Package: refund
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'pfr_plot.gam.Rd':
  plot.random.effect
    Code: function(x, P = NULL, data = NULL, label = "", partial.resids =
                   FALSE, rug = TRUE, se = TRUE, scale = -1, n = 100, n2
                   = 40, n3 = 3, theta = 30, phi = 30, jit = FALSE, xlab
                   = NULL, ylab = NULL, main = NULL, ylim = NULL, xlim =
                   NULL, too.far = 0.1, shade.col = "gray80", shift = 0,
                   trans = I, by.resids = FALSE, scheme = 0, ...)
    Docs: function(x, P = NULL, data = NULL, label = "", se1.mult = 1,
                   se2.mult = 2, partial.resids = FALSE, rug = TRUE, se =
                   TRUE, scale = -1, n = 100, n2 = 40, n3 = 3, theta =
                   30, phi = 30, jit = FALSE, xlab = NULL, ylab = NULL,
                   main = NULL, ylim = NULL, xlim = NULL, too.far = 0.1,
                   shade = FALSE, shade.col = "gray80", shift = 0, trans
                   = I, by.resids = FALSE, scheme = 0, ...)
    Argument names in docs not in code:
      se1.mult se2.mult shade
    Mismatches in argument names (first 3):
      Position: 5 Code: partial.resids Docs: se1.mult
      Position: 6 Code: rug Docs: se2.mult
      Position: 7 Code: se Docs: partial.resids

Package: sspm
Check: tests
New result: ERROR
    Running ‘testthat.R’ [103s/104s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(sspm)
    Loading required package: sf
    Linking to GEOS 3.14.1, GDAL 3.11.4, PROJ 9.6.2; sf_use_s2() is TRUE
    WARNING: different compile-time and runtime versions for GEOS found:
    Linked against: 3.14.1-CAPI-1.20.5 compiled against: 3.13.1-CAPI-1.19.2
    It is probably a good idea to reinstall sf (and maybe lwgeom too)
    Loading required package: mgcv
    Loading required package: nlme
    This is mgcv 1.9-4. For overview type '?mgcv'.
    > 
    > test_check("sspm")
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:nlme':
    
        collapse
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    x Method 'method_not_supported' is not part of the supported methods.
    i See `?spm_methods()`
    ! SSPM assumes areas are supplied in km^2
    ! SSPM assumes areas are supplied in km^2
    i  Casting data matrix into simple feature collection using columns: lon_dec, lat_dec
    !  Warning: sspm is assuming WGS 84 CRS is to be used for casting
    i  Casting data matrix into simple feature collection using columns: lon_dec, lat_dec
    !  Warning: sspm is assuming WGS 84 CRS is to be used for casting
    i  Discretizing using method tesselate_voronoi
    i  Discretizing using method tesselate_voronoi
    i  Discretizing using method tesselate_voronoi
    i  Discretizing using method tesselate_voronoi
    i  Discretizing using method tesselate_voronoi
    i  Discretizing using method Custom
    i  Discretizing using method triangulate_delaunay
    i  Discretizing using method triangulate_delaunay
    i  Discretizing using method triangulate_delaunay
    i  Discretizing using method triangulate_delaunay
    x Method 'wrong_method' is not part of the supported methods.
    i See `?spm_methods()`
    i  Fitting formula: weight_per_km2 ~ sfa + smooth_time(by = sfa) + smooth_space() + smooth_space_time(k = c(NA, 30)) for dataset ''
    i  Note:  response variable temp_at_bottom is NOT a biomass density variable
    i  Fitting formula: temp_at_bottom ~ smooth_time(by = sfa) + smooth_space() + smooth_space_time(k = c(NA, 30)) for dataset ''
    x Method 'method_not_supported' is not part of the supported methods.
    i See `?spm_methods()`
    i See `?spm_smooth_methods()`
    i  Joining smoothed data from all datasets
    [ FAIL 1 | WARN 0 | SKIP 1 | PASS 179 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test-zzzintegration.R:5:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-fit.R:15:3'): Fitting works as expected ──────────────────────
    `intercept` (`actual`) not equal to 7.855774 (`expected`).
    
      `actual`: 7.925
    `expected`: 7.856
    
    [ FAIL 1 | WARN 0 | SKIP 1 | PASS 179 ]
    Error: Test failures
    Execution halted