Check results for 'EcoCleanR'

using R version 4.5.2 Patched (2025-12-16 r89181)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc-14 (Debian 14.3.0-10) 14.3.0 GNU Fortran (Debian 14.3.0-10) 14.3.0
running under: Debian GNU/Linux forky/sid
using session charset: UTF-8
checking for file ‘EcoCleanR/DESCRIPTION’ ... OK
this is package ‘EcoCleanR’ version ‘1.0.1’
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 ‘EcoCleanR’ can be installed ... OK See the install log for details.
checking package directory ... OK
checking for future file timestamps ... 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 ... [12s/15s] OK
checking whether the package can be loaded with stated dependencies ... [12s/14s] OK
checking whether the package can be unloaded cleanly ... [11s/15s] OK
checking whether the namespace can be loaded with stated dependencies ... [11s/17s] OK
checking whether the namespace can be unloaded cleanly ... [11s/19s] OK
checking loading without being on the library search path ... [11s/15s] 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 ... [50s/88s] OK
checking Rd files ... [0s/1s] 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 ... [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 ... [14s/156s] ERROR Running examples in ‘EcoCleanR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ec_geographic_map > ### Title: Map view of occurrence data points > ### Aliases: ec_geographic_map > > ### ** Examples > > data <- data.frame( + scientificName = "Mexacanthina lugubris", + decimalLongitude = c(-117, -117.8, -116.9), + decimalLatitude = c(32.9, 33.5, 31.9), + temperature_mean = c(12, 13, 14), + temperature_min = c(9, 6, 10), + temperature_max = c(14, 16, 18) + ) > ec_geographic_map(data, + latitude = "decimalLatitude", + longitude = "decimalLongitude" + ) The geodata server is temporary out of service for maintenance. It should be back on 20 December. Error: unable to find an inherited method for function ‘crop’ for signature ‘x = "NULL"’ Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed ec_extract_env_layers 1.837 0.207 5.163
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [169s/496s] ERROR Running ‘testthat.R’ [169s/496s] 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(EcoCleanR) > > test_check("EcoCleanR") == 1 queries =============== Retrieving data for taxon 'Mexacanthina lugubris' ✔ Found: Mexacanthina lugubris == Results ================= • Total: 1 • Found: 1 • Not Found: 0 Suggested threshold at 96th percentile: 8801832 Extracting BO_sstmean... Imputation iteration 1 Imputation iteration 2 No more missing values to impute. The geodata server is temporary out of service for maintenance. It should be back on 20 December. Saving _problems/test-data_cleaning-294.R The geodata server is temporary out of service for maintenance. It should be back on 20 December. Saving _problems/test-data_cleaning-329.R [ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • Skipping ec_flag_non_east_atlantic test - big shape files required to load for it (1): 'test-data_cleaning.R:417:3' • Skipping ec_flag_non_west_atlantic test - big shape files required to load for it (1): 'test-data_cleaning.R:438:3' • Skipping ec_flag_non_west_pacific test - big shape files required to load for it (1): 'test-data_cleaning.R:459:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-data_cleaning.R:290:3'): ec_geographic_map_w_flag works ──────── Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"' Backtrace: ▆ 1. └─EcoCleanR::ec_geographic_map_w_flag(...) at test-data_cleaning.R:290:3 2. └─terra::crop(x = world_map, y = geographic_extent) 3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-data_cleaning.R:326:3'): ec_geographic_map works ─────────────── Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"' Backtrace: ▆ 1. └─EcoCleanR::ec_geographic_map(...) at test-data_cleaning.R:326:3 2. └─terra::crop(x = world_map, y = geographic_extent) 3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) [ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ] Error: ! Test failures. Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [31s/314s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘data_cleaning.Rmd’ using rmarkdown Quitting from data_cleaning.Rmd:68-73 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! unable to find an inherited method for function 'crop' for signature 'x = "NULL"' --- Backtrace: ▆ 1. └─EcoCleanR::ec_geographic_map(...) 2. └─terra::crop(x = world_map, y = geographic_extent) 3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'data_cleaning.Rmd' failed with diagnostics: unable to find an inherited method for function 'crop' for signature 'x = "NULL"' --- failed re-building ‘data_cleaning.Rmd’ --- re-building ‘data_merging.Rmd’ using rmarkdown Quitting from data_merging.Rmd:141-147 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! unable to find an inherited method for function 'crop' for signature 'x = "NULL"' --- Backtrace: ▆ 1. └─EcoCleanR::ec_geographic_map(Mixdb.occ, "decimalLatitude", longitude = "decimalLongitude") 2. └─terra::crop(x = world_map, y = geographic_extent) 3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'data_merging.Rmd' failed with diagnostics: unable to find an inherited method for function 'crop' for signature 'x = "NULL"' --- failed re-building ‘data_merging.Rmd’ SUMMARY: processing the following files failed: ‘data_cleaning.Rmd’ ‘data_merging.Rmd’ Error: Vignette re-building failed. Execution halted
checking PDF version of manual ... [5s/6s] OK
checking HTML version of manual ... [1s/2s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 3 ERRORs