Last updated on 2025-04-26 20:50:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 5.51 | 64.80 | 70.31 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 3.34 | 45.33 | 48.67 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 114.24 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 131.06 | ERROR | |||
| r-devel-windows-x86_64 | 0.2.0 | 7.00 | 77.00 | 84.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.0 | 5.49 | 61.61 | 67.10 | ERROR | |
| r-release-linux-x86_64 | 0.2.0 | 5.09 | 61.18 | 66.27 | ERROR | |
| r-release-macos-arm64 | 0.2.0 | 125.00 | OK | |||
| r-release-macos-x86_64 | 0.2.0 | 237.00 | OK | |||
| r-release-windows-x86_64 | 0.2.0 | 7.00 | 80.00 | 87.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.2.0 | 76.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.2.0 | 183.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.2.0 | 9.00 | 102.00 | 111.00 | ERROR |
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’ [15s/20s]
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/10s]
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’ [25s/91s]
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
Flavors: r-devel-windows-x86_64, r-release-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/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-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: 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' [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-oldrel-windows-x86_64
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