Check results for 'BeeBDC'

using R version 4.4.1 (2024-06-14)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.4
using session charset: UTF-8
checking for file ‘BeeBDC/DESCRIPTION’ ... OK
this is package ‘BeeBDC’ version ‘1.2.1’
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 ... [15s/17s] OK See the install log for details.
checking installed package size ... 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 ... [4s/4s] OK
checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
checking whether the package can be unloaded cleanly ... [3s/4s] OK
checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
checking loading without being on the library search path ... [3s/4s] 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 ... [11s/12s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... 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 ... [0s/0s] OK
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 ... [15s/17s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [27s/45s] ERROR Running ‘testthat.R’ [27s/45s] 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 37446. - '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 12061. Nomia maneei is an accpeted name with the taxon id number 37446. Bombus hypnorum is an accpeted name with the taxon id number 9667. - '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, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada 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 12061. Nomia maneei is an accpeted name with the taxon id number 37446. Bombus hypnorum is an accpeted name with the taxon id number 9667. - '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 91 of 100 occurrence records. This leaves a total of 9 unmatched occurrence records. harmoniseR: 9 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 0.3 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 93 of 102 occurrence records. This leaves a total of 9 unmatched occurrence records. harmoniseR: 9 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 0.53 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): /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/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_2025-07-18.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/out_file - Writing attributes file... Written to file called USGS_attribute_files2025-07-18.xml at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/out_file - Fin. trying URL 'https://figshare.com/ndownloader/files/47092720' Download attempt failed... Could not read download... trying URL 'https://figshare.com/ndownloader/files/47092720' Download attempt failed... Could not read download... [1] "Attempt: 2 of 4" trying URL 'https://figshare.com/ndownloader/files/47092720' Download attempt failed... Could not read download... [1] "Attempt: 3 of 4" trying URL 'https://figshare.com/ndownloader/files/47092720' Download attempt failed... Could not read download... [1] "Attempt: 4 of 4" - Checklist download failed. Please check your internet connection. trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969' Download attempt failed... Could not read download... trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969' Download attempt failed... Could not read download... [1] "Attempt: 2 of 4" trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969' Download attempt failed... Could not read download... [1] "Attempt: 3 of 4" trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969' Download attempt failed... Could not read download... [1] "Attempt: 4 of 4" - Taxonomy download failed. Please check your internet connection. Loading required namespace: rnaturalearthdata Spherical geometry (s2) switched off - Extracting continent data from points... - Prepare the neighbouring continent dataset... although coordinates are longitude/latitude, st_intersects assumes that they are planar - Compare points with the checklist... - Combining data... - Finished. We have matched 74 records to their exact continent and 2 to an adjacent continent We failed to match 3 occurrences to any 'exact' or 'neighbouring' continent There are 21 'NA' occurrences for the .continentOutlier column. continentOutlieRs: Flagged 5 for continent outlier and flagged 2 for in the .sea records. Three columns were added to the database: 1. The '.continentOutlier' column was added which is a filtering column. 2. The 'continentMatch' columns indicates exact, neighbour, or noMatch. 3. The '.sea' column was added as a filtering column for points in the ocean. The '.sea' column includes the user input buffer in its calculation. - Completed in 1.83 secs \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. - Extracting country data from points... - Prepare the neighbouring country dataset... although coordinates are longitude/latitude, st_intersects assumes that they are planar - Compare points with the checklist... - Combining data... - Finished. We have matched 72 records to their exact country and 2 to an adjacent country We failed to match 3 occurrences to any 'exact' or 'neighbouring' country. There are 23 'NA' occurrences for the .countryOutlier column. countryOutlieRs: Flagged 5 for country outlier and flagged 2 for in the .sea records. Three columns were added to the database: 1. The '.countryOutlier' column was added which is a filtering column. 2. The 'countryMatch' columns indicates exact, neighbour, or noMatch. 3. The '.sea' column was added as a filtering column for points in the ocean. The '.sea' column includes the user input buffer in its calculation. - Completed in 1.21 secs Loading required namespace: 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_2025-07-18.rds at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/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_2025-07-18.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/out_file... - Writing attribute data file in csv format... Number of rows (sources): 1 Written to file called BeeData_attributes_2025-07-18.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/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: 0.122681140899658 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: 0.13525390625 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 0.14 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: /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFmduplicateRun_collectionInfo_2025-07-18.csv - Across the entire dataset, there are now 3 duplicates from a total of 12 occurrences. - Completed in 0.4 secs - No dates in file name(s). Finding most-recent from file save time... - Found the following file(s): /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/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% - Great, R has detected some files. These files include: /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/USGS_attribute_files2023-01-27.csv /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm/USGS_formatted_2023-01-27.csv - .csv export version found. Loading this file... 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: 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 - Completed in 0.54 secs - We have updated the country names of 0 occurrences that previously had no country name assigned. - 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. - Completed in 0.56 secs - We have updated the country names of 0 occurrences that previously had no country name assigned. - 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 Spherical geometry (s2) switched on Correcting latitude and longitude transposed 8 occurrences will be tested jbd_coordinates_transposed: Corrected 3 records. One columns were added to the database. - Finished chunk 1 of 1. Total records examined: 91 - Completed in 3.23 secs Loading required package: cowplot Loading required package: ggspatial Loading required namespace: bdc Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpWERTFm - 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. Spherical geometry (s2) switched off - Extracting country data from points... although coordinates are longitude/latitude, st_intersects assumes that they are planar although coordinates are longitude/latitude, st_intersects assumes that they are planar Extraction complete. - Buffering naturalearth map by pointBuffer... dist is assumed to be in decimal degrees (arc_degrees). although coordinates are longitude/latitude, st_intersects assumes that they are planar although coordinates are longitude/latitude, st_intersects assumes that they are planar - Downloading taxonomy... - taxadb save the taxonomy to: /Users/pkgbuild/Library/Application Support/org.R-project.R/R/taxadb Removing previous flags generated with this function - 0 duplicates found in the data. - Cleaning complete! From an initial dataset of 196 names, there remain 196 names. - We removed: 0 source1 accepted names, 0 source2 'accepted' names, 0 source2 synonyms internally duplicated, 0 source2 synonyms duplicated with the source1 list, 0 subsequent duplicates after merging, - We flagged: 0 ambiguous validName, 0 ambiguous canonical_withFlags names, 4 ambiguous canonical names, 0 NON-ambiguous, but duplicated, canonical_withFlags names, 4 NON-ambiguous, but duplicated, canonical names, - We removed: 0 ambiguous synonyms associated with accepted names. - We re-assigned: 0 duplicated [non-duplicate] ids [ FAIL 1 | WARN 4 | SKIP 0 | PASS 236 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-formattedCombiner.R:69:1'): (code run outside of `test_that()`) ── Error in `file(.)`: invalid 'description' argument Backtrace: ▆ 1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:69:1 2. │ └─... %>% xml2::read_xml() 3. ├─xml2::read_xml(.) 4. └─base::file(.) [ FAIL 1 | WARN 4 | SKIP 0 | PASS 236 ] Error: Test failures Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [43s/51s] OK
checking PDF version of manual ... [5s/5s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '