CRAN Package Check Results for Package trackr

Last updated on 2019-10-31 00:51:10 CET.

Check Details

Version: 0.10.5
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'images'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.10.5
Check: tests
Result: ERROR
     Running ‘ggplot_extraction.R’ [6s/10s]
     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/RtmpFIRUBR"
    
     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/RtmpFIRUBR/file2f427d0e07c3"
     Field "file":
     [1] "/home/hornik/tmp/scratch/RtmpFIRUBR/file2f427d0e07c3"
    
     > 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/RtmpFIRUBR/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/RtmpFIRUBR/rmarkdown-str2f422e5a3aec.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/RtmpFIRUBR/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:afa7ea580e2f655a635b5eaffd56eb3f
     Adding ObjFeatureSet object with ID SpkyV2:afa7ea580e2f655a635b5eaffd56eb3f...
     ID SpkyV2:afa7ea580e2f655a635b5eaffd56eb3f
     >
     > 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 MD5:544a3943318ba62b16cb91939960a77c
     Adding RawFilesFeatureSet object with ID MD5:544a3943318ba62b16cb91939960a77c...
     ID MD5:544a3943318ba62b16cb91939960a77c
     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/RtmpFIRUBR"
    
     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:afa7ea580e2f655a635b5eaffd56eb3f
     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/RtmpFIRUBR/knitr_test.Rmd
     outfile: /home/hornik/tmp/scratch/RtmpFIRUBR/knitr_test.html
     rmdfileid: SpkyV2:9af395e0438d167f246442ef6aa49594
     figurefiles(9): bootstrap-3.3.5/css/bootstrap.min.css ...
     user: hornik
     regdate: 2019-10-30
     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: 22:33:12
     regdatetime: 2019-10-30T22:33:12Z
     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/RtmpFIRUBR/file2f427d0e07c3"
     Field "file":
     [1] "/home/hornik/tmp/scratch/RtmpFIRUBR/file2f427d0e07c3"
    
     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
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.10.5
Check: package dependencies
Result: ERROR
    Package required but not available: ‘rsolr’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64