• using R Under development (unstable) (2025-03-10 r87922)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘divvy/DESCRIPTION’ ... OK
• this is package ‘divvy’ version ‘1.0.0’
• 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 ‘divvy’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘subsample_circle.R’ ‘subsample_lat_band.R’
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... 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 ... 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 ... [21s/21s] ERROR Running examples in ‘divvy-Ex.R’ failed The error most likely occurred in: > ### Name: rangeSize > ### Title: Calculate common metrics of spatial distribution > ### Aliases: rangeSize > > ### ** Examples > > # generate 20 occurrences for a pseudo-species > # centred on Yellowstone National Park (latitude-longitude) > # normally distributed with a standard deviation ~110 km > set.seed(2) > x <- rnorm(20, 110.5885, 2) > y <- rnorm(20, 44.4280, 1) > pts <- cbind(x,y) > > rangeSize(pts) Error in UseMethod("units") :   no applicable method for 'units' applied to an object of class "c('integer', 'numeric')" Calls: rangeSize -> cbind -> cbind -> units Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [45s/45s] ERROR   Running ‘testthat.R’ [44s/45s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(divvy)   >   > test_check("divvy")   [ FAIL 4 | WARN 0 | SKIP 0 | PASS 22 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_calc_eco_variables.R:4:3'): rangeSize returns appropriate values ──   Error in `UseMethod("units")`: no applicable method for 'units' applied to an object of class "c('integer', 'numeric')"   Backtrace:       ▆    1. └─divvy::rangeSize(xy) at test_calc_eco_variables.R:4:3    2. └─base::cbind(...)    3. └─units (local) cbind(deparse.level, ...)    4. └─base::units(dots[[1]])   ── Error ('test_calc_eco_variables.R:19:3'): sdSumry returns values within basic tolerance limits ──   Error in `UseMethod("units")`: no applicable method for 'units' applied to an object of class "c('integer', 'numeric')"   Backtrace:       ▆    1. └─divvy::sdSumry(...) at test_calc_eco_variables.R:19:3    2. └─divvy (local) dfsumry(dat)    3. └─divvy::rangeSize(coords = locs, crs = crs)    4. └─base::cbind(...)    5. └─units (local) cbind(deparse.level, ...)    6. └─base::units(dots[[1]])   ── Failure ('test_calc_eco_variables.R:42:3'): rangeSize and sdSumry accept projected coords ──   Expected `rangeSize(bivAlt[, xyCell], crs = prj)` to run without any conditions.   i Actually got a <simpleError> with text:     no applicable method for 'units' applied to an object of class "c('integer', 'numeric')"   ── Error ('test_calc_eco_variables.R:43:3'): rangeSize and sdSumry accept projected coords ──   Error in `UseMethod("units")`: no applicable method for 'units' applied to an object of class "c('integer', 'numeric')"   Backtrace:       ▆    1. └─divvy::rangeSize(bivAlt[, xyCell], crs = prj) at test_calc_eco_variables.R:43:3    2. └─base::cbind(...)    3. └─units (local) cbind(deparse.level, ...)    4. └─base::units(dots[[1]])      [ FAIL 4 | WARN 0 | SKIP 0 | PASS 22 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [114s/115s] ERROR Error(s) in re-building vignettes: --- re-building ‘habitat-rangesize-case-study.Rmd’ using rmarkdown --- finished re-building ‘habitat-rangesize-case-study.Rmd’ --- re-building ‘subsampling-vignette.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/divvy.Rcheck/vign_test/divvy/vignettes/subsampling-vignette_files/figure-html/map data-1.png 576x288 pixels, 8 bits/pixel, 168 colors in palette Input IDAT size = 24231 bytes Input file size = 24849 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22782   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22782 Output IDAT size = 22782 bytes (1449 bytes decrease) Output file size = 23376 bytes (1473 bytes = 5.93% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/divvy.Rcheck/vign_test/divvy/vignettes/subsampling-vignette_files/figure-html/map subsample-1.png 576x288 pixels, 8 bits/pixel, 169 colors in palette Input IDAT size = 24253 bytes Input file size = 24874 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22810   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22810 Output IDAT size = 22810 bytes (1443 bytes decrease) Output file size = 23407 bytes (1467 bytes = 5.90% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/divvy.Rcheck/vign_test/divvy/vignettes/subsampling-vignette_files/figure-html/count pool size-1.png 576x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 63158 bytes Input file size = 63320 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37982   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37982 Output IDAT size = 37982 bytes (25176 bytes decrease) Output file size = 38060 bytes (25260 bytes = 39.89% decrease) Quitting from lines 254-271 [meta data] (subsampling-vignette.Rmd) Error: processing vignette 'subsampling-vignette.Rmd' failed with diagnostics: no applicable method for 'units' applied to an object of class "c('integer', 'numeric')" --- failed re-building ‘subsampling-vignette.Rmd’ SUMMARY: processing the following file failed:   ‘subsampling-vignette.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... 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: 3 ERRORs, 1 NOTE