* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/deeptime.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 ‘deeptime/DESCRIPTION’ ... OK
* this is package ‘deeptime’ 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 ‘deeptime’ can be installed ... [28s/32s] 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 ... 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 whether startup messages can be suppressed ... 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 ... [39s/49s] 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 ... [33s/42s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/13s]
 [11s/14s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deeptime)
  > 
  > test_check("deeptime")
  [ FAIL 2 | WARN 0 | SKIP 25 | PASS 14 ]
  
  ══ Skipped tests (25) ══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-coord_geo.R:66:3', 'test-get_scale_data.R:2:3'
  • dispRity cannot be loaded (1): 'test-disparity_through_time.R:2:3'
  • divDyn cannot be loaded (10): 'test-coord_geo.R:2:3',
    'test-coord_geo.R:52:3', 'test-coord_geo.R:89:3', 'test-coord_geo.R:104:3',
    'test-coord_geo.R:119:3', 'test-coord_geo.R:140:3', 'test-facet_color.R:2:3',
    'test-facet_color.R:53:3', 'test-gggeo_scale.R:13:3',
    'test-gggeo_scale_old.R:13:3'
  • ggtree cannot be loaded (4): 'test-coord_geo.R:157:3',
    'test-coord_geo.R:169:3', 'test-coord_geo_polar.R:1:1',
    'test-coord_geo_radial.R:1:1'
  • palaeoverse cannot be loaded (1): 'test-points_range.R:2:3'
  • paleotree cannot be loaded (1): 'test-ggarrange2.R:2:3'
  • vdiffr is not installed. (6): 'test-coord_trans_flip.R:10:3',
    'test-coord_trans_xy.R:22:3', 'test-phylomorpho.R:21:3',
    'test-scales.R:11:3', 'test-scales.R:24:3', 'test-scales.R:37:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-gggeo_scale.R:2:3'): gggeo_scale() is deprecated ───────────────
  Error in `eval(code, test_env)`: object 'coral_div' not found
  Backtrace:
      ▆
   1. └─ggplot2::ggplot(coral_div) at test-gggeo_scale.R:2:3
  ── Error ('test-gggeo_scale_old.R:2:3'): gggeo_scale_old() is deprecated ───────
  Error in `eval(code, test_env)`: object 'coral_div' not found
  Backtrace:
      ▆
   1. └─ggplot2::ggplot(coral_div) at test-gggeo_scale_old.R:2:3
  
  [ FAIL 2 | WARN 0 | SKIP 25 | PASS 14 ]
  Deleting unused snapshots:
  • coord_geo/custom-discrete-scale-new.svg
  • coord_geo/custom-discrete-scale-old.svg
  • coord_geo/geom-fit-text-new.svg
  • coord_geo/geom-fit-text-old.svg
  • coord_geo/scale-on-all-facets-new.svg
  • coord_geo/scale-on-all-facets-old.svg
  • coord_geo/scale-on-discrete-axis-new.svg
  • coord_geo/scale-on-discrete-axis-old.svg
  • coord_geo/scale-on-fossil-ggtree-new.svg
  • coord_geo/scale-on-fossil-ggtree-old.svg
  • coord_geo/scale-on-ggtree-new.svg
  • coord_geo/scale-on-ggtree-old.svg
  • coord_geo/scale-on-only-one-facet-new.svg
  • coord_geo/scale-on-only-one-facet-old.svg
  • coord_geo/scales-on-different-sides1-new.svg
  • coord_geo/scales-on-different-sides1-old.svg
  • coord_geo/scales-on-different-sides2-new.svg
  • coord_geo/scales-on-different-sides2-old.svg
  • coord_geo/stacked-scales-new.svg
  • coord_geo/stacked-scales-old.svg
  • coord_geo_polar/coord-geo-polar-grey-new.svg
  • coord_geo_polar/coord-geo-polar-new.svg
  • coord_geo_polar/coord-geo-polar-old.svg
  • coord_geo_polar/coord-geo-polar-pos-new.svg
  • coord_geo_polar/scale-on-fossil-ggtree-new.svg
  • coord_geo_polar/scale-on-fossil-ggtree-old.svg
  • coord_geo_polar/scale-on-fossil-ggtree-with-labels-new.svg
  • coord_geo_polar/scale-on-fossil-ggtree-with-labels-old.svg
  • coord_geo_polar/stacked-scales-new.svg
  • coord_geo_polar/stacked-scales-old.svg
  • coord_geo_radial/coord-geo-radial-new.svg
  • coord_geo_radial/scale-on-fossil-ggtree-new.svg
  • coord_geo_radial/scale-on-fossil-ggtree-with-labels-new.svg
  • coord_geo_radial/stacked-scales-new.svg
  • coord_trans_flip/coord-trans-flip-new.svg
  • coord_trans_flip/coord-trans-flip-with-different-transforms-new.svg
  • coord_trans_flip/coord-trans-flip-with-different-transforms-old.svg
  • coord_trans_xy/coord-trans-xy-with-expansion-new.svg
  • coord_trans_xy/coord-trans-xy-with-expansion-old.svg
  • coord_trans_xy/coord-trans-xy-with-no-trans-new.svg
  • coord_trans_xy/coord-trans-xy-without-expansion-new.svg
  • disparity_through_time/disparity-through-time-new.svg
  • disparity_through_time/disparity-through-time-old.svg
  • facet_color/facet-grid-color-new.svg
  • facet_color/facet-grid-color-old.svg
  • facet_color/facet-grid-color-with-function-new.svg
  • facet_color/facet-grid-color-with-function-old.svg
  • facet_color/facet-grid-color-with-named-vector-new.svg
  • facet_color/facet-grid-color-with-named-vector-old.svg
  • facet_color/facet-wrap-color-new.svg
  • facet_color/facet-wrap-color-old.svg
  • ggarrange2/double-ggarrange2-layout-new.svg
  • ggarrange2/double-ggarrange2-layout-old.svg
  • ggarrange2/double-ggarrange2-new.svg
  • ggarrange2/double-ggarrange2-old.svg
  • ggarrange2/ggarrange2-layout-new.svg
  • ggarrange2/ggarrange2-layout-old.svg
  • ggarrange2/ggarrange2-new.svg
  • ggarrange2/ggarrange2-no-dims-layout-new.svg
  • ggarrange2/ggarrange2-no-dims-layout-old.svg
  • ggarrange2/ggarrange2-no-dims-new.svg
  • ggarrange2/ggarrange2-no-dims-old.svg
  • ggarrange2/ggarrange2-no-heights-layout-new.svg
  • ggarrange2/ggarrange2-no-heights-layout-old.svg
  • ggarrange2/ggarrange2-no-heights-new.svg
  • ggarrange2/ggarrange2-no-heights-old.svg
  • ggarrange2/ggarrange2-old.svg
  • ggarrange2/ggarrange2-with-layout-layout-new.svg
  • ggarrange2/ggarrange2-with-layout-layout-old.svg
  • ggarrange2/ggarrange2-with-layout-new.svg
  • ggarrange2/ggarrange2-with-layout-old.svg
  • gggeo_scale/gggeo-scale-left-and-right-new.svg
  • gggeo_scale/gggeo-scale-left-and-right-old.svg
  • gggeo_scale/gggeo-scale-new.svg
  • gggeo_scale/gggeo-scale-old.svg
  • gggeo_scale/gggeo-scale-top-new.svg
  • gggeo_scale/gggeo-scale-top-old.svg
  • phylomorpho/geom-phylomorpho-new.svg
  • points_range/geom-points-range-aes-new.svg
  • points_range/geom-points-range-aes-old.svg
  • points_range/geom-points-range-bg-new.svg
  • points_range/geom-points-range-bg-old.svg
  • points_range/geom-points-range-h-new.svg
  • points_range/geom-points-range-h-old.svg
  • points_range/geom-points-range-v-new.svg
  • points_range/geom-points-range-v-old.svg
  • scales/scale-color-geo-new.svg
  • scales/scale-discrete-geo-new.svg
  • scales/scale-fill-geo-new.svg
  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 ... [10s/13s] 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: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/deeptime.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:17.59, 231.75 + 22.76