Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(umap)
  > 
  > test_check("umap")
  
  test_checks
  
  test_print
  
  test_coo
  ── 1. Error: simple add (@test_coo.R#176)  ─────────────────────────────────────
  replacement has 1 row, data has 0
  1: add.coo(c1, c1) at testthat/test_coo.R:176
  2: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  3: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 2. Error: simple subtract (@test_coo.R#185)  ────────────────────────────────
  replacement has 1 row, data has 0
  1: add.coo(c1, c1, a = 1, b = -1) at testthat/test_coo.R:185
  2: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  3: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 3. Error: add to a zero matrix (@test_coo.R#194)  ───────────────────────────
  replacement has 1 row, data has 0
  1: add.coo(c1, c2) at testthat/test_coo.R:194
  2: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  3: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test_embedding
  ── 4. Error: spectral embedding can revert to random (@test_embedding.R#71)  ───
  replacement has 1 row, data has 0
  1: naive.fuzzy.simplicial.set(knn, config) at testthat/test_embedding.R:71
  2: add.coo(add.coo(conn, connT), connP, b = -1)
  3: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  4: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  5: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test_knn
  ── 5. Error: (unknown) (@test_knn.R#5)  ────────────────────────────────────────
  replacement has 1 row, data has 0
  1: source("train_test.R") at testthat/test_knn.R:5
  2: withVisible(eval(ei, envir))
  3: eval(ei, envir)
  4: eval(ei, envir)
  5: umap(i.train, n_neighbors = 10, random_state = 123)
  6: implementations[[method]](d, config)
  7: naive.fuzzy.simplicial.set(knn, config)
  8: add.coo(add.coo(conn, connT), connP, b = -1)
  9: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  10: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  11: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test_methods
  ── 6. Error: reproducible output when seed is set (@test_methods.R#32)  ────────
  replacement has 1 row, data has 0
  1: umap(i4, conf) at testthat/test_methods.R:32
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 7. Error: output with rownames (@test_methods.R#49)  ────────────────────────
  replacement has 1 row, data has 0
  1: umap(data, conf) at testthat/test_methods.R:49
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 8. Error: accept parameters in main function (@test_methods.R#67)  ──────────
  replacement has 1 row, data has 0
  1: umap(data, conf, n_neighbors = 3) at testthat/test_methods.R:67
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 9. Error: supply knn in main (@test_methods.R#79)  ──────────────────────────
  replacement has 1 row, data has 0
  1: umap(data, conf) at testthat/test_methods.R:79
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 10. Error: log messages in verbose mode (@test_methods.R#96)  ───────────────
  replacement has 1 row, data has 0
  1: expect_message(umap(i4, conf), "starting") at testthat/test_methods.R:96
  2: quasi_capture(enquo(object), capture_messages, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, message = function(condition) {
         out$push(condition)
         invokeRestart("muffleMessage")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: umap(i4, conf)
  7: implementations[[method]](d, config)
  8: naive.fuzzy.simplicial.set(knn, config)
  9: add.coo(add.coo(conn, connT), connP, b = -1)
  10: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  11: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  12: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 11. Error: log messages during prediction verbose mode (@test_methods.R#106) 
  replacement has 1 row, data has 0
  1: suppressMessages(umap(i4, conf)) at testthat/test_methods.R:106
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: umap(i4, conf)
  4: implementations[[method]](d, config)
  5: naive.fuzzy.simplicial.set(knn, config)
  6: add.coo(add.coo(conn, connT), connP, b = -1)
  7: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  8: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  9: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 12. Error: progress messages in verbose mode (@test_methods.R#117)  ─────────
  replacement has 1 row, data has 0
  1: expect_message(umap(i4, conf), "12") at testthat/test_methods.R:117
  2: quasi_capture(enquo(object), capture_messages, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, message = function(condition) {
         out$push(condition)
         invokeRestart("muffleMessage")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: umap(i4, conf)
  7: implementations[[method]](d, config)
  8: naive.fuzzy.simplicial.set(knn, config)
  9: add.coo(add.coo(conn, connT), connP, b = -1)
  10: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  11: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  12: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 13. Error: use of supplied knn (@test_methods.R#128)  ───────────────────────
  replacement has 1 row, data has 0
  1: umap(data, conf) at testthat/test_methods.R:128
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 14. Error: spectral layout on two component data (@test_methods.R#144)  ─────
  replacement has 1 row, data has 0
  1: umap(ilarge, conf) at testthat/test_methods.R:144
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  ── 15. Error: spectral layout aborts and uses random init with small datasets (@
  replacement has 1 row, data has 0
  1: expect_warning(umap(ismall, conf), "init") at testthat/test_methods.R:154
  2: quasi_capture(enquo(object), capture_warnings, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, warning = function(condition) {
         out$push(condition)
         invokeRestart("muffleWarning")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: umap(ismall, conf)
  7: implementations[[method]](d, config)
  8: naive.fuzzy.simplicial.set(knn, config)
  9: add.coo(add.coo(conn, connT), connP, b = -1)
  10: check.coo(x, "add")
  11: add.coo(conn, connT)
  12: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  13: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  14: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test_naive
  ── 16. Error: (unknown) (@test_naive.R#5)  ─────────────────────────────────────
  replacement has 1 row, data has 0
  1: source("train_test.R") at testthat/test_naive.R:5
  2: withVisible(eval(ei, envir))
  3: eval(ei, envir)
  4: eval(ei, envir)
  5: umap(i.train, n_neighbors = 10, random_state = 123)
  6: implementations[[method]](d, config)
  7: naive.fuzzy.simplicial.set(knn, config)
  8: add.coo(add.coo(conn, connT), connP, b = -1)
  9: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  10: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  11: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test_predict
  ── 17. Error: (unknown) (@test_predict.R#17)  ──────────────────────────────────
  replacement has 1 row, data has 0
  1: umap(i.train, conf.testing) at testthat/test_predict.R:17
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test_print
  ── 18. Error: print displays summary of umap result (@test_print.R#55)  ────────
  replacement has 1 row, data has 0
  1: umap(mat, n_epochs = 2, n_neighbors = 3) at testthat/test_print.R:55
  2: implementations[[method]](d, config)
  3: naive.fuzzy.simplicial.set(knn, config)
  4: add.coo(add.coo(conn, connT), connP, b = -1)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test_python
  
  test_rcpp
  ── 19. Error: layout optimization (@test_rcpp.R#105)  ──────────────────────────
  replacement has 1 row, data has 0
  1: naive.fuzzy.simplicial.set(knn, conf) at testthat/test_rcpp.R:105
  2: add.coo(add.coo(conn, connT), connP, b = -1)
  3: check.coo(x, "add")
  4: add.coo(conn, connT)
  5: `[<-`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  6: `[<-.data.frame`(`*tmp*`, is.na(added[, "value.x"]), "value.x", value = 0)
  7: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, n), domain = NA)
  
  
  test small
  
  test_spectral
  
  test_synthetic
  
  test_universal
  
  test_utils
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 122 SKIPPED: 0 FAILED: 19
  1. Error: simple add (@test_coo.R#176) 
  2. Error: simple subtract (@test_coo.R#185) 
  3. Error: add to a zero matrix (@test_coo.R#194) 
  4. Error: spectral embedding can revert to random (@test_embedding.R#71) 
  5. Error: (unknown) (@test_knn.R#5) 
  6. Error: reproducible output when seed is set (@test_methods.R#32) 
  7. Error: output with rownames (@test_methods.R#49) 
  8. Error: accept parameters in main function (@test_methods.R#67) 
  9. Error: supply knn in main (@test_methods.R#79) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted