Fix R CMD check lazy-load failure from duplicate R6 method registration#30

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copilot/discuss-transition-probability-estimation

Copilot AI commented May 12, 2026 •

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R CMD check (light) failed during package load because evoland_db_views.R attempted to add public methods that are now already declared in evoland_db.R. The failure was caused by duplicate R6 method registration at load time.

R6 method override compatibility
- Updated evoland_db$set(...) calls in R/evoland_db_views.R to explicitly allow replacing predeclared methods:
  - trans_rates_dinamica_v
  - adjusted_trans_pot_v
  - alloc_params_clumpy_v
- This keeps evoland_db.R as the canonical method declaration surface while preserving view-backed implementations in evoland_db_views.R.
Behavioral impact
- No API shape changes.
- Resolves class initialization/load error by making view implementations intentional overrides instead of duplicate adds.

evoland_db$set(
  "public",
  "trans_rates_dinamica_v",
  overwrite = TRUE,
  function(id_period) { ... }
)

Copilot AI and others added 2 commits

May 12, 2026 13:45


          feat: implement CLUMPY allocation backend and raw/adjusted trans_pot …

b499d9d

…architecture

Agent-Logs-Url: https://github.com/ethzplus/evoland-plus/sessions/39b6065d-0375-4ce9-ae25-40e65e2e68dd

Co-authored-by: mmyrte <24587121+mmyrte@users.noreply.github.com>


          style: address code review: rename abbreviations, fix vignette code b…

c01cc4e

…lock

Agent-Logs-Url: https://github.com/ethzplus/evoland-plus/sessions/39b6065d-0375-4ce9-ae25-40e65e2e68dd

Co-authored-by: mmyrte <24587121+mmyrte@users.noreply.github.com>

Copilot AI assigned Copilot and mmyrte

Copilot created this pull request from a session on behalf of mmyrte

May 12, 2026 13:49

Copilot finished work on behalf of mmyrte

May 12, 2026 13:49

Copilot AI requested a review from mmyrte

May 12, 2026 13:49

mmyrte added 2 commits

June 16, 2026 15:09


          robustness: rbind on names, not position

ddbce6a


          Merge branch 'main' into copilot/discuss-transition-probability-estim…

2cfdcba

…ation

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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

air

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_alloc_params_t.R

Lines 79 to 80 in 2cfdcba

    
           params[c("mean_patch_size", "patch_size_variance", "patch_isometry", 
        
                    "frac_expander", "frac_patcher")],

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_trans_pot_t.R

Line 9 in 2cfdcba

id_trans = 1L,

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_trans_pot_t.R

Lines 11 to 12 in 2cfdcba

    
           id_coord     = 1L, 
        
           value        = 0.3

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_trans_pot_t.R

Lines 37 to 38 in 2cfdcba

    
           id_trans       = c(1L, 2L, 1L, 2L, 1L, 2L), 
        
           id_coord       = c(1L, 1L, 2L, 2L, 3L, 3L),

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_trans_pot_t.R

Line 40 in 2cfdcba

value = c(0.6, 0.2, 0.1, 0.5, 0.3, 0.4)

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_trans_pot_t.R

Lines 43 to 44 in 2cfdcba

    
           id_trans  = c(1L, 2L), 
        
           rate      = c(0.2, 0.1)

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_trans_pot_t.R

Lines 48 to 49 in 2cfdcba

    
           mean_t1 <- mean(raw_vals$value[raw_vals$id_trans == 1L])  # (0.6+0.1+0.3)/3 
        
           mean_t2 <- mean(raw_vals$value[raw_vals$id_trans == 2L])  # (0.2+0.5+0.4)/3

[air] _{reported by reviewdog 🐶}

evoland-plus/inst/tinytest/test_trans_pot_t.R

Lines 81 to 82 in 2cfdcba

    
           expect_true(abs(col_mean_t1_scaled - rates$rate[1L]) <= 
        
                         abs(mean_t1 - rates$rate[1L]) + 1e-9)

R/alloc_clumpy.R

+              #' @return Integer >= 1L, sampled patch area in cells.
+              #' @keywords internal
+              sample_lognorm_area <- function(area_mean, area_var) {
+                if (is.na(area_mean) || area_mean <= 0) return(1L)

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              if (is.na(area_mean) || area_mean <= 0) return(1L)
          
              if (is.na(area_mean) || area_mean <= 0) {
          
                return(1L)
          
              }

R/alloc_clumpy.R

Comment on lines +96 to +99

+                  above = ifelse(rows > 1L,      seq_len(n) - ncol_r, 0L),
+                  below = ifelse(rows < nrow_r,  seq_len(n) + ncol_r, 0L),
+                  left  = ifelse(cols > 1L,      seq_len(n) - 1L,     0L),
+                  right = ifelse(cols < ncol_r,  seq_len(n) + 1L,     0L)

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
                above = ifelse(rows > 1L,      seq_len(n) - ncol_r, 0L),
          
                below = ifelse(rows < nrow_r,  seq_len(n) + ncol_r, 0L),
          
                left  = ifelse(cols > 1L,      seq_len(n) - 1L,     0L),
          
                right = ifelse(cols < ncol_r,  seq_len(n) + 1L,     0L)
          
                above = ifelse(rows > 1L, seq_len(n) - ncol_r, 0L),
          
                below = ifelse(rows < nrow_r, seq_len(n) + ncol_r, 0L),
          
                left = ifelse(cols > 1L, seq_len(n) - 1L, 0L),
          
                right = ifelse(cols < ncol_r, seq_len(n) + 1L, 0L)

R/alloc_clumpy.R

+                n_cells <- nrow_r * ncol_r
+                ant_vec <- as.integer(terra::values(anterior_rast))
+                post_vec <- ant_vec  # will be modified in-place

github-actions Bot Jun 16, 2026

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[air] _{reported by reviewdog 🐶}

Suggested change

      
              post_vec <- ant_vec  # will be modified in-place
          
              post_vec <- ant_vec # will be modified in-place

R/alloc_clumpy.R

+                  # Cells currently in from_class (1-based raster index)
+                  from_cells <- which(!is.na(ant_vec) & ant_vec == from_class)
+                  if (length(from_cells) == 0L) next

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
                if (length(from_cells) == 0L) next
          
                if (length(from_cells) == 0L) {
          
                  next
          
                }

R/alloc_clumpy.R

+                  for (j in seq_along(to_classes)) {
+                    id_trans_j <- trans_for_class$id_trans[j]
+                    pots_j <- adj_pots[id_trans == id_trans_j, .(id_coord, value)]
+                    if (nrow(pots_j) == 0L) next

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
                  if (nrow(pots_j) == 0L) next
          
                  if (nrow(pots_j) == 0L) {
          
                    next
          
                  }

inst/tinytest/test_alloc_clumpy.R

+                from_class   = 1L,
+                to_class     = 2L,
+                eccentricity = 0.5,
+                ncol         = 4L

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              ncol         = 4L
          
              ncol = 4L

inst/tinytest/test_alloc_clumpy.R

+                ncol         = 4L
+              )
+              expect_true(length(patch) <= 4L)
+              expect_true(1L %in% patch)  # pivot always included

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
            expect_true(1L %in% patch)  # pivot always included
          
            expect_true(1L %in% patch) # pivot always included

inst/tinytest/test_alloc_clumpy.R

+              # Pivot with wrong class → empty result
+              landscape_wrong <- as.integer(rep(2L, n))
+              patch_empty <- grow_patch_cpp(
+                landscape    = landscape_wrong,

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              landscape    = landscape_wrong,
          
              landscape = landscape_wrong,

inst/tinytest/test_alloc_clumpy.R

Comment on lines +86 to +94

+                probs        = probs,
+                nbr_above    = nbrs$above,
+                nbr_below    = nbrs$below,
+                nbr_left     = nbrs$left,
+                nbr_right    = nbrs$right,
+                pivot        = 1L,
+                target_area  = 4L,
+                from_class   = 1L,
+                to_class     = 2L,

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              probs        = probs,
          
              nbr_above    = nbrs$above,
          
              nbr_below    = nbrs$below,
          
              nbr_left     = nbrs$left,
          
              nbr_right    = nbrs$right,
          
              pivot        = 1L,
          
              target_area  = 4L,
          
              from_class   = 1L,
          
              to_class     = 2L,
          
              probs = probs,
          
              nbr_above = nbrs$above,
          
              nbr_below = nbrs$below,
          
              nbr_left = nbrs$left,
          
              nbr_right = nbrs$right,
          
              pivot = 1L,
          
              target_area = 4L,
          
              from_class = 1L,
          
              to_class = 2L,

inst/tinytest/test_alloc_clumpy.R

+                from_class   = 1L,
+                to_class     = 2L,
+                eccentricity = 0.5,
+                ncol         = 4L

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              ncol         = 4L
          
              ncol = 4L


          Merge develop into copilot/discuss-transition-probability-estimation

21cd4d6

github-actions Bot reviewed

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inst/tinytest/test_alloc_params_t.R

Comment on lines +79 to +80

		params[c("mean_patch_size", "patch_size_variance", "patch_isometry",
		"frac_expander", "frac_patcher")],

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              params[c("mean_patch_size", "patch_size_variance", "patch_isometry",
          
                       "frac_expander", "frac_patcher")],
          
              params[c(
          
                "mean_patch_size",
          
                "patch_size_variance",
          
                "patch_isometry",
          
                "frac_expander",
          
                "frac_patcher"
          
              )],

inst/tinytest/test_trans_pot_t.R

+              # as_trans_pot_t: basic construction
+              tp <- as_trans_pot_t(data.frame(
+                id_trans     = 1L,

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              id_trans     = 1L,
          
              id_trans = 1L,

inst/tinytest/test_trans_pot_t.R

Comment on lines +11 to +12

		id_coord = 1L,
		value = 0.3

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              id_coord     = 1L,
          
              value        = 0.3
          
              id_coord = 1L,
          
              value = 0.3

inst/tinytest/test_trans_pot_t.R

Comment on lines +37 to +38

		id_trans = c(1L, 2L, 1L, 2L, 1L, 2L),
		id_coord = c(1L, 1L, 2L, 2L, 3L, 3L),

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              id_trans       = c(1L, 2L, 1L, 2L, 1L, 2L),
          
              id_coord       = c(1L, 1L, 2L, 2L, 3L, 3L),
          
              id_trans = c(1L, 2L, 1L, 2L, 1L, 2L),
          
              id_coord = c(1L, 1L, 2L, 2L, 3L, 3L),

inst/tinytest/test_trans_pot_t.R

+                id_trans       = c(1L, 2L, 1L, 2L, 1L, 2L),
+                id_coord       = c(1L, 1L, 2L, 2L, 3L, 3L),
+                id_period_post = 4L,
+                value          = c(0.6, 0.2, 0.1, 0.5, 0.3, 0.4)

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              value          = c(0.6, 0.2, 0.1, 0.5, 0.3, 0.4)
          
              value = c(0.6, 0.2, 0.1, 0.5, 0.3, 0.4)

inst/tinytest/test_trans_pot_t.R

Comment on lines +43 to +44

		id_trans = c(1L, 2L),
		rate = c(0.2, 0.1)

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
              id_trans  = c(1L, 2L),
          
              rate      = c(0.2, 0.1)
          
              id_trans = c(1L, 2L),
          
              rate = c(0.2, 0.1)

inst/tinytest/test_trans_pot_t.R

Comment on lines +48 to +49

		mean_t1 <- mean(raw_vals$value[raw_vals$id_trans == 1L]) # (0.6+0.1+0.3)/3
		mean_t2 <- mean(raw_vals$value[raw_vals$id_trans == 2L]) # (0.2+0.5+0.4)/3

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
            mean_t1 <- mean(raw_vals$value[raw_vals$id_trans == 1L])  # (0.6+0.1+0.3)/3
          
            mean_t2 <- mean(raw_vals$value[raw_vals$id_trans == 2L])  # (0.2+0.5+0.4)/3
          
            mean_t1 <- mean(raw_vals$value[raw_vals$id_trans == 1L]) # (0.6+0.1+0.3)/3
          
            mean_t2 <- mean(raw_vals$value[raw_vals$id_trans == 2L]) # (0.2+0.5+0.4)/3

inst/tinytest/test_trans_pot_t.R

Comment on lines +81 to +82

		expect_true(abs(col_mean_t1_scaled - rates$rate[1L]) <=
		abs(mean_t1 - rates$rate[1L]) + 1e-9)

github-actions Bot Jun 16, 2026

Contributor

[air] _{reported by reviewdog 🐶}

Suggested change

      
            expect_true(abs(col_mean_t1_scaled - rates$rate[1L]) <=
          
                          abs(mean_t1 - rates$rate[1L]) + 1e-9)
          
            expect_true(abs(col_mean_t1_scaled - rates$rate[1L]) <= abs(mean_t1 - rates$rate[1L]) + 1e-9)

Copilot started work on behalf of mmyrte

June 16, 2026 13:37


          fix: allow overriding view methods already declared in evoland_db

c636e3a

Copilot AI changed the title ~~feat: CLUMPY allocation backend + raw/adjusted transition potential architecture~~ Fix R CMD check lazy-load failure from duplicate R6 method registration

Copilot finished work on behalf of mmyrte

June 16, 2026 13:43

mmyrte marked this pull request as ready for review

June 16, 2026 13:54

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