* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/BeeBDC.Rcheck’ * using R Under development (unstable) (2024-04-19 r86451) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘BeeBDC/DESCRIPTION’ ... OK * this is package ‘BeeBDC’ version ‘1.1.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BeeBDC’ can be installed ... [74s/161s] OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [17s/31s] OK * checking whether the package can be loaded with stated dependencies ... [16s/25s] OK * checking whether the package can be unloaded cleanly ... [15s/32s] OK * checking whether the namespace can be loaded with stated dependencies ... [16s/28s] OK * checking whether the namespace can be unloaded cleanly ... [16s/26s] OK * checking loading without being on the library search path ... [16s/28s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [106s/145s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 107 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [19s/27s] ERROR Running examples in ‘BeeBDC-Ex.R’ failed The error most likely occurred in: > ### Name: countryOutlieRs > ### Title: Flag country-level outliers with a provided checklist. > ### Aliases: countryOutlieRs > > ### ** Examples > > library(magrittr) > # Load in the test dataset > beesRaw <- BeeBDC::beesRaw > # For the sake of this example, use the testChecklist > system.file("extdata", "testChecklist.rda", package="BeeBDC") |> load() > # For real examples, you might download the beesChecklist from FigShare using > # [BeeBDC::beesChecklist()] > > beesRaw_out <- countryOutlieRs(checklist = testChecklist, + data = beesRaw %>% + dplyr::filter(dplyr::row_number() %in% 1:50), + keepAdjacentCountry = TRUE, + pointBuffer = 1, + scale = 50, + stepSize = 1000000, + mc.cores = 1) The rnaturalearthdata package needs to be installed. Installing the rnaturalearthdata package. Installing package into ‘/tmp/RtmpUCMlxJ/RLIBS_3fa4a35c9c4cfd’ (as ‘lib’ is unspecified) Error in value[[3L]](cond) : Failed to install the rnaturalearthdata package. Please try installing the package for yourself using the following command: install.packages("rnaturalearthdata") Calls: countryOutlieRs Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [72s/119s] [72s/120s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > requireNamespace("testthat") Loading required namespace: testthat > requireNamespace("BeeBDC") Loading required namespace: BeeBDC > > testthat::test_check("BeeBDC") Loading required package: BeeBDC Loading required namespace: mgsub Starting taxonomy report... Nomia maneei is an accpeted name with the taxon id number 38067. - 'Nomia maneei' has the synonyms: Starting checklist report... - Nomia maneei Cockerell, 1910 is reportedly found in: United States The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'. These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport. Starting taxonomy report... Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12323. Nomia maneei is an accpeted name with the taxon id number 38067. Bombus hypnorum is an accpeted name with the taxon id number 9760. - 'Ceratina nanula Cockerell, 1897' has the synonyms: - 'Nomia maneei' has the synonyms: - 'Bombus hypnorum' has the synonyms: Starting checklist report... - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: Austria, Belarus, Brussels, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, Scotland, Colombia - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: Austria, Belarus, Brussels, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, Scotland, Colombia - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: Austria, Belarus, Brussels, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, Scotland, Colombia The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'. These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport. Starting taxonomy report... Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12323. Nomia maneei is an accpeted name with the taxon id number 38067. Bombus hypnorum is an accpeted name with the taxon id number 9760. - 'Ceratina nanula Cockerell, 1897' has the synonyms: - 'Nomia maneei' has the synonyms: - 'Bombus hypnorum' has the synonyms: The output will be returned as a list with the elements: 'taxonomyReport' and 'SynonymReport'. These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, or 'output'$failedReport. Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union - jbd_GBIFissues: Flagged 5 The .GBIFflags column was added to the database. - Formatting taxonomy for matching... The names_clean column was not found and will be temporarily copied from scientificName - Harmonise the occurrence data with unambiguous names... - Attempting to harmonise the occurrence data with ambiguous names... - Formatting merged datasets... Removing the names_clean column... - We matched valid names to 96 of 100 occurrence records. This leaves a total of 4 unmatched occurrence records. harmoniseR: 4 records were flagged. The column, '.invalidName' was added to the database. - We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName - Completed in 2.11 secs - Formatting taxonomy for matching... The names_clean column was not found and will be temporarily copied from scientificName - Harmonise the occurrence data with unambiguous names... - Attempting to harmonise the occurrence data with ambiguous names... checkVerbatim = TRUE. Checking the verbatimScientificName column... - Formatting merged datasets... Removing the names_clean column... - We matched valid names to 98 of 102 occurrence records. This leaves a total of 4 unmatched occurrence records. harmoniseR: 4 records were flagged. The column, '.invalidName' was added to the database. - We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName - Completed in 3.19 secs - INITIAL match with occurrenceID only 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. - Starting iteration 1 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 2 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 3 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 4 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 5 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 6 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 7 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 8 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Starting iteration 9 Matched 2 of 15 Paige occurrences. There are 13 occurrences remaining to match. This step has found 0 extra occurrences from the last iteration. - Updating Paige datasheet to merge... - Updating the final datasheet with new information from Paige... - No dates in file name(s). Finding most-recent from file save time... - Found the following file(s): /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS/19-Nov-22_USGS_DRO_flat.txt - Reading in data file. This should not take too long. There may be some errors upon reading in depending on the state of the data. One might consider reporting errors to Sam Droege to improve the dataset. Rows: 7 Columns: 35 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "$" chr (22): ID., name, sex, DeterminedBy, WhoScanned, COLLECTION.db, ip, coun... dbl (7): gmt, latitude, longitude, accuracy, elevation, position, how1 lgl (3): SpeciesNotes, days, note dttm (1): DateEntered date (2): DeterminedWhen, DateScanned ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. - Formatting the USGS dataset... - Formatting the dateTime... - Creating samplingProtocol and samplingEffort columns... - Creating the fieldNotes and dataSource columns... - Renaming and selecting columns... - Checking for existing out_file directory... - No existing,out_file directory found. Creating directory... - Writing occurrence data file... Number of rows (records): 7 Written to file called USGS_formatted_2024-04-19.csv at location /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS/out_file - Writing attributes file... Written to file called USGS_attribute_files2024-04-19.xml at location /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS/out_file - Fin. trying URL 'https://figshare.com/ndownloader/files/42320598?private_link=bce1f92848c2ced313ee' Content type 'application/octet-stream' length 764612 bytes (746 KB) ================================================== downloaded 746 KB trying URL 'https://open.flinders.edu.au/ndownloader/files/43331472' Content type 'application/octet-stream' length 1105124 bytes (1.1 MB) ================================================== downloaded 1.1 MB \coordUncerFlagR: Flagged 3 geographically uncertain records: The column '.uncertaintyThreshold' was added to the database. - Using default country names and codes from https:en.wikipedia.org/wiki/ISO_3166-1_alpha-2 - static version from July 2022. The rnaturalearthdata package needs to be installed. Installing the rnaturalearthdata package. Installing package into '/tmp/RtmpUCMlxJ/RLIBS_3fa4a378522668' (as 'lib' is unspecified) Loading required namespace: emld Failed with error: 'there is no package called 'emld'' - Checking for existing out_file directory... - Existing out_filedirectory found. Data will be saved here. - We have removed empty columns. This is standard, but as an FYI, these columns are: - Writing occurrence, attribute, and EML data file in .rds format... Number of records: 5 Number of attribute sources: 1 The 0 eml sources are Writing to file called BeeData_2024-04-19.rds at location /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS/out_file... - dataSaver. Fin. - Checking for existing out_file directory... - Existing out_filedirectory found. Data will be saved here. - We have removed empty columns. This is standard, but as an FYI, these columns are: - Writing occurrence data file in csv format... Number of rows (records): 5 Writing to file called BeeData_combined_2024-04-19.csv at location /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS/out_file... - Writing attribute data file in csv format... Number of rows (sources): 1 Written to file called BeeData_attributes_2024-04-19.csv at location /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS/out_file - dataSaver. Fin. Rows: 5 Columns: 15 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp... dbl (5): collector_number, day_collected, year_collected, latitude, longitude ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 1 Columns: 11 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (11): dataSource, alternateIdentifier, title, pubDate, dateStamp, doi, d... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. - Preparing data... - Extracting dates from year, month, day columns... - Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats... - Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats... - Formating and combining the new data.. - Merging all data, nearly there... - Finished. We now have -1 more full eventDate cells than in the input data. We modified dates in 9 occurrences. - As it stands, there are 9 complete eventDates and 1 missing dates. - There are also 9 complete year occurrences to filter from. This is up from an initial count of 2 At this rate, you will stand to lose 1 occurrences on the basis of missing year - Operation time: 1.11050987243652 secs - Preparing data... - Extracting dates from year, month, day columns... - Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats... - Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats... - Formating and combining the new data.. - Merging all data, nearly there... - Finished. We now have 8 more full eventDate cells than in the input data. We modified dates in 18 occurrences. - As it stands, there are 18 complete eventDates and 1 missing dates. - There are also 19 complete year occurrences to filter from. This is up from an initial count of 6 At this rate, you will stand to lose 0 occurrences on the basis of missing year - Operation time: 0.966851472854614 secs Removing rounded coordinates with BeeBDC::jbd_coordinates_precision... jbd_coordinates_precision: Removed 5 records. - Starting the latitude sequence... - Starting the longitude sequence... - Merging results and adding the .sequential column... diagonAlley: Flagged 17 records The .sequential column was added to the database. - Completed in 0.77 secs Loading required namespace: forcats Loading required namespace: cowplot Loading required namespace: igraph - Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns. This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows. - Updating the .summary column to sort by... - We will NOT flag the following columns. However, they will remain in the data file. .gridSummary, .lonFlag, .latFlag, .uncer_terms, .uncertaintyThreshold, .unLicensed - summaryFun: Flagged 0 The .summary column was added to the database. - Working on CustomComparisonsRAW duplicates... Completed iteration 1 of 1: - Identified 2 duplicate records and kept 1 unique records using the column(s): catalogNumber, institutionCode, scientificName - Working on CustomComparisons duplicates... Completed iteration 1 of 4: - Identified 0 duplicate records and kept 0 unique records using the column(s): gbifID, scientificName Completed iteration 2 of 4: - Identified 1 duplicate records and kept 1 unique records using the column(s): occurrenceID, scientificName Completed iteration 3 of 4: - Identified 0 duplicate records and kept 0 unique records using the column(s): recordId, scientificName Completed iteration 4 of 4: - Identified 0 duplicate records and kept 0 unique records using the column(s): id, scientificName - Working on collectionInfo duplicates... Completed iteration 1 of 2: - Identified 0 duplicate records and kept 0 unique records using the columns: decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and catalogNumber Completed iteration 2 of 2: - Identified 0 duplicate records and kept 0 unique records using the columns: decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and otherCatalogNumbers - Clustering duplicate pairs... Duplicate pairs clustered. There are 3 duplicates across 2 kept duplicates. - Ordering prefixs... - Ordering data by 1. dataSource, 2. completeness and 3. .summary column... - Find and FIRST duplicate to keep and assign other associated duplicates to that one (i.e., across multiple tests a 'kept duplicate', could otherwise be removed)... - Duplicates have been saved in the file and location: /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydSduplicateRun_collectionInfo_2024-04-19.csv - Across the entire dataset, there are now 3 duplicates from a total of 12 occurrences. - Completed in 1.91 secs - No dates in file name(s). Finding most-recent from file save time... - Found the following file(s): /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS/testData.csv \.occurrenceAbsent: Flagged 18 absent records: One column was added to the database. No dataSource provided. Filling this column with NAs... No license provided. Filling this column with NAs... \.unLicensed: Flagged 11 records that may NOT be used. One column was added to the database. - We will flag all columns starting with '.' - summaryFun: Flagged 77 The .summary column was added to the database. The percentages of species impacted by each flag in your analysis are as follows: .coordinates_empty = 23.46% .coordinates_outOfRange = 0% .basisOfRecords_notStandard = 1.23% .coordinates_country_inconsistent = 1.23% .occurrenceAbsent = 8.64% .unLicensed = 0% .GBIFflags = 0% .uncer_terms = 0% .rou = 29.63% .val = 0% .equ = 0% .zer = 0% .cap = 0% .cen = 0% .gbf = 0% .inst = 0% .sequential = 0% .lonFlag = 0% .latFlag = 2.47% .gridSummary = 0% .uncertaintyThreshold = 12.35% .countryOutlier = 0% .sea = 1.23% .eventDate_empty = 13.58% .year_outOfRange = 13.58% .duplicates = 56.79% Loading required namespace: emld Failed with error: 'there is no package called 'emld'' Warning message: - No completeness_cols provided. Using default of: c('decimalLatitude', 'decimalLongitude', 'scientificName', and 'eventDate') - Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns. This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows. - Starting core loop... - we matched 26 records using gbifID. This leaves 24 unmatched data in the priorData file - we matched 20 records using catalogNumber, institutionCode, dataSource. This leaves 4 unmatched data in the priorData file - we matched 4 records using occurrenceID, dataSource. This leaves 0 unmatched data in the priorData file - we matched 0 records using recordId, dataSource. This leaves 0 unmatched data in the priorData file - we matched 0 records using id. This leaves 0 unmatched data in the priorData file - we matched 0 records using catalogNumber, institutionCode. This leaves 0 unmatched data in the priorData file - Combining ids and assigning new ones where needed... - We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 49 unmatched occurrences. Warning message: - No completeness_cols provided. Using default of: c('decimalLatitude', 'decimalLongitude', 'scientificName', and 'eventDate') - Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns. This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows. - Starting core loop... - we matched 26 records using gbifID. This leaves 24 unmatched data in the priorData file - we matched 20 records using catalogNumber, institutionCode, dataSource. This leaves 4 unmatched data in the priorData file - we matched 4 records using occurrenceID, dataSource. This leaves 0 unmatched data in the priorData file - we matched 0 records using recordId, dataSource. This leaves 0 unmatched data in the priorData file - we matched 0 records using id. This leaves 0 unmatched data in the priorData file - we matched 0 records using catalogNumber, institutionCode. This leaves 0 unmatched data in the priorData file - Combining ids and assigning new ones where needed... - We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 50 unmatched occurrences. Loading required namespace: htmlwidgets Failed with error: 'there is no package called 'htmlwidgets'' Loading required namespace: leaflet Failed with error: 'there is no package called 'leaflet'' The column .expertOutlier was not found. One will be created with all values = TRUE. - Running chunker with: stepSize = 50 chunkStart = 1 chunkEnd = 50 - Starting parallel operation. Unlike the serial operation (mc.cores = 1) , a parallel operation will not provide running feedback. Please be patient as this function may take some time to complete. Each chunk will be run on a seperate thread so also be aware of RAM usage. Loading required package: rnaturalearth - Running chunker with: stepSize = 100 chunkStart = 1 chunkEnd = 100 append = FALSE - Starting chunk 1... From 1 to 100 Loading required package: readr Attaching package: 'readr' The following objects are masked from 'package:testthat': edition_get, local_edition The rnaturalearthdata package needs to be installed. Installing the rnaturalearthdata package. Installing package into '/tmp/RtmpUCMlxJ/RLIBS_3fa4a378522668' (as 'lib' is unspecified) Loading required package: cowplot Loading required package: ggspatial Loading required namespace: bdc Failed with error: 'there is no package called 'bdc'' Check figures in /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS Loading required namespace: bdc Failed with error: 'there is no package called 'bdc'' Check figures in /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS Loading required namespace: bdc Failed with error: 'there is no package called 'bdc'' Check figures in /tmp/RtmpUCMlxJ/working_dir/RtmpcAcydS Loading required namespace: bdc Failed with error: 'there is no package called 'bdc'' - Preparing data to plot... - Building plot... Loading required namespace: openxlsx A .csv data type was chosen... Rows: 5 Columns: 15 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp... dbl (5): collector_number, day_collected, year_collected, latitude, longitude ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... Rows: 4 Columns: 21 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (15): family, subfamily, Tribe, genus, subgenus, Morphospecies, specific... dbl (5): catalogNumber, decimalLatitude, decimalLongitude, coordinateUncert... lgl (1): associatedTaxa ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... Rows: 4 Columns: 24 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (20): catalogNumber, Phylum, higherClassification, Order, family, genus,... dbl (2): decimalLatitude, decimalLongitude lgl (2): dateIdentified, county ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... Rows: 6 Columns: 41 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (30): occurence_lsid, language, basisOfRecord, catalogNumber, scientifi... dbl (4): organismQuantity, decimalLatitude, decimalLongitude, dateIdentified lgl (6): municipality, eventTime, fieldNumber, typeStatus, infraspecificEp... dttm (1): modified ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... Rows: 4 Columns: 91 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (27): institutionCode, collectionCode, basisOfRecord, occurrenceID, high... dbl (12): id, taxonID, year, month, day, startDayOfYear, cultivationStatus, ... lgl (52): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... Rows: 4 Columns: 48 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (34): institutionCode, Collection Code, collection.var, catalogNumber, ... dbl (10): Other Catalog Number, SampleRound, TempStart, TempEnd, WindStart,... lgl (2): sex, subspecies time (2): eventTime, EndTime ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .xlsx data type was chosen... A .csv data type was chosen... A .csv data type was chosen... Rows: 6 Columns: 6 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (2): Collection, Species dbl (4): ID_project, Longitude, Latitude, Year ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... - We have read in 6 occurrence records from the 'GEOLOCATE HIGH' sheet. - We have read in 5 occurrence records from the 'BELS High' sheet. - We have kept 6 occurrences from GeoLocate, and 5 records from BELS (11 in total). BELS was given preference over GeoLocate A .csv data type was chosen... A .xlsx data type was chosen... A .xlsx data type was chosen... A .csv data type was chosen... Rows: 4 Columns: 91 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (32): institutionCode, collectionCode, basisOfRecord, catalogNumber, hig... dbl (10): id, taxonID, year, month, day, startDayOfYear, localitySecurity, d... lgl (49): ownerInstitutionCode, occurrenceID, otherCatalogNumbers, subgenus,... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... Rows: 5 Columns: 18 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (13): organismName, county, stateProvince, locale, observationDate, coll... dbl (3): individualCount, latitude, longitude lgl (2): determiner, Notes ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .xlsx data type was chosen... A .csv data type was chosen... Rows: 6 Columns: 25 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (17): eventID, occurrenceID, basisOfRecord, eventDate, Kingdom, Order, F... dbl (5): Morphospecies, individualCount, sampleSizeValue, decimalLatitude, ... lgl (3): Species, adult, sex ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .xlsx data type was chosen... A .csv data type was chosen... Rows: 6 Columns: 30 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (23): basisOfRecord, recordNumber, locationID, family, subfamily, genus... dbl (5): individualCount, decimalLatitude, decimalLongitude, elevationInMe... lgl (1): catalogNumber time (1): eventTime ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .xlsx data type was chosen... A .csv data type was chosen... Rows: 5 Columns: 36 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (22): CodeBBdatabase_curated, Scientific name corrected, Native.to.Brazi... dbl (8): Day, Month, Year, Latitude_dec.degrees, Longitude_dec.degrees, Spc... lgl (6): Date_precision, NotasLatLong, NotesOnLocality, Spcslink.county, Sp... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .xlsx data type was chosen... A .csv data type was chosen... Rows: 3 Columns: 92 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (28): institutionCode, collectionCode, collectionID, basisOfRecord, occu... dbl (8): Catalognumber, taxonID, year, month, day, startDayOfYear, decimalL... lgl (56): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus... ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .csv data type was chosen... Rows: 3 Columns: 19 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (15): Country, Muninciplaity, Gender, Site, Latitud, Longitude, elevatio... lgl (4): Type, othercatalognumber, AssociatedTaxa, Citation ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. A .xlsx data type was chosen... A .xlsx data type was chosen... - We will flag all columns starting with '.' - summaryFun: Flagged 30 The .summary column was added to the database. The rnaturalearthdata package needs to be installed. Installing the rnaturalearthdata package. Installing package into '/tmp/RtmpUCMlxJ/RLIBS_3fa4a378522668' (as 'lib' is unspecified) Loading required namespace: taxadb Failed with error: 'there is no package called 'taxadb'' Loading required namespace: taxadb Failed with error: 'there is no package called 'taxadb'' - Downloading taxonomy... [ FAIL 7 | WARN 0 | SKIP 0 | PASS 209 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-countryOutlieRs.R:16:1'): (code run outside of `test_that()`) ── Error in `value[[3L]](cond)`: Failed to install the rnaturalearthdata package. Please try installing the package for yourself using the following command: install.packages("rnaturalearthdata") Backtrace: ▆ 1. ├─BeeBDC::countryOutlieRs(...) at test-countryOutlieRs.R:16:1 2. │ ├─base::suppressWarnings(...) 3. │ │ └─base::withCallingHandlers(...) 4. │ ├─... %>% ... 5. │ └─rnaturalearth::ne_countries(...) 6. │ └─rnaturalearth:::get_data(scale = scale, type = type) 7. │ └─rnaturalearth::check_rnaturalearthdata() 8. │ └─rnaturalearth::install_rnaturalearthdata() 9. │ └─base::tryCatch(...) 10. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. │ └─base (local) tryCatchOne(...) 12. │ └─value[[3L]](cond) 13. ├─dplyr::mutate(...) 14. ├─dplyr::select(...) 15. └─sf::st_make_valid(.) ── Error ('test-formattedCombiner.R:57:1'): (code run outside of `test_that()`) ── Error in `loadNamespace(x)`: there is no package called 'emld' Backtrace: ▆ 1. └─base::loadNamespace(x) at test-formattedCombiner.R:57:1 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-interactiveMapR.R:9:1'): (code run outside of `test_that()`) ─── Error in `loadNamespace(x)`: there is no package called 'leaflet' Backtrace: ▆ 1. ├─BeeBDC::interactiveMapR(...) at test-interactiveMapR.R:9:1 2. └─base::loadNamespace(x) 3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. └─base (local) withOneRestart(expr, restarts[[1L]]) 5. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-jbd_CfC_chunker.R:18:1'): (code run outside of `test_that()`) ── Error in `loadNamespace("bdc")`: there is no package called 'bdc' Backtrace: ▆ 1. ├─BeeBDC::jbd_CfC_chunker(...) at test-jbd_CfC_chunker.R:18:1 2. │ └─... %>% dplyr::bind_rows() 3. ├─dplyr::bind_rows(.) 4. │ └─rlang::list2(...) 5. └─parallel::mclapply(., funCoordCountry, mc.cores = mc.cores) 6. └─base::lapply(X = X, FUN = FUN, ...) 7. └─BeeBDC (local) FUN(X[[i]], ...) 8. └─base::loadNamespace("bdc") 9. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 10. └─base (local) withOneRestart(expr, restarts[[1L]]) 11. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-jbd_Ctrans_chunker.R:13:1'): (code run outside of `test_that()`) ── Error in `value[[3L]](cond)`: Failed to install the rnaturalearthdata package. Please try installing the package for yourself using the following command: install.packages("rnaturalearthdata") Backtrace: ▆ 1. └─BeeBDC::jbd_Ctrans_chunker(...) at test-jbd_Ctrans_chunker.R:13:1 2. └─BeeBDC::jbd_coordinates_transposed(...) 3. └─BeeBDC:::jbd_get_world_map(scale = scale) 4. ├─base::suppressWarnings(...) 5. │ └─base::withCallingHandlers(...) 6. └─rnaturalearth::ne_countries(scale = scale, returnclass = "sf") 7. └─rnaturalearth:::get_data(scale = scale, type = type) 8. └─rnaturalearth::check_rnaturalearthdata() 9. └─rnaturalearth::install_rnaturalearthdata() 10. └─base::tryCatch(...) 11. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 12. └─base (local) tryCatchOne(...) 13. └─value[[3L]](cond) ── Error ('test-summaryMaps.R:7:1'): (code run outside of `test_that()`) ─────── Error in `value[[3L]](cond)`: Failed to install the rnaturalearthdata package. Please try installing the package for yourself using the following command: install.packages("rnaturalearthdata") Backtrace: ▆ 1. ├─BeeBDC::summaryMaps(...) at test-summaryMaps.R:7:1 2. │ ├─... %>% sf::st_make_valid() 3. │ └─rnaturalearth::ne_countries(...) 4. │ └─rnaturalearth:::get_data(scale = scale, type = type) 5. │ └─rnaturalearth::check_rnaturalearthdata() 6. │ └─rnaturalearth::install_rnaturalearthdata() 7. │ └─base::tryCatch(...) 8. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ └─base (local) tryCatchOne(...) 10. │ └─value[[3L]](cond) 11. ├─sf::st_make_valid(.) 12. └─dplyr::select(...) ── Error ('test-taxadbToBeeBDC.R:7:2'): (code run outside of `test_that()`) ──── Error in `loadNamespace(x)`: there is no package called 'taxadb' Backtrace: ▆ 1. ├─BeeBDC::taxadbToBeeBDC(...) at test-taxadbToBeeBDC.R:7:2 2. └─base::loadNamespace(x) 3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. └─base (local) withOneRestart(expr, restarts[[1L]]) 5. └─base (local) doWithOneRestart(return(expr), restart) [ FAIL 7 | WARN 0 | SKIP 0 | PASS 209 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [11s/16s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-Suggests/BeeBDC.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 15:55.44, 564.51 + 30.43