Package: bigsnpr [Old version: 1.12.18, New version: 1.12.21]
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [109s/119s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(bigsnpr)
    Loading required package: bigstatsr
    > 
    > for (k in 1:9)
    +   test_check("bigsnpr", filter = paste0(k, '-'))
    [ FAIL 0 | WARN 0 | SKIP 1 | PASS 268 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • is_cran is TRUE (1): 'test-1-readBed.R:53:3'
    
    [ FAIL 0 | WARN 0 | SKIP 1 | PASS 268 ]
    [ FAIL 0 | WARN 0 | SKIP 3 | PASS 219 ]
    
    ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
    • is_cran is TRUE (3): 'test-2-autoSVD.R:28:3', 'test-2-autoSVD.R:76:3',
      'test-2-bed-clumping-SVD.R:7:1'
    
    [ FAIL 0 | WARN 0 | SKIP 3 | PASS 219 ]
    [ FAIL 0 | WARN 0 | SKIP 2 | PASS 11 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • is_cran is TRUE (2): 'test-3-fastImpute.R:12:3', 'test-3-plink-QC.R:6:1'
    
    [ FAIL 0 | WARN 0 | SKIP 2 | PASS 11 ]
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 98 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-4-pcadapt.R:35:3'): Same as pcadapt ──────────────────────────
    abs(obj.svd$u) not equal to abs(obj.pcadapt$scores).
    1496/5170 mismatches (average diff: 1.09e-05)
    [3620] 0.0198 - 0.0198 ==  3.39e-07
    [3621] 0.0606 - 0.0606 == -3.12e-08
    [3622] 0.0163 - 0.0163 == -1.04e-07
    [3623] 0.0531 - 0.0531 ==  2.78e-08
    [3624] 0.0140 - 0.0140 == -7.50e-08
    [3625] 0.0492 - 0.0492 == -7.07e-08
    [3626] 0.0410 - 0.0410 == -2.05e-08
    [3627] 0.0447 - 0.0447 == -9.29e-08
    [3628] 0.0436 - 0.0436 == -2.53e-08
    ...
    ── Failure ('test-4-pcadapt.R:36:3'): Same as pcadapt ──────────────────────────
    abs(obj.svd$v) not equal to abs(obj.pcadapt$loadings).
    11724/45420 mismatches (average diff: 4e-06)
    [31795] 0.02490 - 0.02490 ==  2.49e-08
    [31796] 0.01777 - 0.01777 == -2.73e-08
    [31797] 0.01465 - 0.01465 == -2.49e-08
    [31798] 0.01236 - 0.01236 == -1.70e-08
    [31800] 0.01005 - 0.01005 ==  2.90e-08
    [31803] 0.02747 - 0.02747 == -5.27e-08
    [31804] 0.00998 - 0.00998 ==  5.06e-08
    [31806] 0.00953 - 0.00953 ==  6.10e-08
    [31807] 0.00818 - 0.00818 == -4.49e-08
    ...
    
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 98 ]
    Error: Test failures
    Execution halted

Package: fad
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: knockoff
Check: examples
New result: ERROR
  Running examples in ‘knockoff-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: knockoff.filter
  > ### Title: The Knockoff Filter
  > ### Aliases: knockoff.filter
  > 
  > ### ** Examples
  > 
  > set.seed(2022)
  > p=100; n=80; k=15
  > mu = rep(0,p); Sigma = diag(p)
  > X = matrix(rnorm(n*p),n)
  > nonzero = sample(p, k)
  > beta = 3.5 * (1:p %in% nonzero)
  > y = X %*% beta + rnorm(n)
  > 
  > # Basic usage with default arguments
  > result = knockoff.filter(X, y)
  Error in solve.default(Sigma, diag_s) : 
    system is computationally singular: reciprocal condition number = 1.78743e-19
  Calls: knockoff.filter ... knockoffs -> create.gaussian -> solve -> solve.default
  Execution halted

Package: rainette
Check: tests
New result: ERROR
    Running ‘testthat.R’ [12s/12s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(rainette)
    
    Attaching package: 'rainette'
    
    The following object is masked from 'package:stats':
    
        cutree
    
    > 
    > test_check("rainette")
    [ FAIL 1 | WARN 0 | SKIP 1 | PASS 182 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test_plots.R:6:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_rainette1.R:98:3'): Stopping if tab too small ──────────────────
    <std::runtime_error/C++Error/error/condition>
    Error: TridiagEigen: eigen decomposition failed
    Backtrace:
         ▆
      1. ├─testthat::expect_message(...) at test_rainette1.R:98:3
      2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
      3. │   ├─testthat (local) .capture(...)
      4. │   │ └─base::withCallingHandlers(...)
      5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      6. └─rainette::rainette(dtm, k = 12, min_segment_size = 10, min_split_members = 3)
      7.   ├─progressr::with_progress(...)
      8.   └─rainette:::cluster_tab(tab, cc_test = cc_test, tsj = tsj)
      9.     └─rainette:::order_docs(m)
     10.       ├─RSpectra::svds(s, k = 1, nv = 0)
     11.       └─RSpectra:::svds.matrix(s, k = 1, nv = 0)
     12.         └─RSpectra (local) fun(A, k, nu, nv, opts, mattype = "matrix")
    
    [ FAIL 1 | WARN 0 | SKIP 1 | PASS 182 ]
    Deleting unused snapshots:
    • plots/base-rainette-plot-measure-docprop.svg
    • plots/base-rainette-plot-measure-frequency.svg
    • plots/base-rainette-plot-measure-lr.svg
    • plots/base-rainette-plot-with-free-scales.svg
    • plots/base-rainette-plot-with-k-and-without-negative.svg
    • plots/base-rainette-plot-with-k-n-terms-and-font-size.svg
    • plots/base-rainette-plot.svg
    • plots/base-rainette2-plot-measure-docprop.svg
    • plots/base-rainette2-plot-measure-frequency.svg
    • plots/base-rainette2-plot-measure-lr.svg
    • plots/base-rainette2-plot-with-complete-groups.svg
    • plots/base-rainette2-plot-with-free-scales.svg
    • plots/base-rainette2-plot-with-k-5.svg
    • plots/base-rainette2-plot-with-k-and-without-negative.svg
    • plots/base-rainette2-plot-with-k-n-terms-and-font-size.svg
    • plots/base-rainette2-plot.svg
    Error: Test failures
    Execution halted

Package: vsp
Check: examples
New result: ERROR
  Running examples in ‘vsp-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_varimax_z_pairs
  > ### Title: Create a pairs plot of select Y factors
  > ### Aliases: plot_varimax_z_pairs plot_varimax_y_pairs plot_svd_u
  > ###   plot_svd_v
  > 
  > ### ** Examples
  > 
  > 
  > data(enron, package = "igraphdata")
  > 
  > fa <- vsp(enron, rank = 3)
  This graph was created by an old(er) igraph version.
  ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
  For now we convert it on the fly...
  > 
  > plot_varimax_z_pairs(fa)
  Error in `dplyr::sample_n()`:
  ! Can't compute indices.
  Caused by error in `sample.int()`:
  ! too few positive probabilities
  Backtrace:
       ▆
    1. ├─vsp::plot_varimax_z_pairs(fa)
    2. │ └─... %>% GGally::ggpairs(ggplot2::aes(alpha = 0.001), ...)
    3. ├─GGally::ggpairs(., ggplot2::aes(alpha = 0.001), ...)
    4. ├─dplyr::select(., -leverage)
    5. ├─dplyr::sample_n(., min(nrow(.), 1000), weight = leverage^2)
    6. ├─dplyr:::sample_n.data.frame(., min(nrow(.), 1000), weight = leverage^2)
    7. │ ├─dplyr::slice(...)
    8. │ └─dplyr:::slice.data.frame(...)
    9. │   └─dplyr:::slice_rows(.data, dots, by)
   10. │     └─dplyr:::slice_eval(mask, dots, error_call = error_call, user_env = user_env)
   11. │       ├─base::withCallingHandlers(...)
   12. │       └─mask$eval_all(quo(impl(!!!dots)))
   13. ├─dplyr (local) impl(...)
   14. │ └─dplyr:::...elt2(i)
   15. │   └─rlang::eval_bare(sym(paste0("..", i)), frame)
   16. ├─rlang (local) local(...)
   17. ├─base::local(...)
   18. │ └─base::eval.parent(substitute(eval(quote(expr), envir)))
   19. │   └─base::eval(expr, p)
   20. │     └─base::eval(expr, p)
   21. │       └─base::eval(...)
   22. │         └─base::eval(...)
   23. │           └─base::sample.int(n(), size, replace = replace, prob = leverage^2)
   24. └─base::.handleSimpleError(...)
   25.   └─dplyr (local) h(simpleError(msg, call))
   26.     └─rlang::abort(bullets, call = error_call, parent = cnd)
  Execution halted