CRAN Package Check Results for Package traitdataform

Last updated on 2019-05-02 08:50:02 CEST.

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: 65 SKIPPED: 1 WARNINGS: 4 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

Version: 0.5.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [4s/13s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(traitdataform)
     >
     > test_check("traitdataform")
    
     *** caught segfault ***
     address (nil), cause 'unknown'
    
     Traceback:
     1: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
     2: crul_fetch(opts)
     3: private$make_request(rr)
     4: cli$get(query = args, ...)
     5: gbif_name_backbone(sciname)
     6: FUN(X[[i]], ...)
     7: lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method)
     8: setNames(lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method), sciname)
     9: taxize::get_gbifid_(x, messages = verbose)
     10: (function (x, subspecies = TRUE, higherrank = FALSE, verbose = FALSE, fuzzy = TRUE, conf_threshold = 90, resolve_synonyms = TRUE) { matchtype = status = confidence = NULL temp <- taxize::get_gbifid_(x, messages = verbose) for (i in 1:length(temp)) { warning_i = "" synonym_i = FALSE if (nrow(temp[[i]]) == 0) { warning_i <- paste("No matching species concept!") temp[[i]] <- data.frame(scientificName = x[i], matchtype = "NONE", status = "NA", rank = "species") } if (!fuzzy & nrow(temp[[i]]) > 0) { temp[[i]] <- subset(temp[[i]], matchtype != "FUZZY") if (nrow(temp[[i]]) == 0) { warning_i <- paste(warning_i, "Fuzzy matching might yield results.") } } if (!is.null(conf_threshold) & nrow(temp[[i]]) > 0) { temp[[i]] <- subset(temp[[i]], confidence >= conf_threshold) if (nrow(temp[[i]]) == 0) { temp[[i]] <- data.frame(scientificName = x[i], matchtype = "NONE", status = "NA", rank = "species") warning_i <- paste(warning_i, "No match! Check spelling or lower confidence threshold!") } } if (any(temp[[i]]$status == "ACCEPTED")) { temp[[i]] <- subset(temp[[i]], status == "ACCEPTED") temp[[i]] <- subset(temp[[i]], temp[[i]]$confidence == max(temp[[i]]$confidence)) if (nrow(temp[[i]]) > 1) { temp[[i]] <- temp[[i]][1, ] warning_i <- paste(warning_i, "Selected first of multiple equally ranked concepts!") } } if (!any(temp[[i]]$status == "ACCEPTED") & any(temp[[i]]$status == "SYNONYM")) { if (resolve_synonyms) { keep <- temp[i] temp[i] <- taxize::get_gbifid_(temp[[i]]$species[which.max(temp[[i]]$confidence)], messages = verbose) if (temp[[i]][1, ]$status == "ACCEPTED") { temp[[i]] <- subset(temp[[i]], matchtype == "EXACT" & status == "ACCEPTED") temp[[i]] <- subset(temp[[i]], temp[[i]]$confidence == max(temp[[i]]$confidence)) if (nrow(temp[[i]]) > 1) { temp[[i]] <- temp[[i]][1, ] warning_i <- paste(warning_i, "Selected first of multiple equally ranked concepts!") } warning_i <- paste(warning_i, "A synonym was mapped to the accepted species concept!", sep = " ") synonym_i = TRUE } else { status <- temp[[i]][1, ]$status temp[i] <- keep if (nrow(temp[[i]]) > 1) { temp[[i]] <- temp[[i]][1, ] warning_i <- paste(warning_i, "Selected first of multiple equally ranked concepts!") } warning_i <- paste0(warning_i, " Resolved synonym '", temp[[i]]$species, "' is labelled '", status, "'. Clarification required!") } } else { temp[[i]] <- subset(temp[[i]], status == "SYNONYM") temp[[i]] <- subset(temp[[i]], temp[[i]]$confidence == max(temp[[i]]$confidence)) warning_i <- paste(warning_i, "The provided taxon seems to be a synonym of '", temp[[i]]$species, "'!", sep = "") } } if (all(temp[[i]]$status == "DOUBTFUL")) { temp[[i]] <- subset(temp[[i]], status == "DOUBTFUL") warning_i <- paste(warning_i, "Mapped concept is labelled 'DOUBTFUL'!") temp[[i]] <- subset(temp[[i]], temp[[i]]$confidence == max(temp[[i]]$confidence)) if (nrow(temp[[i]]) > 1) { temp[[i]] <- temp[[i]][1, ] warning_i <- paste(warning_i, "Selected first of multiple equally ranked concepts!") } } rankorder <- c("kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies") if (match(temp[[i]]$rank, rankorder) > 7 & !subspecies) { if (length(strsplit(as.character(temp[[i]]$canonicalname), " ")[[1]]) > 2) { temp[i] <- taxize::get_gbifid_(paste(strsplit(names(temp[i]), " ")[[1]][1:2], collapse = " "), messages = verbose) temp[[i]] <- subset(temp[[i]], temp[[i]]$confidence == max(temp[[i]]$confidence)) warning_i <- paste(warning_i, "Subspecies has been remapped to species concept!", sep = " ") } else { temp[[i]] <- data.frame(scientificName = x[i], matchtype = "NONE", rank = "subspecies") warning_i <- paste(warning_i, "No mapping of subspecies name to species was possible!", sep = " ") } } if (temp[[i]]$matchtype == "HIGHERRANK") { if (higherrank) { temp[[i]] <- subset(temp[[i]], temp[[i]]$confidence == max(temp[[i]]$confidence)) warning_i <- paste(warning_i, "No matching species concept! Entry has been mapped to higher taxonomic level.") } else { temp[[i]] <- data.frame(scientificName = x[i], matchtype = "NONE", rank = "highertaxon") warning_i <- paste("No matching species concept!", warning_i) } } if (temp[[i]]$matchtype != "NONE") { temp[[i]] <- data.frame(scientificName = x[i], synonym = synonym_i, scientificNameStd = temp[[i]]$canonicalname, author = sub(paste0(temp[[i]]$canonicalname, " "), "", temp[[i]]$scientificname), taxonRank = temp[[i]]$rank, confidence = temp[[i]]$confidence, kingdom = if (is.null(temp[[i]]$kingdom)) NA else temp[[i]]$kingdom, phylum = if (is.null(temp[[i]]$phylum)) NA else temp[[i]]$phylum, class = if (is.null(temp[[i]]$class)) NA else temp[[i]]$class, order = if (is.null(temp[[i]]$order)) NA else temp[[i]]$order, family = if (is.null(temp[[i]]$family)) NA else temp[[i]]$family, genus = if (is.null(temp[[i]]$genus)) NA else temp[[i]]$genus, taxonomy = "GBIF Backbone Taxonomy", taxonID = paste0("http://www.gbif.org/species/", temp[[i]]$usagekey, ""), warnings = NA) } else { temp[[i]] <- data.frame(scientificName = x[i], warnings = NA) } temp[[i]]$warnings <- warning_i if (verbose & nchar(warning_i) >= 1) warning(warning_i) } out <- data.table::rbindlist(temp, fill = TRUE) class(out) <- c("data.frame", "taxonomy") return(out)})(c("Abax_parallelepipedus", "Calathus_cinctus", "Dromius_angustus", "Limodromus_assimilis", "Miscodira_artica", "Notiophilus_aquaticus", "Trichocellus_placidus"), subspecies = 1, higherrank = 0, verbose = 0, fuzzy = 1, conf_threshold = 90, resolve_synonyms = 1)
     11: do.call(method, c(list(levels(droplevels(as.factor(x$scientificName)))), method_options))
     12: standardise_taxa(dataset1[c(1, 83, 166, 206, 240, 286, 320, 323, 361, 306, 440), ])
     13: eval(code, test_env)
     14: eval(code, test_env)
     15: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     16: doTryCatch(return(expr), name, parentenv, handler)
     17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     19: doTryCatch(return(expr), name, parentenv, handler)
     20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     21: tryCatchList(expr, classes, parentenv, handlers)
     22: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     23: test_code(desc, code, env = parent.frame())
     24: test_that("mapping of taxa works", { pulldata("carabids") dataset1 <- as.traitdata(carabids) dd1 <- standardise_taxa(dataset1[c(1, 83, 166, 206, 240, 286, 320, 323, 361, 306, 440), ]) expect_equal(as.character(dd1$scientificNameStd), c("Abax parallelepipedus", "Abax parallelepipedus", "Calathus cinctus", "Calathus cinctus", "Dromius angustus", "Platynus assimilis", "Platynus assimilis", NA, NA, "Notiophilus aquaticus", "Dicheirotrichus placidus")) expect_true(all(c("scientificNameStd", "taxonID", "warnings") %in% names(dd1))) dd1 <- standardise_taxa(dataset1[c(1, 83, 166, 206, 240, 286, 320, 323, 361, 306, 440), ], method_options = c(resolve_synonyms = FALSE)) expect_equal(as.character(dd1$scientificNameStd), c("Abax parallelepipedus", "Abax parallelepipedus", "Calathus cinctus", "Calathus cinctus", "Dromius angustus", "Limodromus assimilis", "Limodromus assimilis", NA, NA, "Notiophilus aquaticus", "Trichocellus placidus")) expect_true(all(c("scientificNameStd", "taxonID", "warnings") %in% names(dd1))) pulldata("arthropodtraits") dataset2 <- as.traitdata(arthropodtraits) dd2 <- standardise_taxa(dataset2[c(215, 476, 774, 975, 1445, 1706, 3437, 3905, 4667, 5396, 5896, 8755, 8966), ]) expect_equal(as.character(dd2$scientificNameStd), c("Acalypta parvula", "Kosswigianella denticauda", "Kosswigianella spinosa", "Kosswigianella spinosa", "Kosswigianella spinosa", "Aspidapion radiolus", "Aspidapion radiolus", "Aspidapion radiolus", "Mocyta fungi", "Gymnetron ictericus", "Gymnetron ictericus", "Gymnetron ictericus", "Trigonocranus emmeae")) expect_true(all(c("scientificNameStd", "taxonID", "warnings") %in% names(dd2)))})
     25: eval(code, test_env)
     26: eval(code, test_env)
     27: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     28: doTryCatch(return(expr), name, parentenv, handler)
     29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     31: doTryCatch(return(expr), name, parentenv, handler)
     32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     33: tryCatchList(expr, classes, parentenv, handlers)
     34: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     35: test_code(NULL, exprs, env)
     36: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     37: force(code)
     38: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$end_context() reporter$end_file() })
     39: FUN(X[[i]], ...)
     40: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     41: force(code)
     42: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     43: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     44: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     45: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     46: test_check("traitdataform")
     An irrecoverable exception occurred. R is aborting now ...
     Segmentation fault
Flavor: r-patched-linux-x86_64