Running ‘testthat.R’ [26s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # load packages
  > library(testthat)
  > library(oppr)
  > 
  > # run tests
  > test_check("oppr")
  list()
  attr(,"class")
  [1] "Waiver"
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  Starting checking the validity of sim_tree...
  Found number of tips: n = 5 
  Found number of nodes: m = 4 
  Done.
  ── 1. Error: no phylogenetic data (@test_plot.R#30)  ───────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot.R:30
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot.R:33
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ── 2. Error: phylogenetic data (@test_plot.R#70)  ──────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot.R:70
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot.R:73
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ── 3. Error: some projects funded (@test_plot_feature_persistence.R#29)  ───────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot_feature_persistence.R:29
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot_feature_persistence.R:32
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ── 4. Error: all projects funded (@test_plot_feature_persistence.R#65)  ────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot_feature_persistence.R:65
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot_feature_persistence.R:68
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ── 5. Error: no projects funded (@test_plot_feature_persistence.R#101)  ────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot_feature_persistence.R:101
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot_feature_persistence.R:104
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ── 6. Error: some projects funded (@test_plot_phylo_persistence.R#31)  ─────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot_phylo_persistence.R:31
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot_phylo_persistence.R:34
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ── 7. Error: all projects funded (@test_plot_phylo_persistence.R#69)  ──────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot_phylo_persistence.R:69
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot_phylo_persistence.R:72
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ── 8. Error: no projects funded (@test_plot_phylo_persistence.R#107)  ──────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_true({
         f <- tempfile(fileext = ".png")
         png(f)
         print(g)
         dev.off()
         unlink(f)
         TRUE
     }) at testthat/test_plot_phylo_persistence.R:107
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: print(g) at testthat/test_plot_phylo_persistence.R:110
  5: print(g)
  6: print.ggplot(g)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  
  Model name:  'project prioritization problem' - run #1    
  Objective:   Maximize(R0)
   
  SUBMITTED
  Model size:       23 constraints,      23 variables,           52 non-zeros.
  Sets:                                   0 GUB,                  0 SOS.
   
  Using DUAL simplex for phase 1 and PRIMAL simplex for phase 2.
  The primal and dual simplex pricing strategy set to 'Devex'.
   
  
  Relaxed solution            1.697466 after         20 iter is B&B base.
   
  Feasible solution            1.07805 after         24 iter,         5 nodes (gap 23.0%)
  Improved solution            1.09488 after         27 iter,         9 nodes (gap 22.3%)
  Improved solution             1.6536 after         29 iter,        10 nodes (gap 1.6%)
   
  Optimal solution              1.6536 after         29 iter,        10 nodes (gap 1.6%).
  
  Excellent numeric accuracy ||*|| = 1.11022e-16
  
   MEMO: lp_solve version 5.5.2.0 for 64 bit OS, with 64 bit LPSREAL variables.
        In the total iteration count 29, 4 (13.8%) were bound flips.
        There were 5 refactorizations, 0 triggered by time and 0 by density.
         ... on average 5.0 major pivots per refactorization.
        The largest [LUSOL v2.2.1.0] fact(B) had 58 NZ entries, 1.1x largest basis.
        The maximum B&B level was 4, 0.1x MIP order, 3 at the optimal solution.
        The constraint matrix inf-norm is 1, with a dynamic range of 10.
        Time to load data was 0.033 seconds, presolve used 0.000 seconds,
         ... 0.000 seconds in simplex solver, in total 0.033 seconds.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1473 SKIPPED: 35 FAILED: 8
  1. Error: no phylogenetic data (@test_plot.R#30) 
  2. Error: phylogenetic data (@test_plot.R#70) 
  3. Error: some projects funded (@test_plot_feature_persistence.R#29) 
  4. Error: all projects funded (@test_plot_feature_persistence.R#65) 
  5. Error: no projects funded (@test_plot_feature_persistence.R#101) 
  6. Error: some projects funded (@test_plot_phylo_persistence.R#31) 
  7. Error: all projects funded (@test_plot_phylo_persistence.R#69) 
  8. Error: no projects funded (@test_plot_phylo_persistence.R#107) 
  
  Error: testthat unit tests failed
  Execution halted