CRAN Package Check Results for Package traitdataform

Last updated on 2019-04-21 01:48:09 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.5.3 6.45 60.96 67.41 ERROR
r-devel-linux-x86_64-debian-gcc 0.5.3 6.13 57.23 63.36 OK
r-devel-linux-x86_64-fedora-clang 0.5.3 88.09 OK
r-devel-linux-x86_64-fedora-gcc 0.5.3 84.40 OK
r-devel-windows-ix86+x86_64 0.5.3 25.00 148.00 173.00 OK
r-patched-linux-x86_64 0.5.3 7.07 67.76 74.83 OK
r-patched-solaris-x86 0.5.3 133.40 OK
r-release-linux-x86_64 0.5.3 4.06 66.22 70.28 OK
r-release-windows-ix86+x86_64 0.5.2 10.00 146.00 156.00 OK
r-release-osx-x86_64 0.5.3 OK
r-oldrel-windows-ix86+x86_64 0.5.3 13.00 136.00 149.00 OK
r-oldrel-osx-x86_64 0.5.2 OK

Check Details

Version: 0.5.3
Check: examples
Result: ERROR
    Running examples in 'traitdataform-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: mutate.traitdata
    > ### Title: Mutate traits within a traitdata object.
    > ### Aliases: mutate.traitdata
    >
    > ### ** Examples
    >
    >
    > ## Not run:
    > ##D pulldata("arthropodtraits")
    > ##D dataset3 <- as.traitdata(arthropodtraits,
    > ##D taxa = "SpeciesID",
    > ##D traits = c("Body_Size", "Dispersal_ability",
    > ##D "Feeding_guild","Feeding_guild_short",
    > ##D "Feeding_mode", "Feeding_specialization",
    > ##D "Feeding_tissue", "Feeding_plant_part",
    > ##D "Endophagous_lifestyle", "Stratum_use",
    > ##D "Stratum_use_short"),
    > ##D units = c(Body_Size = "mm", Dispersal_ability = "unitless"),
    > ##D keep = c(measurementRemark = "Remark"),
    > ##D metadata = list(
    > ##D license = "http://creativecommons.org/publicdomain/zero/1.0/"
    > ##D )
    > ##D )
    > ##D head(dataset3)
    > ##D
    > ##D updated <- mutate.traitdata(dataset3, predator = Feeding_guild == "c" )
    > ##D
    > ##D head(updated[updated$traitName == "predator",])
    > ##D
    > ##D levels(updated$traitName)
    > ## End(Not run)
    >
    > ##
    >
    > pulldata("heteroptera_raw")
    Warning in read.table(file = file, header = header, sep = sep, quote = quote, :
     invalid input found on input connection 'https://ndownloader.figshare.com/files/5633883'
    Warning in read.table(file = file, header = header, sep = sep, quote = quote, :
     incomplete final line found by readTableHeader on 'https://ndownloader.figshare.com/files/5633883'
    The dataset 'heteroptera_raw' is now available for use!
    
    > dataset2 <- as.traitdata(heteroptera_raw,
    + traits = c("Body_length", "Body_width", "Body_height", "Thorax_length",
    + "Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1",
    + "Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5",
    + "Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length",
    + "Front.Femur_length", "Hind.Femur_length", "Front.Femur_width",
    + "Hind.Femur_width", "Rostrum_length", "Rostrum_width",
    + "Wing_length", "Wing_width"),
    + taxa = "SpeciesID",
    + occurrences = "ID"
    + )
    Input is taken to be an occurrence table/an observation -- trait matrix
    (i.e. with individual specimens per row and multiple trait measurements in columns).
    If this is not the case, please provide parameters!
    Error in `$<-.data.frame`(`*tmp*`, "measurementID", value = 2:1) :
     replacement has 2 rows, data has 0
    Calls: as.traitdata -> $<- -> $<-.data.frame
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.5.3
Check: tests
Result: ERROR
     Running 'testthat.R' [6s/19s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(traitdataform)
     >
     > test_check("traitdataform")
     -- 1. Failure: encoding and read-in successful (@test.columns_to_ETS.R#19) ----
     as.character(heteroptera_raw[13, 6]) not equal to "(Herrich-Schäffer, 1841)".
     1/1 mismatches
     x[1]: NA
     y[1]: "(Herrich-Schäffer, 1841)"
    
     -- 2. Error: reformat observation data, with trait columns provided as attribute
     replacement has 2 rows, data has 0
     1: as.traitdata(heteroptera_raw) at testthat/test.columns_to_ETS.R:74
     2: `$<-`(`*tmp*`, "measurementID", value = structure(2:1, .Label = c("0", "1"), class = "factor"))
     3: `$<-.data.frame`(`*tmp*`, "measurementID", value = structure(2:1, .Label = c("0",
     "1"), class = "factor"))
     4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"),
     N, nrows), domain = NA)
    
     -- 3. Error: mapping of traits based on thesaurus works (@test.standardize.R#31)
     replacement has 2 rows, data has 0
     1: as.traitdata(heteroptera_raw) at testthat/test.standardize.R:31
     2: `$<-`(`*tmp*`, "measurementID", value = structure(2:1, .Label = c("0", "1"), class = "factor"))
     3: `$<-.data.frame`(`*tmp*`, "measurementID", value = structure(2:1, .Label = c("0",
     "1"), class = "factor"))
     4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"),
     N, nrows), domain = NA)
    
     == testthat results ===========================================================
     OK: 69 SKIPPED: 1 FAILED: 3
     1. Failure: encoding and read-in successful (@test.columns_to_ETS.R#19)
     2. Error: reformat observation data, with trait columns provided as attributes (@test.columns_to_ETS.R#74)
     3. Error: mapping of traits based on thesaurus works (@test.standardize.R#31)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.5.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'traitdataform.Rmd' using rmarkdown
    Quitting from lines 94-118 (traitdataform.Rmd)
    Error: processing vignette 'traitdataform.Rmd' failed with diagnostics:
    replacement has 2 rows, data has 0
    --- failed re-building 'traitdataform.Rmd'
    
    SUMMARY: processing the following file failed:
     'traitdataform.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang