CRAN Package Check Results for Maintainer ‘Martina Sánchez-Pinillos <martina.sanchez.pinillos at gmail.com>’

Last updated on 2025-04-21 14:49:58 CEST.

Package	ERROR	OK
ecoregime	9	4

Package ecoregime

Current CRAN status: ERROR: 9, OK: 4

Version: 0.2.0
Check: Rd cross-references
Result: WARN Missing link(s) in Rd file 'EDR_metrics.Rd': ‘[ecotraj:trajectorymetrics]{ecotraj::trajectoryDistances()}’ Missing link(s) in Rd file 'dist_edr.Rd': ‘[ecotraj:trajectorymetrics]{ecotraj::trajectoryDistances()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64

Version: 0.2.0
Check: examples
Result: ERROR Running examples in ‘ecoregime-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: EDR_metrics > ### Title: Metrics of Ecological Dynamic Regimes > ### Aliases: EDR_metrics dDis dBD dEve > > ### ** Examples > > # Data to compute dDis, dBD, and dEve > dStates <- EDR_data$EDR1$state_dissim > dTraj <- EDR_data$EDR1$traj_dissim > trajectories <- paste0("T", EDR_data$EDR1$abundance$traj) > states <- EDR_data$EDR1$abundance$state > > # Dynamic dispersion taking the first trajectory as reference > dDis(d = dTraj, d.type = "dTraj", trajectories = unique(trajectories), + reference = "T1") dDis (ref. T1) 0.267622 > > # Dynamic dispersion weighting trajectories by their length > dDis(d = dStates, d.type = "dStates", trajectories = trajectories, states = states, + reference = "T1", w.type = "length") Error in ecotraj::trajectoryLengths(d = as.matrix(d)[trajectories %in% : unused arguments (d = as.matrix(d)[trajectories %in% noRef, trajectories %in% noRef], sites = noRef, surveys = noRef_states) Calls: dDis Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [14s/18s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘EDR_framework.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18802 bytes Input file size = 18904 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15029 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 = 15029 Output IDAT size = 15029 bytes (3773 bytes decrease) Output file size = 15107 bytes (3797 bytes = 20.09% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/traj_state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29948 bytes Input file size = 30062 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24425 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 = 24425 Output IDAT size = 24425 bytes (5523 bytes decrease) Output file size = 24503 bytes (5559 bytes = 18.49% decrease) Quitting from EDR_framework.Rmd:166-174 [traj_dissim] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EDR_framework.Rmd' failed with diagnostics: unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) --- failed re-building ‘EDR_framework.Rmd’ --- re-building ‘Resilience.Rmd’ using rmarkdown Quitting from Resilience.Rmd:70-126 [dDis] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = trajectories, surveys = states) --- Backtrace: ▆ 1. └─base::sapply(...) 2. └─base::lapply(X = X, FUN = FUN, ...) 3. └─global FUN(X[[i]], ...) 4. └─ecoregime::dDis(...) 5. └─base::as.matrix(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Resilience.Rmd' failed with diagnostics: unused arguments (sites = trajectories, surveys = states) --- failed re-building ‘Resilience.Rmd’ SUMMARY: processing the following files failed: ‘EDR_framework.Rmd’ ‘Resilience.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [9s/12s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘EDR_framework.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18802 bytes Input file size = 18904 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15029 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 = 15029 Output IDAT size = 15029 bytes (3773 bytes decrease) Output file size = 15107 bytes (3797 bytes = 20.09% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/traj_state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29948 bytes Input file size = 30062 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24425 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 = 24425 Output IDAT size = 24425 bytes (5523 bytes decrease) Output file size = 24503 bytes (5559 bytes = 18.49% decrease) Quitting from EDR_framework.Rmd:166-174 [traj_dissim] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EDR_framework.Rmd' failed with diagnostics: unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) --- failed re-building ‘EDR_framework.Rmd’ --- re-building ‘Resilience.Rmd’ using rmarkdown Quitting from Resilience.Rmd:70-126 [dDis] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = trajectories, surveys = states) --- Backtrace: ▆ 1. └─base::sapply(...) 2. └─base::lapply(X = X, FUN = FUN, ...) 3. └─global FUN(X[[i]], ...) 4. └─ecoregime::dDis(...) 5. └─base::as.matrix(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Resilience.Rmd' failed with diagnostics: unused arguments (sites = trajectories, surveys = states) --- failed re-building ‘Resilience.Rmd’ SUMMARY: processing the following files failed: ‘EDR_framework.Rmd’ ‘Resilience.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: examples
Result: ERROR Running examples in ‘ecoregime-Ex.R’ failed The error most likely occurred in: > ### Name: EDR_metrics > ### Title: Metrics of Ecological Dynamic Regimes > ### Aliases: EDR_metrics dDis dBD dEve > > ### ** Examples > > # Data to compute dDis, dBD, and dEve > dStates <- EDR_data$EDR1$state_dissim > dTraj <- EDR_data$EDR1$traj_dissim > trajectories <- paste0("T", EDR_data$EDR1$abundance$traj) > states <- EDR_data$EDR1$abundance$state > > # Dynamic dispersion taking the first trajectory as reference > dDis(d = dTraj, d.type = "dTraj", trajectories = unique(trajectories), + reference = "T1") dDis (ref. T1) 0.267622 > > # Dynamic dispersion weighting trajectories by their length > dDis(d = dStates, d.type = "dStates", trajectories = trajectories, states = states, + reference = "T1", w.type = "length") Error in ecotraj::trajectoryLengths(d = as.matrix(d)[trajectories %in% : unused arguments (d = as.matrix(d)[trajectories %in% noRef, trajectories %in% noRef], sites = noRef, surveys = noRef_states) Calls: dDis Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [23s/58s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘EDR_framework.Rmd’ using rmarkdown Quitting from EDR_framework.Rmd:166-174 [traj_dissim] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EDR_framework.Rmd' failed with diagnostics: unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) --- failed re-building ‘EDR_framework.Rmd’ --- re-building ‘Resilience.Rmd’ using rmarkdown Quitting from Resilience.Rmd:70-126 [dDis] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = trajectories, surveys = states) --- Backtrace: ▆ 1. └─base::sapply(...) 2. └─base::lapply(X = X, FUN = FUN, ...) 3. └─global FUN(X[[i]], ...) 4. └─ecoregime::dDis(...) 5. └─base::as.matrix(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Resilience.Rmd' failed with diagnostics: unused arguments (sites = trajectories, surveys = states) --- failed re-building ‘Resilience.Rmd’ SUMMARY: processing the following files failed: ‘EDR_framework.Rmd’ ‘Resilience.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [21s/25s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.0
Check: tests
Result: ERROR Running 'testthat.R' [12s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64

Version: 0.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [14s/16s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘EDR_framework.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18802 bytes Input file size = 18904 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15029 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 = 15029 Output IDAT size = 15029 bytes (3773 bytes decrease) Output file size = 15107 bytes (3797 bytes = 20.09% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/traj_state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29948 bytes Input file size = 30062 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24425 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 = 24425 Output IDAT size = 24425 bytes (5523 bytes decrease) Output file size = 24503 bytes (5559 bytes = 18.49% decrease) Quitting from EDR_framework.Rmd:166-174 [traj_dissim] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EDR_framework.Rmd' failed with diagnostics: unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) --- failed re-building ‘EDR_framework.Rmd’ --- re-building ‘Resilience.Rmd’ using rmarkdown Quitting from Resilience.Rmd:70-126 [dDis] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = trajectories, surveys = states) --- Backtrace: ▆ 1. └─base::sapply(...) 2. └─base::lapply(X = X, FUN = FUN, ...) 3. └─global FUN(X[[i]], ...) 4. └─ecoregime::dDis(...) 5. └─base::as.matrix(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Resilience.Rmd' failed with diagnostics: unused arguments (sites = trajectories, surveys = states) --- failed re-building ‘Resilience.Rmd’ SUMMARY: processing the following files failed: ‘EDR_framework.Rmd’ ‘Resilience.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64

Version: 0.2.0
Check: tests
Result: ERROR Running ‘testthat.R’ [14s/17s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-release-linux-x86_64

Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘EDR_framework.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18802 bytes Input file size = 18904 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15029 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 = 15029 Output IDAT size = 15029 bytes (3773 bytes decrease) Output file size = 15107 bytes (3797 bytes = 20.09% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ecoregime.Rcheck/vign_test/ecoregime/vignettes/EDR_framework_files/figure-html/traj_state_mds-1.png 480x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29948 bytes Input file size = 30062 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24425 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 = 24425 Output IDAT size = 24425 bytes (5523 bytes decrease) Output file size = 24503 bytes (5559 bytes = 18.49% decrease) Quitting from EDR_framework.Rmd:166-174 [traj_dissim] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EDR_framework.Rmd' failed with diagnostics: unused arguments (sites = rep(ID_sampling, each = 3), surveys = rep(ID_obs, 10)) --- failed re-building ‘EDR_framework.Rmd’ --- re-building ‘Resilience.Rmd’ using rmarkdown Quitting from Resilience.Rmd:70-126 [dDis] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `ecotraj::trajectoryDistances()`: ! unused arguments (sites = trajectories, surveys = states) --- Backtrace: ▆ 1. └─base::sapply(...) 2. └─base::lapply(X = X, FUN = FUN, ...) 3. └─global FUN(X[[i]], ...) 4. └─ecoregime::dDis(...) 5. └─base::as.matrix(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Resilience.Rmd' failed with diagnostics: unused arguments (sites = trajectories, surveys = states) --- failed re-building ‘Resilience.Rmd’ SUMMARY: processing the following files failed: ‘EDR_framework.Rmd’ ‘Resilience.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64

Version: 0.2.0
Check: tests
Result: ERROR Running 'testthat.R' [11s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Version: 0.2.0
Check: Rd cross-references
Result: WARN Missing link or links in Rd file 'EDR_metrics.Rd': '[ecotraj:trajectorymetrics]{ecotraj::trajectoryDistances()}' Missing link or links in Rd file 'dist_edr.Rd': '[ecotraj:trajectorymetrics]{ecotraj::trajectoryDistances()}' See section 'Cross-references' in the 'Writing R Extensions' manual. Flavor: r-oldrel-windows-x86_64

Version: 0.2.0
Check: tests
Result: ERROR Running 'testthat.R' [19s] 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 > > library(testthat) > library(ecoregime) > > test_check("ecoregime") [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-plot.R:2:3', 'test-plot.R:16:3', 'test-plot.R:33:3', 'test-plot.R:50:3', 'test-plot.R:67:3', 'test-plot.R:84:3', 'test-plot.R:101:3', 'test-plot.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-EDR_metrics.R:36:3'): dDis is smaller when the reference trajectory belongs to the EDR than if it is external ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:36:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:72:3'): dDis decreases when the weight of trajectories close to the reference increases ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dDis(...) at test-EDR_metrics.R:72:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:94:3'): dBD is greater when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = d, sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dBD(...) at test-EDR_metrics.R:94:3 2. └─stats::as.dist(...) ── Error ('test-EDR_metrics.R:112:3'): dEve is smaller when trajectories belong to different EDRs ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:112:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:130:3'): dEve is smaller when trajectories of the same EDR have greater weight ── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::dEve(...) at test-EDR_metrics.R:130:3 2. └─base::as.matrix(...) ── Error ('test-EDR_metrics.R:264:3'): dEve returns errors ───────────────────── Error in `ecotraj::trajectoryDistances(d = as.matrix(d), sites = trajectories, surveys = states, ...)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-EDR_metrics.R:264:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ecoregime::dEve(...) 8. └─base::as.matrix(...) ── Error ('test-define_retra.R:60:3'): returns same results when data is defined from 'retra' ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:60:3 ── Error ('test-define_retra.R:111:3'): attributes change for a selection of states ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:111:3 ── Error ('test-define_retra.R:303:3'): returns errors ───────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-define_retra.R:303:3 ── Error ('test-dist_edr.R:10:3'): dissimilarity of an EDR to itself is zero ─── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:45:3'): symmetrize argument works ─────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:125:3'): the properties of dDR are fit ────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state)`: unused arguments (sites = paste0(abun$EDR, "_", abun$traj), surveys = abun$state) ── Error ('test-dist_edr.R:157:3'): trajectories can be disordered ───────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-dist_edr.R:208:3'): returns errors ───────────────────────────── Error in `ecotraj::trajectoryDistances(d = dStates, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:6:3'): returns an object of class 'RETRA' ────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:6:3 ── Error ('test-retra_edr.R:37:3'): returns same results for dSegs and coordSegs ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-retra_edr.R:84:3'): minSegs and eps work ─────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:84:3 ── Error ('test-retra_edr.R:106:3'): attributes are correct when there is only a segment ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-retra_edr.R:106:3 ── Error ('test-retra_edr.R:124:3'): returns errors ──────────────────────────── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) ── Error ('test-summary.R:5:3'): summarizes representative trajectories from retra_edr and define_retra ── Error in `ecotraj::segmentDistances(d = d, sites = trajectories, surveys = states)`: unused arguments (sites = trajectories, surveys = states) Backtrace: ▆ 1. └─ecoregime::retra_edr(...) at test-summary.R:5:3 [ FAIL 20 | WARN 0 | SKIP 8 | PASS 164 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64