Running ‘ggplot_extraction.R’ [8s/8s]
  Running ‘trackr-tests.R’ [8s/10s]
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/Rtmpu5ohUx"
  
  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/Rtmpu5ohUx/file54403d8a164c"
  Field "file":
  [1] "/tmp/Rtmpu5ohUx/file54403d8a164c"
  
  > 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/Rtmpu5ohUx/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+smart --output knitr_test.html --email-obfuscation none --standalone --section-divs --template /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/Rtmpu5ohUx/rmarkdown-str544018397aaa.html --lua-filter /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rmarkdown/rmd/lua/latex-div.lua 
  
  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/Rtmpu5ohUx/knitr_test.Rmd
  No existing record found for id SpkyV2:a5430dcddb0a957c73d3140a5d4b7f6f
  Adding RmdFeatureSet object with ID SpkyV2:a5430dcddb0a957c73d3140a5d4b7f6f...
  ID  SpkyV2:a5430dcddb0a957c73d3140a5d4b7f6f 
  No existing record found for id SpkyV2:649972ba8a4253f4080a48e9e16b6c30
  Adding ObjFeatureSet object with ID SpkyV2:649972ba8a4253f4080a48e9e16b6c30...
  ID  SpkyV2:649972ba8a4253f4080a48e9e16b6c30 
  > 
  > f = function(paths) readLines(paths)
  > fil = system.file("test_docs", "knitr_test.Rmd", package = "trackr")
  > recordFiles(fil, ingestfun = f, verbose = TRUE)
    adding: home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/trackr/test_docs/knitr_test.Rmd (deflated 35%)
  No existing record found for id SpkyV2:aa80b4d9353a4be08088ba36c7ca87d9
  Adding ObjFeatureSet object with ID SpkyV2:aa80b4d9353a4be08088ba36c7ca87d9...
  ID  SpkyV2:aa80b4d9353a4be08088ba36c7ca87d9 
  No existing record found for id MD5:e802c1aed82bdfa1c0f183d91578aeb3
  Adding RawFilesFeatureSet object with ID MD5:e802c1aed82bdfa1c0f183d91578aeb3...
  ID  MD5:e802c1aed82bdfa1c0f183d91578aeb3 
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "/tmp/Rtmpu5ohUx"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (4x76)
  First document 
  id:                         SpkyV2:a5430dcddb0a957c73d3140a5d4b7f6f
  chunks(3):                  ---\ntitle: "knitr support test for recordr"\naut...
  numouts:                    1
  numplots:                   0
  title:                      
  author:                     Gabriel Becker and Sara Moore
  textkeywords:               
  codekeywords:               
  inputfiles:                 
  outputids:                  SpkyV2:649972ba8a4253f4080a48e9e16b6c30
  fullcode(12):               ## ----plot--------------------------------------...
  fullcodeinfo.files:         
  fullcodeinfo.strings:       
  fullcodeinfo.libraries:     ggplot2
  fullcodeinfo.inputs:        mtcars
  fullcodeinfo.outputs(2):    p fit
  fullcodeinfo.updates:       
  fullcodeinfo.functions(5):  { qplot $ lm ~
  fullcodeinfo.removes:       
  fullcodeinfo.nsevalVars(2): hp wt
  fullcodeinfo.sideEffects:   
  fullcodeinfo.code:          {\n    library(ggplot2)\n    p = qplot(mtcars$wt,...
  rmdfile:                    /tmp/Rtmpu5ohUx/knitr_test.Rmd
  outfile:                    /tmp/Rtmpu5ohUx/knitr_test.html
  rmdfileid:                  SpkyV2:2bf056300cc95934c5ed2918cce47d25
  figurefiles(10):            bootstrap-3.3.5/css/bootstrap.min.css ...
  user:                       hornik
  regdate:                    2020-01-23
  uniqueid:                   SpkyV2:a5430dcddb0a957c73d3140a5d4b7f6f
  tags:                       
  analysisfile:               <NA>
  rstudioproject:             <NA>
  generatedin:                
  code:                       
  sessioninfo.R.version(14):  x86_64-pc-linux-gnu ... Dark and Stormy Night
  sessioninfo.platform:       x86_64-pc-linux-gnu (64-bit)
  sessioninfo.locale:         LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.U...
  sessioninfo.running:        Debian GNU/Linux bullseye/sid
  sessioninfo.RNGkind(3):     Mersenne-Twister Inversion Rejection
  sessioninfo.basePkgs(7):    stats graphics grDevices utils datasets methods base
  sessioninfo.otherPkgs(4):   ggplot2:3.2.1 trackr:0.10.5 knitr:1.27 histry:0.2.4
  sessioninfo.loadedOnly(60): tidyselect:0.2.5 xfun:0.12 ... compiler:3.6.2
  sessioninfo.matprod:        default
  sessioninfo.BLAS:           /home/hornik/tmp/R.check/r-release-gcc/Work/build...
  sessioninfo.LAPACK:         /home/hornik/tmp/R.check/r-release-gcc/Work/build...
  isplot:                     FALSE
  fsetklass:                  RmdFeatureSet
  trackrversion:              
  clineargs:                  
  resultURI:                  
  titles:                     knitr support test for recordr
  regtime:                    09:04:54
  regdatetime:                2020-01-23T09:04:54Z
  study:                      12345
  important:                  Hi Nolan! It's me, trackr!
  preview.path:               SpkyV2_a5430dcddb0a957c73d3140a5d4b7f6f_thumb.png
  image.path:                 SpkyV2_a5430dcddb0a957c73d3140a5d4b7f6f.png
  
  Field ".file":
  [1] "/tmp/Rtmpu5ohUx/file54403d8a164c"
  Field "file":
  [1] "/tmp/Rtmpu5ohUx/file54403d8a164c"
  
  Warning message:
  In flatten5(as(object, "list")) :
    got a provtable field I don't understand. NULLing it.
  > recs = recs + 2 ## file and read-in value
  > res= findRecords("test_docs")
  > stopifnot(length(res) == 1, # it doesn't find anything from the Rmd because the copy disassociates with original path
  +           length(findRecords("*")) == recs)
  > 
  > ## for now just ensure that it works
  > library(switchr)
  Error in library(switchr) : there is no package called 'switchr'
  Execution halted