• using R version 4.4.1 (2024-06-14)
  • using platform: x86_64-apple-darwin20
  • R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 12.2.0
  • running under: macOS Ventura 13.3.1
  • using session charset: UTF-8
  • checking for file ‘metamorphr/DESCRIPTION’ ... OK
  • this is package ‘metamorphr’ version ‘0.1.1’
  • package encoding: UTF-8
  • checking package namespace information ... OK
  • checking package dependencies ... NOTE Package suggested but not available for checking: ‘qsmooth’
  • checking if this is a source package ... OK
  • checking if there is a namespace ... OK
  • checking for executable files ... OK
  • checking for hidden files and directories ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking whether package ‘metamorphr’ can be installed ... [3s/5s] OK See the install log for details.
  • checking installed package size ... OK
  • checking package directory ... OK
  • checking ‘build’ directory ... OK
  • checking DESCRIPTION meta-information ... OK
  • checking top-level files ... OK
  • checking for left-over files ... OK
  • checking index information ... OK
  • checking package subdirectories ... OK
  • checking code files for non-ASCII characters ... OK
  • checking R files for syntax errors ... OK
  • checking whether the package can be loaded ... [0s/0s] OK
  • checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the package can be unloaded cleanly ... [0s/0s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
  • checking loading without being on the library search path ... [0s/0s] OK
  • checking dependencies in R code ... OK
  • checking S3 generic/method consistency ... OK
  • checking replacement functions ... OK
  • checking foreign function calls ... OK
  • checking R code for possible problems ... [3s/4s] OK
  • checking Rd files ... [1s/1s] OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... OK
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking Rd contents ... OK
  • checking for unstated dependencies in examples ... OK
  • checking contents of ‘data’ directory ... OK
  • checking data for non-ASCII characters ... [0s/0s] OK
  • checking LazyData ... OK
  • checking data for ASCII and uncompressed saves ... OK
  • checking R/sysdata.rda ... OK
  • checking installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [6s/10s] OK
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [43s/69s] ERROR   Running ‘testthat.R’ [42s/68s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview   > # * https://testthat.r-lib.org/articles/special-files.html   >   > library(testthat)   > library(metamorphr)   >   > test_check("metamorphr")   `impute_bpca` output:         `impute_bpca` output:         `impute_bpca` output:         `impute_bpca` output:         Cluster size 2308 broken into 1247 1061   Done cluster 1247   Done cluster 1061   Cluster size 2308 broken into 1406 902   Done cluster 1406   Done cluster 902   Cluster size 2308 broken into 1247 1061   Done cluster 1247   Done cluster 1061   Finished iteration 2.   Finished iteration 3.   Successfully ran 3 iterations.   Finished iteration 1.   Finished iteration 2.   Finished iteration 3.   11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      0 % missing values (NA): 0 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      0 % missing values (NA): 0 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      0 % missing values (NA): 0 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      0 % missing values (NA): 0 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      0 % missing values (NA): 0 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      0 % missing values (NA): 0 out of 110.      Finished iteration 1.   Finished iteration 2.   Finished iteration 3.   Finished iteration 4.   Finished iteration 5.   Finished iteration 6.   Finished iteration 1.   nipals calculated PCA   Importance of component(s):                    PC1 PC2   R2 0.4315 0.2422   Cumulative R2 0.4315 0.6736   10 Variables   11 Samples   33 NAs ( 30 %)   2 Calculated component(s)   Data was mean centered before running PCA   Data was NOT scaled before running PCA   Scores structure:   [1] 11 2   Loadings structure:   [1] 10 2   # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      30 % missing values (NA): 33 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      # 5 more features      # Use the n_features_max argument to see more      30 % missing values (NA): 33 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      30 % missing values (NA): 33 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      Replicates detected: 1...3      1 Batches: 1      30 % missing values (NA): 33 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      4 Groups: control, treatment, QC, blank      1 Batches: 1      30 % missing values (NA): 33 out of 110.      11 Samples: Sample1, Sample2, Sample3, Sample4, Sample5      # 6 more samples      # Use the n_samples_max argument to see more      10 Features: 161.10519 Da 26.98 s, 276.13647 Da 27.28 s, 304.24023 Da 32.86 s, 417.23236 Da 60.08 s, 104.10753 Da 170.31 s      # 5 more features      # Use the n_features_max argument to see more      4 Groups: control, treatment, QC, blank      Replicates detected: 1...3      30 % missing values (NA): 33 out of 110.      [ FAIL 2 | WARN 0 | SKIP 0 | PASS 362 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-impute_knn.R:206:3'): test check_installed_wrapper function ──   `check_installed_wrapper("abc")` did not throw the expected error.   ── Error ('test-normalize_quantile_smooth.R:91:3'): normalize_quantile_smooth returns the same values as qsmooth::qsmooth() ──   <packageNotFoundError/error/condition>   Error in `loadNamespace(x)`: there is no package called 'qsmooth'   Backtrace:       ▆    1. └─base::loadNamespace(x) at test-normalize_quantile_smooth.R:91:3    2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)    3. └─base (local) withOneRestart(expr, restarts[[1L]])    4. └─base (local) doWithOneRestart(return(expr), restart)      [ FAIL 2 | WARN 0 | SKIP 0 | PASS 362 ]   Error: Test failures   Execution halted
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes ... OK
  • checking re-building of vignette outputs ... [43s/80s] OK
  • checking PDF version of manual ... [8s/11s] OK
  • DONE Status: 1 ERROR, 1 NOTE
  • using check arguments '--no-clean-on-error '