Check results for 'palaeoverse'

using R version 4.6.0 (2026-04-24)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc-16 (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22] GNU Fortran (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22]
running under: Debian GNU/Linux forky/sid
using session charset: UTF-8 * current time: 2026-05-16 19:15:42 UTC
checking for file ‘palaeoverse/DESCRIPTION’ ... OK
this is package ‘palaeoverse’ version ‘1.4.0’
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 ‘palaeoverse’ 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 ... [2s/3s] OK
checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
checking whether the package can be unloaded cleanly ... [2s/3s] OK
checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
checking loading without being on the library search path ... [2s/3s] 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 ... [19s/27s] OK
checking Rd files ... [1s/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/1s] 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 ... [2s/63s] ERROR Running examples in ‘palaeoverse-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: axis_geo > ### Title: Add an axis with a geological timescale > ### Aliases: axis_geo axis_geo_phylo > > ### ** Examples > > # track user par > oldpar <- par(no.readonly = TRUE) > # single scale on bottom > par(mar = c(6.1, 4.1, 4.1, 2.1)) # modify margin > plot(0:100, axes = FALSE, xlim = c(100, 0), ylim = c(100, 0), + xlab = NA, ylab = "Depth (m)") > box() > axis(2) > axis_geo(side = 1, intervals = "period") > # the line argument here depends on the absolute size of the plot > title(xlab = "Time (Ma)", line = 4) > > # stack multiple scales, abbreviate only one set of labels > par(mar = c(7.1, 4.1, 4.1, 2.1)) # further expand bottom margin > plot(0:100, axes = FALSE, xlim = c(100, 0), ylim = c(100, 0), + xlab = NA, ylab = "Depth (m)") > box() > axis(2) > axis_geo(side = 1, intervals = list("epoch", "period"), + abbr = list(TRUE, FALSE)) > # the line argument here depends on the absolute size of the plot > title(xlab = "Time (Ma)", line = 6) > > # scale with MacroStrat intervals > par(mar = c(6.1, 4.1, 4.1, 2.1)) # modify margin > plot(0:30, axes = FALSE, xlim = c(30, 0), ylim = c(30, 0), + xlab = NA, ylab = "Depth (m)") > box() > axis(2) > axis_geo(side = 1, intervals = "North American land mammal ages") Warning in open.connection(file, "rt") : URL 'https://macrostrat.org/api/v2/defs/intervals?format=csv&timescale=North%20American%20land%20mammal%20ages': Timeout of 60 seconds was reached Error: `name` does not match a built-in or Macrostrat time scale. Execution halted
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [86s/286s] ERROR Running ‘testthat.R’ [86s/285s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(palaeoverse) > > test_check("palaeoverse") Saving _problems/test-axis_geo-64.R Loading required package: ape Loading required package: maps Presence of occurrences falling on boundaries detected. Occurrences assigned to upper bin. Average spacing between adjacent cells in the primary grid was set to 274.09 km. H3 resolution: 2 Average spacing between adjacent cells in the primary grid was set to 725.17 km. H3 resolution: 1 Average spacing between adjacent cells in the primary grid was set to 274.09 km. H3 resolution: 2 Average spacing between adjacent cells in the primary grid was set to 725.17 km. H3 resolution: 1 Bin size set to 12 degrees to fit latitudinal range. Bin size set to 12 degrees to fit latitudinal range. Target equal length time bins was set to 10.02 Myr. Generated time bins have a mean length of 10.82 Myr and a standard deviation of 2.41 Myr. Target equal length time bins was set to 6.01 Myr. Generated time bins have a mean length of 7.31 Myr and a standard deviation of 2.98 Myr. Target equal length time bins was set to 10.02 Myr. Generated time bins have a mean length of 10.61 Myr and a standard deviation of 2.52 Myr. Target equal length time bins was set to 20.13 Myr. Generated time bins have a mean length of 50.33 Myr and a standard deviation of 23.5 Myr. Target equal length time bins was set to 10.02 Myr. Generated time bins have a mean length of 10.82 Myr and a standard deviation of 2.41 Myr. Target equal length time bins was set to 49.18 Myr. Generated time bins have a mean length of 49.18 Myr and a standard deviation of 3.18 Myr. Target equal length time bins was set to 24.59 Myr. Generated time bins have a mean length of 24.59 Myr and a standard deviation of 3.08 Myr. Target equal length time bins was set to 13.25 Myr. Generated time bins have a mean length of 13.25 Myr and a standard deviation of 4.11 Myr. [ FAIL 1 | WARN 3 | SKIP 13 | PASS 314 ] ══ Skipped tests (13) ══════════════════════════════════════════════════════════ • On CRAN (13): 'test-axis_geo.R:1:1', 'test-axis_geo.R:14:1', 'test-axis_geo.R:28:1', 'test-axis_geo.R:68:1', 'test-lat_bins_area.R:17:1', 'test-palaeorotate.R:26:3', 'test-palaeorotate.R:82:3', 'test-tax_range_strat.R:25:1', 'test-tax_range_strat.R:37:1', 'test-tax_range_strat.R:49:1', 'test-tax_range_strat.R:61:1', 'test-tax_range_strat.R:73:1', 'test-time_bins.R:3:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-axis_geo.R:61:5'): axis_geo() can be used on multiple sides ──── Error: `name` does not match a built-in or Macrostrat time scale. Backtrace: ▆ 1. └─vdiffr::expect_doppelganger(...) at test-axis_geo.R:46:3 2. └─vdiffr (local) writer(fig, testcase, title) 3. ├─vdiffr:::print_plot(plot, title) 4. └─vdiffr:::print_plot.function(plot, title) 5. └─palaeoverse (local) p() 6. └─palaeoverse::axis_geo(...) at test-axis_geo.R:61:5 7. └─palaeoverse::time_bins(scale = scale_intervals) 8. └─base::tryCatch(...) 9. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. └─value[[3L]](cond) [ FAIL 1 | WARN 3 | SKIP 13 | PASS 314 ] Error: ! Test failures. Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [6s/8s] OK
checking PDF version of manual ... [7s/12s] OK
checking HTML version of manual ... [5s/8s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 2 ERRORs