Package: embed Check: tests New result: ERROR Running ‘testthat.R’ [68s/68s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(embed) Loading required package: recipes Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'recipes' The following object is masked from 'package:stats': step > > test_check("embed") Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Saving _problems/test-umap-273.R Saving _problems/test-umap-431.R [ FAIL 2 | WARN 0 | SKIP 103 | PASS 364 ] ══ Skipped tests (103) ═════════════════════════════════════════════════════════ • On CRAN (102): 'test-collapse_cart.R:110:1', 'test-collapse_cart.R:125:1', 'test-collapse_cart.R:142:1', 'test-collapse_cart.R:179:1', 'test-collapse_stringdist.R:198:1', 'test-collapse_stringdist.R:215:1', 'test-collapse_stringdist.R:234:1', 'test-collapse_stringdist.R:271:1', 'test-discretize_cart.R:17:1', 'test-discretize_cart.R:46:1', 'test-discretize_cart.R:75:1', 'test-discretize_cart.R:95:1', 'test-discretize_cart.R:115:1', 'test-discretize_cart.R:127:1', 'test-discretize_cart.R:157:1', 'test-discretize_cart.R:207:1', 'test-discretize_cart.R:231:1', 'test-discretize_cart.R:247:1', 'test-discretize_cart.R:284:1', 'test-discretize_xgb.R:4:1', 'test-embed.R:5:3', 'test-embed.R:83:3', 'test-embed.R:154:3', 'test-embed.R:226:3', 'test-embed.R:302:3', 'test-embed.R:333:1', 'test-embed.R:351:3', 'test-embed.R:373:3', 'test-embed.R:419:3', 'test-embed.R:459:3', 'test-embed.R:478:3', 'test-extension_check.R:1:1', 'test-feature_hash.R:1:1', 'test-lencode.R:1:1', 'test-lencode.R:60:1', 'test-lencode.R:129:1', 'test-lencode.R:306:1', 'test-lencode.R:326:1', 'test-lencode.R:377:1', 'test-lencode.R:391:1', 'test-lencode.R:433:1', 'test-lencode_bayes.R:13:3', 'test-lencode_bayes.R:86:3', 'test-lencode_bayes.R:160:3', 'test-lencode_bayes.R:236:3', 'test-lencode_bayes.R:309:3', 'test-lencode_bayes.R:383:3', 'test-lencode_bayes.R:427:1', 'test-lencode_bayes.R:437:1', 'test-lencode_bayes.R:454:1', 'test-lencode_bayes.R:496:1', 'test-lencode_glm.R:1:1', 'test-lencode_glm.R:58:1', 'test-lencode_glm.R:115:1', 'test-lencode_glm.R:228:1', 'test-lencode_glm.R:241:1', 'test-lencode_glm.R:269:1', 'test-lencode_glm.R:283:1', 'test-lencode_glm.R:325:1', 'test-lencode_mixed.R:1:1', 'test-lencode_mixed.R:119:1', 'test-lencode_mixed.R:238:1', 'test-lencode_mixed.R:254:1', 'test-lencode_mixed.R:286:1', 'test-lencode_mixed.R:303:1', 'test-lencode_mixed.R:345:1', 'test-pca_sparse.R:1:1', 'test-pca_sparse.R:50:1', 'test-pca_sparse.R:110:1', 'test-pca_sparse.R:132:1', 'test-pca_sparse.R:164:1', 'test-pca_sparse.R:249:1', 'test-pca_sparse.R:271:1', 'test-pca_sparse_bayes.R:1:1', 'test-pca_sparse_bayes.R:55:1', 'test-pca_sparse_bayes.R:119:1', 'test-pca_sparse_bayes.R:147:1', 'test-pca_sparse_bayes.R:179:1', 'test-pca_sparse_bayes.R:262:1', 'test-pca_sparse_bayes.R:284:1', 'test-pca_truncated.R:47:1', 'test-pca_truncated.R:88:1', 'test-pca_truncated.R:104:1', 'test-pca_truncated.R:134:1', 'test-pca_truncated.R:217:1', 'test-pca_truncated.R:239:1', 'test-umap.R:218:1', 'test-umap.R:276:1', 'test-umap.R:328:1', 'test-umap.R:344:1', 'test-umap.R:438:1', 'test-woe.R:18:1', 'test-woe.R:25:1', 'test-woe.R:146:1', 'test-woe.R:189:1', 'test-woe.R:206:1', 'test-woe.R:280:1', 'test-woe.R:326:1', 'test-woe.R:342:1', 'test-woe.R:361:1', 'test-woe.R:437:1', 'test-woe.R:455:1' • empty test (1): ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-umap.R:270:3'): backwards compatible for initial and target_weight args (#213) ── Error in `step_umap()`: Error in `step_umap()`: Caused by error in `prep()`: ! `initial` must be a string or character vector. ── Error ('test-umap.R:429:3'): keep_original_cols - can prep recipes with it missing ── Error in `step_umap()`: Error in `step_umap()`: Caused by error in `uwot()`: ! 'n_components' must be a positive integer Backtrace: ▆ 1. ├─recipes::prep(rec) 2. ├─recipes:::prep.recipe(rec) 3. │ ├─recipes:::recipes_error_context(...) 4. │ │ ├─base::withCallingHandlers(...) 5. │ │ └─base::force(expr) 6. │ ├─recipes::prep(x$steps[[i]], training = training, info = x$term_info) 7. │ └─embed:::prep.step_umap(x$steps[[i]], training = training, info = x$term_info) 8. │ ├─withr::with_seed(...) 9. │ │ └─withr::with_preserve_seed(...) 10. │ └─rlang::eval_tidy(umap_fit_call(x, y = y_name)) 11. ├─uwot::umap(...) 12. │ └─uwot:::uwot(...) 13. │ └─base::stop("'n_components' must be a positive integer") 14. └─base::.handleSimpleError(...) 15. └─recipes (local) h(simpleError(msg, call)) 16. └─recipes:::stop_recipes_step(call = call(step_name), parent = cnd) 17. └─recipes:::stop_recipes(...) 18. └─rlang::abort(...) [ FAIL 2 | WARN 0 | SKIP 103 | PASS 364 ] Error: ! Test failures. Execution halted Package: metR Check: examples New result: ERROR Running examples in ‘metR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ImputeEOF > ### Title: Impute missing values > ### Aliases: ImputeEOF > > ### ** Examples > > library(data.table) Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% > data(geopotential) > geopotential <- copy(geopotential) > geopotential[, gh.t := Anomaly(gh), by = .(lat, lon, month(date))] > > # Add gaps to field > geopotential[, gh.gap := gh.t] > set.seed(42) > geopotential[sample(1:.N, .N*0.3), gh.gap := NA] > > max.eof <- 5 # change to a higher value > geopotential[, gh.impute := ImputeEOF(gh.gap ~ lat + lon | date, max.eof, + verbose = TRUE, max.iter = 2000)] With 1 eof - rmse = 27.147 Warning in rbind(B, c(rep(0, j - 1), S)) : number of columns of result is not a multiple of vector length (arg 2) Package: metR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Visualization-tools.Rmd’ using knitr --- finished re-building ‘Visualization-tools.Rmd’ --- re-building ‘Working-with-data.Rmd’ using knitr Quitting from Working-with-data.Rmd:148-154 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! cannot allocate vector of size 17318.1 Gb --- Backtrace: ▆ 1. ├─...[] 2. └─data.table:::`[.data.table`(...) 3. └─base::eval(jsub, SDenv, parent.frame()) 4. └─base::eval(jsub, SDenv, parent.frame()) 5. └─metR::ImputeEOF(gh.na ~ lon + lat | date, max.eof = 5) 6. └─metR:::.ImputeEOF1(...) 7. └─irlba::irlba(X.rec, nv = n.eof, v = prev) 8. ├─base::cbind(diag(d), 0) 9. ├─base::diag(d) 10. └─base::diag(d) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics: cannot allocate vector of size 17318.1 Gb --- failed re-building ‘Working-with-data.Rmd’ SUMMARY: processing the following file failed: ‘Working-with-data.Rmd’ Error: Vignette re-building failed. Execution halted Package: metR Check: tests New result: ERROR Running ‘testthat.R’ [0m/30m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(metR) > # library(vdiffr) > > on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false"))) > if (on_cran) data.table::setDTthreads(2) > > test_check("metR") Package: Seurat Check: tests New result: ERROR Running ‘testthat.R’ [190s/190s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t > # > # # Run tests for 'v3' > # message('Run tests for v3 assay') > # options(Seurat.object.assay.version = 'v3') > # test_check("Seurat") > > # Run tests for 'v5' > message('Run tests for v5 assay') Run tests for v5 assay > options(Seurat.object.assay.version = 'v5') > test_check("Seurat") | | | 0% | |======================================================================| 100% Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running smart local moving algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Saving _problems/test_integratedata-101.R Saving _problems/test_integration-35.R 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Saving _problems/test_transferdata-33.R Saving _problems/test_transferdata-59.R Saving _problems/test_transferdata-60.R Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 2045 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: -0.0613 Number of communities: 64 Elapsed time: 0 seconds Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | 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|============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 5 | WARN 0 | SKIP 37 | PASS 653 ] ══ Skipped tests (37) ══════════════════════════════════════════════════════════ • On CRAN (37): 'test_differential_expression.R:19:3', 'test_differential_expression.R:64:3', 'test_differential_expression.R:85:3', 'test_differential_expression.R:99:3', 'test_differential_expression.R:112:3', 'test_differential_expression.R:160:3', 'test_differential_expression.R:189:3', 'test_differential_expression.R:206:3', 'test_differential_expression.R:219:3', 'test_differential_expression.R:316:3', 'test_differential_expression.R:358:3', 'test_differential_expression.R:380:3', 'test_differential_expression.R:465:3', 'test_integratedata.R:111:3', 'test_integration.R:74:3', 'test_integration.R:105:3', 'test_integration.R:136:3', 'test_integration.R:170:3', 'test_integration.R:202:3', 'test_integration.R:234:3', 'test_integration.R:264:3', 'test_integration.R:306:3', 'test_integration.R:335:3', 'test_integration.R:365:3', 'test_integration5.R:38:3', 'test_integration5.R:331:3', 'test_objects.R:6:3', 'test_preprocessing.R:140:3', 'test_preprocessing.R:158:3', 'test_preprocessing.R:433:3', 'test_preprocessing.R:560:3', 'test_preprocessing.R:581:3', 'test_transferdata.R:65:3', 'test_transferdata.R:88:3', 'test_transferdata.R:100:3', 'test_transferdata.R:112:3', 'test_transferdata.R:128:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_integratedata.R:101:3'): IntegrateData with three objects default work ── Expected `sum(GetAssayData(int3[["integrated"]], layer = "data")[1, ])` to equal 372.829. Differences: 1/1 mismatches [1] 373 - 373 == -0.0389 ── Failure ('test_integration.R:35:3'): FindTransferAnchors defaults work ────── Expected `Embeddings(co[["pcaproject.l2"]])[1, 1]` to equal 0.05175486778. Differences: 1/1 mismatches [1] 0.0518 - 0.0518 == 2.79e-07 ── Failure ('test_transferdata.R:33:3'): TransferData default work ───────────── Expected `preds.standard[1, 5]` to equal 0.4280746. Differences: 1/1 mismatches [1] 0.428 - 0.428 == -1.37e-06 ── Failure ('test_transferdata.R:59:3'): TransferData can return predictions assay, ── Expected `sum(GetAssayData(pred.assay)[1, ])` to equal 26.59365. Differences: 1/1 mismatches [1] 26.6 - 26.6 == 4.21e-05 ── Failure ('test_transferdata.R:60:3'): TransferData can return predictions assay, ── Expected `sum(GetAssayData(pred.assay)[, 1])` to equal 1.428075. Differences: 1/1 mismatches [1] 1.43 - 1.43 == -1.77e-06 [ FAIL 5 | WARN 0 | SKIP 37 | PASS 653 ] Error: ! Test failures. Execution halted Package: SuperCell Check: tests New result: ERROR Running ‘testthat.R’ [6s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(SuperCell) Thank you for installing SuperCell! SuperCell is developed by the group of David Gfeller at University of Lausanne. SuperCell can be used freely by academic groups for non-commercial purposes (see license). The product is provided free of charge, and, therefore, on an 'as is' basis, without warranty of any kind. FOR-PROFIT USERS If you plan to use SuperCell or any data provided with the script in any for-profit application, you are required to obtain a separate license. To do so, please contact eauffarth@licr.org at the Ludwig Institute for Cancer Research Ltd. If required, FOR-PROFIT USERS are also expected to have proper licenses for the tools used in SuperCell, including the R packages igraph, RANN, WeightedCluster, corpora, weights, Hmisc, Matrix, ply, irlba, grDevices, patchwork, ggplot2 and velocyto.R For scientific questions, please contact Mariia Bilous (mariia.bilous@unil.ch) or David Gfeller (David.Gfeller@unil.ch). > > test_check("SuperCell") Loading required namespace: Matrix Saving _problems/test_data_load_and_manipulations-145.R Saving _problems/test_data_load_and_manipulations-146.R [ FAIL 2 | WARN 0 | SKIP 0 | PASS 26 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_data_load_and_manipulations.R:145:3'): Metacell PCA of demo data (cell_lines) works as before ── Expected `abs(SC_test.PCA$x)` to equal `abs(SC.PCA$x)`. Differences: actual vs expected [, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] - actual[1, ] 21.3266304 4.2175459 16.68397541 5.1435219 15.3458658 1.79532235 6.2972716 1.19819827 0.51646089 3.96007475 3.50311418 4.7453620243 0.13520676 0.842127742 0.900001987 1.51799001 0.60682054 0.68602689 0.3431028934 0.87161625 + expected[1, ] 21.3266304 4.2175459 16.68397541 5.1435219 15.3458658 1.79532235 6.2972716 1.19819827 0.51646089 3.96007475 3.50311418 4.7453620243 0.13520676 0.842127742 0.900001987 1.51799001 0.60682041 0.68602895 0.3431058253 0.87151309 - actual[2, ] 5.1754672 22.0564014 2.29133718 3.2714814 1.5311393 1.58378640 8.5605252 0.98153479 3.52821329 2.41277020 2.46699588 0.4648696684 0.02844812 1.972911063 0.105897020 0.96162272 1.06820837 0.73641341 1.0782920609 0.31046654 + expected[2, ] 5.1754672 22.0564014 2.29133718 3.2714814 1.5311393 1.58378640 8.5605252 0.98153479 3.52821329 2.41277020 2.46699588 0.4648696684 0.02844812 1.972911063 0.105897020 0.96162272 1.06820845 0.73641468 1.0782901917 0.31054222 - actual[3, ] 20.8212510 10.6236387 13.27437025 7.4311886 5.2249630 3.52669416 1.6770089 6.14353626 3.02549755 0.90467464 3.56360797 2.2800000636 0.81826128 0.655054247 0.719997134 0.26759567 2.06701480 0.96042610 0.7823370640 0.81154115 + expected[3, ] 20.8212510 10.6236387 13.27437025 7.4311886 5.2249630 3.52669416 1.6770089 6.14353626 3.02549755 0.90467464 3.56360797 2.2800000636 0.81826128 0.655054247 0.719997134 0.26759567 2.06701499 0.96042916 0.7823414365 0.81138754 - actual[4, ] 3.6893045 17.9518433 6.88057916 14.3103533 13.0399180 7.22667789 2.7258798 1.02382371 3.85000062 2.09234149 0.12099447 2.5607794236 0.45926391 2.821640762 1.583769704 1.47161691 1.62814455 0.37379740 3.9917540810 2.71100890 + expected[4, ] 3.6893045 17.9518433 6.88057916 14.3103533 13.0399180 7.22667789 2.7258798 1.02382371 3.85000062 2.09234149 0.12099447 2.5607794236 0.45926391 2.821640762 1.583769704 1.47161691 1.62814418 0.37379157 3.9917624261 2.71130673 - actual[5, ] 1.1276481 11.9989793 26.58896159 1.3048571 0.6032117 8.87478170 0.8743610 0.77330669 0.55184291 0.95962308 0.53768864 1.0062945365 0.08607750 0.671991622 0.908971357 1.44902533 0.25773906 0.27267660 1.5535637077 0.51027229 + expected[5, ] 1.1276481 11.9989793 26.58896159 1.3048571 0.6032117 8.87478170 0.8743610 0.77330669 0.55184291 0.95962308 0.53768864 1.0062945365 0.08607750 0.671991622 0.908971357 1.44902533 0.25773904 0.27267633 1.5535640892 0.51028476 - actual[6, ] 3.2847719 8.0440490 22.59787965 0.7121210 4.9581818 18.56209180 0.8201641 5.55770889 5.52979814 3.23158732 0.34216477 2.5250553536 1.40813333 0.393790128 0.225346367 1.95009198 2.58490363 0.84078302 0.1956382449 0.20447809 + expected[6, ] 3.2847719 8.0440490 22.59787965 0.7121210 4.9581818 18.56209180 0.8201641 5.55770889 5.52979814 3.23158732 0.34216477 2.5250553536 1.40813333 0.393790128 0.225346367 1.95009198 2.58490369 0.84078208 0.1956395678 0.20451937 - actual[7, ] 1.3123215 21.1782936 9.99778006 11.3925415 7.3753713 1.34403676 3.7883440 1.46721557 2.34736506 2.50359397 3.16859669 3.8592591333 0.38047887 0.587506712 0.665754471 2.31167981 1.15369425 1.30925426 0.0908905552 1.08687952 + expected[7, ] 1.3123215 21.1782936 9.99778006 11.3925415 7.3753713 1.34403676 3.7883440 1.46721557 2.34736506 2.50359397 3.16859669 3.8592591333 0.38047887 0.587506712 0.665754471 2.31167981 1.15369433 1.30925305 0.0908888448 1.08693669 - actual[8, ] 21.6159970 15.5394601 20.87720208 7.8905303 2.0290961 3.77964159 8.8058460 5.01951848 0.92158325 1.95100906 4.18622719 4.3628783842 4.15092078 3.437047936 3.268156947 0.49723707 2.69230749 1.29569146 3.5806759361 0.38206899 + expected[8, ] 21.6159970 15.5394601 20.87720208 7.8905303 2.0290961 3.77964159 8.8058460 5.01951848 0.92158325 1.95100906 4.18622719 4.3628783842 4.15092078 3.437047936 3.268156947 0.49723707 2.69230746 1.29569197 3.5806767035 0.38203065 - actual[9, ] 1.9021823 12.6136336 16.26887023 11.7896651 1.8819092 8.64309261 5.7725532 3.79485087 0.47821966 1.67254497 0.41369407 0.9122177931 0.06519662 0.972154928 0.102448344 0.16051152 1.07042409 2.07194408 0.0732424680 0.61663533 + expected[9, ] 1.9021823 12.6136336 16.26887023 11.7896651 1.8819092 8.64309261 5.7725532 3.79485087 0.47821966 1.67254497 0.41369407 0.9122177931 0.06519662 0.972154928 0.102448344 0.16051152 1.07042402 2.07194525 0.0732441270 0.61657930 - actual[10, ] 15.8405239 12.2516398 10.22228291 9.4803173 11.5044169 0.66426670 2.9144206 4.24188999 2.83490211 1.12994190 3.06414940 3.8876363840 0.23627326 1.481718224 1.812193024 0.58893322 0.13915762 0.12677383 0.4938597493 2.28809409 + expected[10, ] 15.8405239 12.2516398 10.22228291 9.4803173 11.5044169 0.66426670 2.9144206 4.24188999 2.83490211 1.12994190 3.06414940 3.8876363840 0.23627326 1.481718224 1.812193024 0.58893322 0.13915731 0.12676892 0.4938527364 2.28834463 and 88 more ... ── Failure ('test_data_load_and_manipulations.R:146:3'): Metacell PCA of demo data (cell_lines) works as before ── Expected `dist(SC_test.PCA$x[1:10, ])` to equal `dist(SC.PCA$x[1:10, ])`. Differences: actual | expected [1] 44.962363990 - 44.962363298 [1] [2] 47.464789773 - 47.464789860 [2] [3] 48.835318410 - 48.835334543 [3] [4] 53.845005379 - 53.845004735 [4] [5] 52.683169942 - 52.683168710 [5] [6] 53.382990877 - 53.382989230 [6] [7] 51.317592065 - 51.317588980 [7] [8] 46.264882050 - 46.264881772 [8] [9] 50.440285644 - 50.440295619 [9] [10] 42.112851553 - 42.112849599 [10] ... ... ... and 35 more ... [ FAIL 2 | WARN 0 | SKIP 0 | PASS 26 ] Error: ! Test failures. Execution halted