Running 'ggplot_extraction.R' [6s]
  Running 'trackr-tests.R' [12s]
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] "D:\\temp\\RtmpQDHjYU"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (0x0)
  Field ".file":
  [1] "D:\\temp\\RtmpQDHjYU\\file1954c57ee78be"
  Field "file":
  [1] "D:\\temp\\RtmpQDHjYU\\file1954c57ee78be"
  
  > 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: D:\temp\RtmpQDHjYU/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
  
  "D:/compiler/pandoc/pandoc" +RTS -K512m -RTS knitr_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output knitr_test.html --email-obfuscation none --standalone --section-divs --template "D:\temp\RtmpqoXnZh\RLIBS_e5605eb57da2\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:bootstrap" --include-in-header "D:\temp\RtmpQDHjYU\rmarkdown-str1954c5313561.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: D:\temp\RtmpQDHjYU/knitr_test.Rmd
  No existing record found for id SpkyV2:b88224e4e222b49f76fbca4d13d3b876
  Adding RmdFeatureSet object with ID SpkyV2:b88224e4e222b49f76fbca4d13d3b876...
  ID  SpkyV2:b88224e4e222b49f76fbca4d13d3b876 
  No existing record found for id SpkyV2:4f0688b4e7db8b1efd76689b1333facc
  Adding ObjFeatureSet object with ID SpkyV2:4f0688b4e7db8b1efd76689b1333facc...
  ID  SpkyV2:4f0688b4e7db8b1efd76689b1333facc 
  > 
  > f = function(paths) readLines(paths)
  > fil = system.file("test_docs", "knitr_test.Rmd", package = "trackr")
  > recordFiles(fil, ingestfun = f, verbose = TRUE)
    adding: temp/RtmpqoXnZh/RLIBS_e5605eb57da2/trackr/test_docs/knitr_test.Rmd (deflated 35%)
  No existing record found for id SpkyV2:6a34fe2b50a67be5b0af333df9b2e2cd
  Adding ObjFeatureSet object with ID SpkyV2:6a34fe2b50a67be5b0af333df9b2e2cd...
  ID  SpkyV2:6a34fe2b50a67be5b0af333df9b2e2cd 
  No existing record found for id MD5:7a4140e9aea62c4fba393f23ae55d9c2
  Adding RawFilesFeatureSet object with ID MD5:7a4140e9aea62c4fba393f23ae55d9c2...
  ID  MD5:7a4140e9aea62c4fba393f23ae55d9c2 
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "D:\\temp\\RtmpQDHjYU"
  
  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:b88224e4e222b49f76fbca4d13d3b876
  chunks(3):                  ---\ntitle: "knitr support test for recordr"\naut...
  numouts:                    1
  numplots:                   0
  title:                      
  author:                     Gabriel Becker and Sara Moore
  textkeywords:               
  codekeywords:               
  inputfiles:                 
  outputids:                  SpkyV2:4f0688b4e7db8b1efd76689b1333facc
  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:                    D:\\temp\\RtmpQDHjYU/knitr_test.Rmd
  outfile:                    D:/temp/RtmpQDHjYU/knitr_test.html
  rmdfileid:                  SpkyV2:4a3e41357c5f7effc6cdeaab365951cc
  figurefiles(9):             d:\\Rcompile\\CRANpkg\\local\\3.6\\trackr.Rcheck\...
  user:                       CRAN
  regdate:                    2020-08-26
  uniqueid:                   SpkyV2:b88224e4e222b49f76fbca4d13d3b876
  tags:                       
  analysisfile:               <NA>
  rstudioproject:             <NA>
  generatedin:                
  code:                       
  sessioninfo.R.version(14):  x86_64-w64-mingw32 x86_64 ... Holding the Windsock
  sessioninfo.platform:       x86_64-w64-mingw32/x64 (64-bit)
  sessioninfo.locale:         LC_COLLATE=C;LC_CTYPE=German_Germany.1252;LC_MONE...
  sessioninfo.running:        Windows Server 2008 x64 (build 6003) Service Pack 2
  sessioninfo.RNGkind(3):     Mersenne-Twister Inversion Rejection
  sessioninfo.basePkgs(7):    stats graphics grDevices utils datasets methods base
  sessioninfo.otherPkgs(4):   ggplot2:3.3.2 trackr:0.10.6 knitr:1.29 histry:0.2.4
  sessioninfo.loadedOnly(61): tidyselect:1.1.0 xfun:0.16 ... compiler:3.6.3
  sessioninfo.matprod:        default
  sessioninfo.BLAS:           
  sessioninfo.LAPACK:         
  isplot:                     FALSE
  fsetklass:                  RmdFeatureSet
  trackrversion:              
  clineargs:                  
  resultURI:                  
  titles:                     knitr support test for recordr
  regtime:                    17:30:59
  regdatetime:                2020-08-26T17:30:59Z
  study:                      12345
  important:                  Hi Nolan! It's me, trackr!
  preview.path:               SpkyV2_b88224e4e222b49f76fbca4d13d3b876_thumb.png
  image.path:                 SpkyV2_b88224e4e222b49f76fbca4d13d3b876.png
  
  Field ".file":
  [1] "D:\\temp\\RtmpQDHjYU\\file1954c57ee78be"
  Field "file":
  [1] "D:\\temp\\RtmpQDHjYU\\file1954c57ee78be"
  
  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)$type)))
  + }
  Switchr needs a default CRAN mirror set via R options. Using the cloud mirror. This happens only when no CRAN mirror is selected *and* the BiocInstaller package is not installed.
  Error: all(!is.na(manifest_df(man)$type)) is not TRUE
  Execution halted