CRAN Package Check Results for Package traitdataform

Last updated on 2019-08-24 04:47:10 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.5.5 7.38 70.60 77.98 OK
r-devel-linux-x86_64-debian-gcc 0.5.5 6.05 55.25 61.30 OK
r-devel-linux-x86_64-fedora-clang 0.5.5 94.48 OK
r-devel-linux-x86_64-fedora-gcc 0.5.5 93.39 OK
r-devel-windows-ix86+x86_64 0.5.5 20.00 104.00 124.00 OK
r-patched-linux-x86_64 0.5.5 6.88 68.95 75.83 OK
r-patched-solaris-x86 0.5.5 124.30 OK
r-release-linux-x86_64 0.5.5 6.66 69.06 75.72 OK
r-release-windows-ix86+x86_64 0.5.5 35.00 526.00 561.00 ERROR
r-release-osx-x86_64 0.5.5 OK
r-oldrel-windows-ix86+x86_64 0.5.5 18.00 130.00 148.00 OK
r-oldrel-osx-x86_64 0.5.5 OK

Check Details

Version: 0.5.5
Check: examples
Result: ERROR
    Running examples in 'traitdataform-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: get_gbif_taxonomy
    > ### Title: Get accepted canonical names and taxonomy for a given species
    > ### name
    > ### Aliases: get_gbif_taxonomy
    >
    > ### ** Examples
    >
    >
    > get_gbif_taxonomy(c("Chorthippus albomarginatus", "Chorthippus apricarius",
    + "Chorthippus biguttulus", "Chorthippus dorsatus", "Chorthippus montanus",
    + "Chorthippus parallelus", "Chrysochraon dispar", "Conocephalus dorsalis",
    + "Conocephalus fuscus", "Decticus verrucivorus", "Euthystira brachyptera",
    + "Gomphocerippus rufus", "Gryllus campestris", "Metrioptera roeselii",
    + "Omocestus viridulus", "Phaneroptera falcata", "Platycleis albopunctata",
    + "Spec", "Stenobothrus lineatus", "Stenobothrus stigmaticus",
    + "Stethophyma grossum", "Tetrix kraussi", "Tetrix subulata",
    + "Tetrix tenuicornis", "Tetrix undulata", "Tettigonia cantans",
    + "Tettigonia viridissima")
    + )
    Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) :
     Empty reply from server
    Calls: get_gbif_taxonomy ... <Anonymous> -> <Anonymous> -> crul_fetch -> <Anonymous>
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.5.5
Check: tests
Result: ERROR
     Running 'testthat.R' [205s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(traitdataform)
     >
     > test_check("traitdataform")
     -- 1. Error: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10) -----------
     Timeout was reached: Operation timed out after 10006 milliseconds with 0 out of 0 bytes received
     1: expect_known_hash(get_gbif_taxonomy(as.character(carabids$name_correct[1:12])), hash = "22e476b7d0") at testthat/test.map_gbif_taxonomy.R:10
     2: quasi_label(enquo(object), arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: get_gbif_taxonomy(as.character(carabids$name_correct[1:12]))
     5: taxize::get_gbifid_(x, messages = verbose)
     6: setNames(lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method),
     sciname)
     7: lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method)
     8: FUN(X[[i]], ...)
     9: gbif_name_backbone(sciname)
     10: cli$get(query = args, ...)
     11: private$make_request(rr)
     12: crul_fetch(opts)
     13: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
    
     -- 2. Error: mapping synonyms (@test.map_gbif_taxonomy.R#24) ------------------
     Timeout was reached: Operation timed out after 10013 milliseconds with 0 out of 0 bytes received
     1: expect_true(get_gbif_taxonomy("Limodromus_assimilis")$scientificNameStd == "Platynus assimilis") at testthat/test.map_gbif_taxonomy.R:24
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: get_gbif_taxonomy("Limodromus_assimilis")
     5: taxize::get_gbifid_(temp[[i]]$species[which.max(temp[[i]]$confidence)], messages = verbose)
     6: setNames(lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method),
     sciname)
     7: lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method)
     8: FUN(X[[i]], ...)
     9: gbif_name_backbone(sciname)
     10: cli$get(query = args, ...)
     11: private$make_request(rr)
     12: crul_fetch(opts)
     13: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
    
     -- 3. Error: mapping doubtful taxa (@test.map_gbif_taxonomy.R#34) -------------
     Empty reply from server
     1: expect_match(get_gbif_taxonomy("Rhynchaenus fagi")$warnings, "DOUBTFUL") at testthat/test.map_gbif_taxonomy.R:34
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: get_gbif_taxonomy("Rhynchaenus fagi")
     5: taxize::get_gbifid_(x, messages = verbose)
     6: setNames(lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method),
     sciname)
     7: lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method)
     8: FUN(X[[i]], ...)
     9: gbif_name_backbone(sciname)
     10: cli$get(query = args, ...)
     11: private$make_request(rr)
     12: crul_fetch(opts)
     13: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
    
     -- 4. Error: mapping lower or higher taxa (@test.map_gbif_taxonomy.R#41) ------
     Empty reply from server
     1: expect_true(get_gbif_taxonomy("Acrocephalus familiaris kingi")$scientificNameStd ==
     "Acrocephalus familiaris kingi") at testthat/test.map_gbif_taxonomy.R:41
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: get_gbif_taxonomy("Acrocephalus familiaris kingi")
     5: taxize::get_gbifid_(x, messages = verbose)
     6: setNames(lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method),
     sciname)
     7: lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method)
     8: FUN(X[[i]], ...)
     9: gbif_name_backbone(sciname)
     10: cli$get(query = args, ...)
     11: private$make_request(rr)
     12: crul_fetch(opts)
     13: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
    
     -- 5. Error: not matching (@test.map_gbif_taxonomy.R#52) ----------------------
     Timeout was reached: Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
     1: expect_true(get_gbif_taxonomy("No_species")$warnings == " No match! Check spelling or lower confidence threshold!") at testthat/test.map_gbif_taxonomy.R:52
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: get_gbif_taxonomy("No_species")
     5: taxize::get_gbifid_(x, messages = verbose)
     6: setNames(lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method),
     sciname)
     7: lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method)
     8: FUN(X[[i]], ...)
     9: gbif_name_backbone(sciname)
     10: cli$get(query = args, ...)
     11: private$make_request(rr)
     12: crul_fetch(opts)
     13: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
    
     -- 6. Error: mapping of taxa works (@test.standardize.R#9) --------------------
     Empty reply from server
     1: standardise_taxa(dataset1[c(1, 83, 166, 206, 240, 286, 320, 323, 361, 306, 440),
     ]) at testthat/test.standardize.R:9
     2: do.call(method, c(list(levels(droplevels(as.factor(x$scientificName)))), method_options))
     3: (function (x, subspecies = TRUE, higherrank = FALSE, verbose = FALSE, fuzzy = TRUE,
     conf_threshold = 90, resolve_synonyms = TRUE)
     {
     matchtype = status = confidence = NULL
     temp <- taxize::get_gbifid_(x, messages = verbose)
     for (i in 1:length(temp)) {
     warning_i = ""
     synonym_i = FALSE
     if (nrow(temp[[i]]) == 0) {
     warning_i <- paste("No matching species concept!")
     temp[[i]] <- data.frame(scientificName = x[i], matchtype = "NONE", status = "NA",
     rank = "species")
     }
     if (!fuzzy & nrow(temp[[i]]) > 0) {
     temp[[i]] <- subset(temp[[i]], matchtype != "FUZZY")
     if (nrow(temp[[i]]) == 0) {
     warning_i <- paste(warning_i, "Fuzzy matching might yield results.")
     }
     }
     if (!is.null(conf_threshold) & nrow(temp[[i]]) > 0) {
     temp[[i]] <- subset(temp[[i]], confidence >= conf_threshold)
     if (nrow(temp[[i]]) == 0) {
     temp[[i]] <- data.frame(scientificName = x[i], matchtype = "NONE",
     status = "NA", rank = "species")
     warning_i <- paste(warning_i, "No match! Check spelling or lower confidence threshold!")
     }
     }
     if (any(temp[[i]]$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)
     4: taxize::get_gbifid_(x, messages = verbose)
     5: setNames(lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method),
     sciname)
     6: lapply(sciname, get_gbifd_help, messages = messages, rows = rows, method = method)
     7: FUN(X[[i]], ...)
     8: gbif_name_backbone(sciname)
     9: cli$get(query = args, ...)
     10: private$make_request(rr)
     11: crul_fetch(opts)
     12: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
    
     == testthat results ===========================================================
     [ OK: 37 | SKIPPED: 2 | WARNINGS: 2 | FAILED: 6 ]
     1. Error: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10)
     2. Error: mapping synonyms (@test.map_gbif_taxonomy.R#24)
     3. Error: mapping doubtful taxa (@test.map_gbif_taxonomy.R#34)
     4. Error: mapping lower or higher taxa (@test.map_gbif_taxonomy.R#41)
     5. Error: not matching (@test.map_gbif_taxonomy.R#52)
     6. Error: mapping of taxa works (@test.standardize.R#9)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.5.5
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'traitdataform.Rmd' using rmarkdown
    Quitting from lines 451-454 (traitdataform.Rmd)
    Error: processing vignette 'traitdataform.Rmd' failed with diagnostics:
    Timeout was reached: Operation timed out after 10006 milliseconds with 0 out of 0 bytes received
    --- failed re-building 'traitdataform.Rmd'
    
    SUMMARY: processing the following file failed:
     'traitdataform.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-windows-ix86+x86_64