Running ‘ggplot_extraction.R’ [6s/9s]
  Running ‘trackr-tests.R’ [7s/11s]
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] "/home/hornik/tmp/scratch/RtmppAj3AQ"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (0x0)
  Field ".file":
  [1] "/home/hornik/tmp/scratch/RtmppAj3AQ/filee95db538b4"
  Field "file":
  [1] "/home/hornik/tmp/scratch/RtmppAj3AQ/filee95db538b4"
  
  > 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: /home/hornik/tmp/scratch/RtmppAj3AQ/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-devel-gcc/Work/build/Packages/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /home/hornik/tmp/scratch/RtmppAj3AQ/rmarkdown-stre9541ab9e36.html --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-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: /home/hornik/tmp/scratch/RtmppAj3AQ/knitr_test.Rmd
  No existing record found for id SpkyV2:f8fbfeff6b575c0f5600100f9468bfdd
  Adding RmdFeatureSet object with ID SpkyV2:f8fbfeff6b575c0f5600100f9468bfdd...
  ID  SpkyV2:f8fbfeff6b575c0f5600100f9468bfdd 
  No existing record found for id SpkyV2:7ecfe1733e9be11159d6063c16129c83
  Adding ObjFeatureSet object with ID SpkyV2:7ecfe1733e9be11159d6063c16129c83...
  ID  SpkyV2:7ecfe1733e9be11159d6063c16129c83 
  > 
  > 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-devel-gcc/Work/build/Packages/trackr/test_docs/knitr_test.Rmd (deflated 35%)
  No existing record found for id SpkyV2:2949e0a32a91147f713c312fdb6be0ef
  Adding ObjFeatureSet object with ID SpkyV2:2949e0a32a91147f713c312fdb6be0ef...
  ID  SpkyV2:2949e0a32a91147f713c312fdb6be0ef 
  No existing record found for id MD5:21f3ad0969433ac77fad1fd51315f765
  Adding RawFilesFeatureSet object with ID MD5:21f3ad0969433ac77fad1fd51315f765...
  ID  MD5:21f3ad0969433ac77fad1fd51315f765 
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "/home/hornik/tmp/scratch/RtmppAj3AQ"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (4x78)
  First document 
  id:                          SpkyV2:f8fbfeff6b575c0f5600100f9468bfdd
  chunks(3):                   ---\ntitle: "knitr support test for recordr"\nau...
  numouts:                     1
  numplots:                    0
  title:                       
  author:                      Gabriel Becker and Sara Moore
  textkeywords:                
  codekeywords:                
  inputfiles:                  
  outputids:                   SpkyV2:7ecfe1733e9be11159d6063c16129c83
  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:                     /home/hornik/tmp/scratch/RtmppAj3AQ/knitr_test.Rmd
  outfile:                     /home/hornik/tmp/scratch/RtmppAj3AQ/knitr_test.html
  rmdfileid:                   SpkyV2:9af395e0438d167f246442ef6aa49594
  figurefiles(9):              bootstrap-3.3.5/css/bootstrap.min.css ...
  user:                        hornik
  regdate:                     2019-11-08
  uniqueid:                    SpkyV2:f8fbfeff6b575c0f5600100f9468bfdd
  tags:                        
  analysisfile:                <NA>
  rstudioproject:              <NA>
  generatedin:                 
  code:                        
  sessioninfo.R.version(14):   x86_64-pc-linux-gnu ... Unsuffered Consequences
  sessioninfo.platform:        x86_64-pc-linux-gnu (64-bit)
  sessioninfo.locale:          LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US....
  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:1.25 histry:0.2.4
  sessioninfo.loadedOnly(58):  tidyselect:0.2.5 xfun:0.10 ... compiler:4.0.0
  sessioninfo.matprod:         default
  sessioninfo.BLAS:            /home/hornik/tmp/R.check/r-devel-gcc/Work/build/...
  sessioninfo.LAPACK:          /home/hornik/tmp/R.check/r-devel-gcc/Work/build/...
  sessioninfo.system.codepage: NULL
  sessioninfo.codepage:        NULL
  isplot:                      FALSE
  fsetklass:                   RmdFeatureSet
  trackrversion:               
  clineargs:                   
  resultURI:                   
  titles:                      knitr support test for recordr
  regtime:                     22:38:30
  regdatetime:                 2019-11-08T22:38:30Z
  study:                       12345
  important:                   Hi Nolan! It's me, trackr!
  preview.path:                SpkyV2_f8fbfeff6b575c0f5600100f9468bfdd_thumb.png
  image.path:                  SpkyV2_f8fbfeff6b575c0f5600100f9468bfdd.png
  
  Field ".file":
  [1] "/home/hornik/tmp/scratch/RtmppAj3AQ/filee95db538b4"
  Field "file":
  [1] "/home/hornik/tmp/scratch/RtmppAj3AQ/filee95db538b4"
  
  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)
  > if(any(grepl("bioc", defaultRepos(), ignore.case = TRUE)) &&
  +    !anyNA(defaultRepos())) { #on some systems bioc repos not available. this will fail.
  +     man = manifestFromRecord(res[[1]])
  +     stopifnot(all(!is.na(manifest_df(man)$type)))
  + }
  Error: Bioconductor version '3.10' requires R version '3.6'; see
    https://bioconductor.org/install
  Execution halted