Running ‘testthat.R’ [102s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mashr)
  Loading required package: ashr
  > test_check("mashr")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Cannot test it due to numerical differences between chol in armadillo and R ... (1)
  • file.exists("estimate_null_cor.rds") is not TRUE (1)
  • file.exists("estimate_null_cor_alpha.rds") is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_cpp_computation.R:172:3): compare posterior computation R vs C++ in simulated data common cov ──
  `out1` not equal to `out2`.
  Component "PosteriorMean": Mean relative difference: 0.5
  Component "PosteriorSD": 'is.NA' value mismatch: 0 in current 5 in target
  Component "lfdr": Mean relative difference: 0.5
  Component "NegativeProb": Mean relative difference: 0.5
  Component "lfsr": Mean relative difference: 0.5
  ── Failure (test_cpp_computation.R:211:3): compare transformed posterior computation R vs C++ in simulated data common cov ──
  `out1` not equal to `out2`.
  Component "PosteriorMean": Mean relative difference: 0.5
  Component "PosteriorSD": 'is.NA' value mismatch: 0 in current 2 in target
  Component "lfdr": Mean relative difference: 0.5
  Component "NegativeProb": Mean relative difference: 0.5
  Component "lfsr": Mean relative difference: 0.5
  ── Failure (test_cpp_computation.R:243:3): compare commonbaseline and transformed computation R vs C++ in simulated data common cov ──
  `out1` not equal to `out2`.
  Component "result": Component "PosteriorSD": Mean relative difference: 0.2928932
  Component "result": Component "lfdr": Mean relative difference: 0.5
  ── Failure (test_cpp_computation.R:270:3): compare nobaseline computation R vs C++ in simulated data common cov ──
  `out1` not equal to `out2`.
  Component "result": Component "PosteriorMean": Mean relative difference: 0.5
  Component "result": Component "PosteriorSD": Mean relative difference: 0.243658
  Component "result": Component "lfdr": Mean relative difference: 0.5
  Component "result": Component "NegativeProb": Mean relative difference: 0.5
  Component "result": Component "lfsr": Mean relative difference: 0.08430693
  ── Failure (test_ed.R:58:3): test title goes here. ─────────────────────────────
  res$avgloglikedata not equal to -1.31147446552581.
  1/1 mismatches
  [1] NaN - -1.31 == NaN
  ── Failure (test_ed.R:59:3): test title goes here. ─────────────────────────────
  res$xmean[1, 1] not equal to 2.30368235.
  1/1 mismatches
  [1] NaN - 2.3 == NaN
  ── Failure (test_ed.R:60:3): test title goes here. ─────────────────────────────
  res$xmean[1, 2] not equal to 1.70701517.
  1/1 mismatches
  [1] NaN - 1.71 == NaN
  ── Failure (test_ed.R:61:3): test title goes here. ─────────────────────────────
  res$xmean[2, 1] not equal to 1.08009397.
  1/1 mismatches
  [1] NaN - 1.08 == NaN
  ── Failure (test_ed.R:62:3): test title goes here. ─────────────────────────────
  res$xmean[2, 2] not equal to 0.8888667.
  1/1 mismatches
  [1] NaN - 0.889 == NaN
  ── Failure (test_ed.R:63:3): test title goes here. ─────────────────────────────
  res$xcovar[[1]][1, 1] not equal to 0.445645987259.
  1/1 mismatches
  [1] NaN - 0.446 == NaN
  ── Failure (test_ed.R:64:3): test title goes here. ─────────────────────────────
  res$xamp[1] not equal to 0.11968415.
  1/1 mismatches
  [1] NaN - 0.12 == NaN
  ── Failure (test_ed.R:65:3): test title goes here. ─────────────────────────────
  res$xamp[2] not equal to 0.880315852981.
  1/1 mismatches
  [1] NaN - 0.88 == NaN
  ── Failure (test_posterior.R:19:3): diag of posterior covariance matches posterior sd ──
  res$PosteriorSD not equal to do.call(...).
  6/6 mismatches (average diff: 0.33)
  [1] 0.822 - 1.16 == -0.340
  [2] 0.899 - 1.27 == -0.372
  [3] 0.460 - 0.65 == -0.190
  [4] 0.874 - 1.24 == -0.362
  [5] 0.820 - 1.16 == -0.340
  [6] 0.908 - 1.28 == -0.376
  ── Failure (test_posterior.R:34:3): diag of posterior covariance matches posterior sd: alpha=1 ──
  res$PosteriorSD not equal to do.call(...).
  6/6 mismatches (average diff: 0.335)
  [1] 0.881 - 1.247 == -0.365
  [2] 0.881 - 1.246 == -0.365
  [3] 0.442 - 0.625 == -0.183
  [4] 0.881 - 1.246 == -0.365
  [5] 0.883 - 1.249 == -0.366
  [6] 0.881 - 1.246 == -0.365
  ── Failure (test_posterior_common_cov.R:13:3): posterior calculations with common cov match regular version ──
  `out1` not equal to `out2`.
  Component "post_mean": Mean relative difference: 0.5
  Component "post_sd": 'is.NA' value mismatch: 0 in current 5 in target
  Component "post_zero": Mean relative difference: 0.5
  Component "post_neg": Mean relative difference: 0.5
  ── Failure (test_simple_sims.R:15:3): simple simulations look right ────────────
  mean(abs(test$B - ashr::get_pm(res))) is not strictly less than mean(abs(test$B - test$Bhat)). Difference: 0.434
  ── Failure (test_simple_sims.R:33:3): simple simulations look right; larger error ──
  mean(abs(test$B - ashr::get_pm(res))) is not strictly less than mean(abs(test$B - test$Bhat)). Difference: 0.0697
  ── Failure (test_simple_sims.R:36:3): simple simulations look right; larger error ──
  mean(abs(test$B[, 1] - ashr::get_pm(res)[, 1])) is not strictly less than mean(abs(test$B[, 1] - ashr::get_pm(ashres))). Difference: 0.31
  
  [ FAIL 18 | WARN 0 | SKIP 3 | PASS 111 ]
  Error: Test failures
  Execution halted