(x, type = "w", allowNA = TRUE) : 
    invalid multibyte string, element 4
  Calls: recordFiles ... withVisible -> str -> str.default -> maybe_truncate -> nchar.w
  Execution halted