Check results for 'metamorphr'

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/1s] 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/1s] OK
checking loading without being on the library search path ... [0s/1s] 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 ... [7s/18s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [43s/77s] ERROR Running ‘testthat.R’ [43s/77s] 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 ... [44s/70s] OK
checking PDF version of manual ... [7s/11s] OK
DONE Status: 1 ERROR, 1 NOTE
using check arguments '--no-clean-on-error '