Package: climenv
Check: tests
New result: ERROR
    Running ‘testthat.R’ [20s/97s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > suppressPackageStartupMessages(library("sp", quietly = TRUE)) # Until Oct 2023
    > library("testthat")
    > library("climenv")
    > 
    > test_check("climenv")
    [ FAIL 1 | WARN 2 | SKIP 6 | PASS 64 ]
    
    ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
    • Could not connect to https://srtm.csi.cgiar.org (2): 'test-elev.R:60:3',
      'test-elev.R:200:3'
    • On CRAN (4): 'test-elev.R:93:3', 'test-elev.R:129:3', 'test-plot.R:89:3',
      'test-worldclim.R:21:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-elev.R:168:3'): elev() downloads polygon from GeoData ──────────
    Error in `if (error == 0) {
        rs <- terra::rast(tif)
        terra::crs(rs) <- "+proj=longlat +datum=WGS84"
        rs
    } else {
        NULL
    }`: argument is of length zero
    Backtrace:
        ▆
     1. ├─testthat::expect_true(...) at test-elev.R:168:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::inherits(...)
     5. └─climenv::elev(...)
     6.   └─climenv:::.elev_geodata(location_sf, output_dir, ...)
     7.     └─base::lapply(...)
     8.       └─climenv (local) FUN(X[[i]], ...)
    
    [ FAIL 1 | WARN 2 | SKIP 6 | PASS 64 ]
    Deleting unused snapshots:
    • plot/py-test-c-plot-low.svg
    • plot/py-test-c-plot.svg
    • plot/py-test-h-plot.svg
    Error: Test failures
    Execution halted

Package: sdmTMB
Check: tests
New result: ERROR
    Running ‘testthat.R’ [53s/32s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > options(Matrix.warnDeprecatedCoerce = 2)
    > 
    > library(testthat)
    > library(sdmTMB)
    > 
    > test_check("sdmTMB")
    Starting 2 test processes
    [ FAIL 1 | WARN 0 | SKIP 146 | PASS 151 ]
    
    ══ Skipped tests (146) ═════════════════════════════════════════════════════════
    • On CRAN (146): 'test-2-fit-less-basic.R:2:3', 'test-2-fit-less-basic.R:33:3',
      'test-2-fit-less-basic.R:86:3', 'test-2-fit-less-basic.R:103:3',
      'test-2-fit-less-basic.R:175:3', 'test-2-fit-less-basic.R:194:3',
      'test-2-fit-less-basic.R:245:3', 'test-2-fit-less-basic.R:253:3',
      'test-2-fit-less-basic.R:283:3', 'test-2-fit-less-basic.R:302:3',
      'test-2-fit-less-basic.R:326:3', 'test-2-fit-less-basic.R:371:3',
      'test-2-fit-less-basic.R:383:3', 'test-2-fit-less-basic.R:437:3',
      'test-2-fit-less-basic.R:512:3', 'test-2-print-anisotropy.R:2:3',
      'test-3-families.R:40:3', 'test-3-families.R:61:3', 'test-3-families.R:81:3',
      'test-3-families.R:97:3', 'test-3-families.R:133:3',
      'test-3-families.R:148:3', 'test-3-families.R:162:3',
      'test-3-families.R:180:3', 'test-3-families.R:204:3',
      'test-3-spatial-varying.R:2:3', 'test-3-spatial-varying.R:95:3',
      'test-3-spatial-varying.R:121:3', 'test-3-spatial-varying.R:142:3',
      'test-4-index-calculation.R:4:3', 'test-4-index-calculation.R:60:3',
      'test-5-residuals.R:21:3', 'test-5-residuals.R:184:3',
      'test-5-residuals.R:285:3', 'test-5-residuals.R:298:3',
      'test-5-residuals.R:339:3', 'test-6-tmb-simulation.R:3:3',
      'test-6-tmb-simulation.R:36:3', 'test-6-tmb-simulation.R:72:3',
      'test-6-tmb-simulation.R:125:3', 'test-7-visreg.R:2:3',
      'test-8-delta2.R:2:3', 'test-8-delta2.R:78:3', 'test-8-delta2.R:148:3',
      'test-8-delta2.R:255:3', 'test-8-delta2.R:349:3', 'test-8-delta2.R:429:3',
      'test-8-delta2.R:479:3', 'test-9-mvn-simulation.R:2:3',
      'test-9-mvn-simulation.R:27:3', 'test-9-mvn-simulation.R:53:3',
      'test-9-mvn-simulation.R:137:3', 'test-9-mvn-simulation.R:163:3',
      'test-9-mvn-simulation.R:237:3', 'test-9-mvn-simulation.R:313:3',
      'test-aniso-plots.R:3:3', 'test-cross-validation.R:3:3',
      'test-cross-validation.R:53:3', 'test-cross-validation.R:70:3',
      'test-cross-validation.R:98:3', 'test-cross-validation.R:236:3',
      'test-delta-population-predictions.R:2:3', 'test-delta.R:6:3',
      'test-delta.R:53:3', 'test-delta.R:66:3', 'test-delta.R:83:3',
      'test-delta.R:97:3', 'test-delta.R:112:3', 'test-delta.R:126:3',
      'test-deprecated-args.R:2:3', 'test-deprecated-args.R:67:3',
      'test-dharma.R:3:3', 'test-extra-optimization.R:2:3',
      'test-extra-time.R:3:3', 'test-extra-time.R:42:3', 'test-extra-time.R:116:3',
      'test-factor-levels.R:2:3', 'test-factor-levels.R:37:3',
      'test-factor-levels.R:91:3', 'test-forecasting.R:2:3', 'test-index.R:3:3',
      'test-link-prediction.R:5:3', 'test-link-prediction.R:67:3',
      'test-links.R:2:3', 'test-methods.R:3:3', 'test-methods.R:33:3',
      'test-mix.R:3:3', 'test-mix.R:62:3', 'test-mix.R:78:3', 'test-mix.R:97:3',
      'test-mix.R:117:3', 'test-nonstationary.R:118:3',
      'test-nonstationary.R:164:3', 'test-nonstationary.R:211:3',
      'test-nonstationary.R:239:3', 'test-nonstationary.R:290:3',
      'test-offset.R:2:3', 'test-offset.R:20:3', 'test-offset.R:81:3',
      'test-offset.R:101:3', 'test-parameter-bounds.R:11:3',
      'test-prediction-missing-years.R:2:3', 'test-priors.R:23:3',
      'test-priors.R:69:3', 'test-priors.R:124:3', 'test-random-intercepts.R:11:3',
      'test-random-intercepts.R:125:3', 'test-random-intercepts.R:160:3',
      'test-random-intercepts.R:264:3', 'test-reml.R:2:3', 'test-reml.R:74:3',
      'test-sanity.R:2:3', 'test-sdmTMB-simulate.R:2:3', 'test-smooths.R:4:3',
      'test-smooths.R:16:3', 'test-smooths.R:52:3', 'test-smooths.R:89:3',
      'test-smooths.R:127:3', 'test-smooths.R:205:3', 'test-smooths.R:256:3',
      'test-smooths.R:279:3', 'test-smooths.R:302:3', 'test-smooths.R:323:3',
      'test-smooths.R:345:3', 'test-smooths.R:366:3', 'test-smooths.R:383:3',
      'test-smooths.R:400:3', 'test-smooths.R:417:3', 'test-smooths.R:434:3',
      'test-smooths.R:445:3', 'test-smooths.R:462:3', 'test-smooths.R:481:3',
      'test-threshold-models.R:2:3', 'test-threshold-models.R:18:3',
      'test-threshold-models.R:32:3', 'test-time-varying.R:2:3',
      'test-time-varying.R:76:3', 'test-tmb-simulation.R:3:3',
      'test-tmb-simulation.R:36:3', 'test-tmb-simulation.R:74:3',
      'test-tmb-simulation.R:125:3', 'test-utm-conversions.R:2:3',
      'test-without-spatial.R:2:3', 'test-1-fit-basic.R:129:3',
      'test-1-fit-basic.R:178:3', 'test-1-fit-basic.R:221:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-5-residuals.R:254:3'): Pearson residuals work ────────────────
    as.numeric(r) (`actual`) not equal to as.numeric(r1) (`expected`).
    
         actual      | expected                    
     [1] 0.14953175  - 0.14953169  [1]             
     [2] 0.23286508  - 0.23286503  [2]             
     [3] 0.05429365  - 0.05429360  [3]             
     [4] 0.48286508  - 0.48286503  [4]             
     [5] -0.01713492 - -0.01713497 [5]             
     [6] -0.37427778 - -0.37427783 [6]             
     [7] -0.01713492 - -0.01713497 [7]             
     [8] 0.14953175  - 0.14953169  [8]             
     [9] -0.51713492 - -0.51713497 [9]             
    [10] 0.08286508  - 0.08286503  [10]            
     ... ...           ...         and 290 more ...
    
    [ FAIL 1 | WARN 0 | SKIP 146 | PASS 151 ]
    Error: Test failures
    Execution halted

Package: smile
Check: examples
New result: ERROR
  Running examples in ‘smile-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: predict_spm
  > ### Title: Prediction over the same or a different set of regions (or
  > ###   points).
  > ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
  > 
  > ### ** Examples
  > 
  > 
  > data(liv_lsoa) ## loading the LSOA data
  > data(liv_msoa) ## loading the MSOA data
  > 
  > msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
  +                       type = "regular", by_polygon = FALSE,
  +                       poly_ids = "msoa11cd",
  +                       var_ids = "leb_est")
  > ## fitting model
  > theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
  > 
  > fit_msoa <-
  +    fit_spm(x = msoa_spm,
  +            theta_st = theta_st_msoa,
  +            model = "matern",
  +            nu = .5,
  +            apply_exp  = TRUE,
  +            opt_method = "L-BFGS-B",
  +            control    = list(maxit = 500))
  > 
  > pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
  Error in `[.data.frame`(x, i) : undefined columns selected
  Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
  Execution halted

Package: smile
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘fit-and-pred.Rmd’ using rmarkdown
  
  Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
  Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
  undefined columns selected
  --- failed re-building ‘fit-and-pred.Rmd’
  
  --- re-building ‘sai.Rmd’ using rmarkdown
  --- finished re-building ‘sai.Rmd’
  
  --- re-building ‘sf-to-spm.Rmd’ using rmarkdown
  
  Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
  Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
  names do not match previous names
  --- failed re-building ‘sf-to-spm.Rmd’
  
  --- re-building ‘sp-cov-functions.Rmd’ using rmarkdown
  --- finished re-building ‘sp-cov-functions.Rmd’
  
  --- re-building ‘theory.Rmd’ using rmarkdown
  --- finished re-building ‘theory.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘fit-and-pred.Rmd’ ‘sf-to-spm.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted