CRAN Package Check Results for Package trackr

Last updated on 2020-08-07 01:50:04 CEST.

Check Details

Version: 0.10.6
Check: tests
Result: ERROR
     Running 'ggplot_extraction.R' [9s]
     Running 'trackr-tests.R' [15s]
    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\\RtmpKYSAdB"
    
     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\\RtmpKYSAdB\\file75f02a97af2"
     Field "file":
     [1] "D:\\temp\\RtmpKYSAdB\\file75f02a97af2"
    
     > 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\RtmpKYSAdB/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\Rtmp8mpjMl\RLIBS_a8987e155c94\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:bootstrap" --include-in-header "D:\temp\RtmpKYSAdB\rmarkdown-str75f089449b.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\RtmpKYSAdB/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:f012c7e0ed9d13463a6dda2e19fdc684
     Adding ObjFeatureSet object with ID SpkyV2:f012c7e0ed9d13463a6dda2e19fdc684...
     ID SpkyV2:f012c7e0ed9d13463a6dda2e19fdc684
     >
     > f = function(paths) readLines(paths)
     > fil = system.file("test_docs", "knitr_test.Rmd", package = "trackr")
     > recordFiles(fil, ingestfun = f, verbose = TRUE)
     adding: temp/Rtmp8mpjMl/RLIBS_a8987e155c94/trackr/test_docs/knitr_test.Rmd (deflated 35%)
     No existing record found for id SpkyV2:b13c898215c1ab8414d03169681624b5
     Adding ObjFeatureSet object with ID SpkyV2:b13c898215c1ab8414d03169681624b5...
     ID SpkyV2:b13c898215c1ab8414d03169681624b5
     No existing record found for id MD5:9af617c24b1c94563e64036eaaf2db93
     Adding RawFilesFeatureSet object with ID MD5:9af617c24b1c94563e64036eaaf2db93...
     ID MD5:9af617c24b1c94563e64036eaaf2db93
     An object of class "TrackrDB"
     Slot "opts":
     An object of class "TrackrOptions"
     Slot "insert_delay":
     [1] 0
    
     Slot "img_dir":
     [1] "D:\\temp\\RtmpKYSAdB"
    
     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:f012c7e0ed9d13463a6dda2e19fdc684
     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\\RtmpKYSAdB/knitr_test.Rmd
     outfile: D:/temp/RtmpKYSAdB/knitr_test.html
     rmdfileid: SpkyV2:4a3e41357c5f7effc6cdeaab365951cc
     figurefiles(9): d:\\Rcompile\\CRANpkg\\local\\3.6\\trackr.Rcheck\...
     user: CRAN
     regdate: 2020-08-06
     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: 01:46:12
     regdatetime: 2020-08-06T01:46:12Z
     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\\RtmpKYSAdB\\file75f02a97af2"
     Field "file":
     [1] "D:\\temp\\RtmpKYSAdB\\file75f02a97af2"
    
     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
Flavor: r-oldrel-windows-ix86+x86_64