Running 'spelling.R' [0s]
  Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MiscMetabar)
  Loading required package: phyloseq
  Loading required package: ggplot2
  Loading required package: dada2
  Loading required package: Rcpp
  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
  
  Loading required package: purrr
  > 
  > test_check("MiscMetabar")
  Starting 2 test processes.
  > test_blast.R: blast_to_phyloseq(), filter_asv_blast(), blast_to_derep(),
  > test_blast.R:           add_blast_info, and blast_pq() can't be tested when
  > test_blast.R:           vsearch is not installed
  > test_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
  > test_clean_pq.R: Taxa are now in rows.
  > test_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
  > test_controls.R: Loading required package: BiocGenerics
  > test_controls.R: Loading required package: generics
  > test_controls.R: 
  > test_controls.R: Attaching package: 'generics'
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:dplyr':
  > test_controls.R: 
  > test_controls.R:     explain
  > test_controls.R: 
  > test_controls.R: The following objects are masked from 'package:base':
  > test_controls.R: 
  > test_controls.R:     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
  > test_controls.R:     setequal, union
  > test_controls.R: 
  > test_controls.R: 
  > test_controls.R: Attaching package: 'BiocGenerics'
  > test_controls.R: 
  > test_controls.R: The following objects are masked from 'package:stats':
  > test_controls.R: 
  > test_controls.R:     IQR, mad, sd, var, xtabs
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:dplyr':
  > test_controls.R: 
  > test_controls.R:     combine
  > test_controls.R: 
  > test_controls.R: The following objects are masked from 'package:base':
  > test_controls.R: 
  > test_controls.R:     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
  > test_controls.R:     as.data.frame, basename, cbind, colnames, dirname, do.call,
  > test_controls.R:     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
  > test_controls.R:     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
  > test_controls.R:     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
  > test_controls.R:     unsplit, which.max, which.min
  > test_controls.R: 
  > test_controls.R: Loading required package: S4Vectors
  > test_controls.R: Loading required package: stats4
  > test_clean_pq.R: Change the samples names in refseq slot
  > test_controls.R: 
  > test_controls.R: Attaching package: 'S4Vectors'
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:utils':
  > test_controls.R: 
  > test_controls.R:     findMatches
  > test_controls.R: 
  > test_controls.R: The following objects are masked from 'package:dplyr':
  > test_controls.R: 
  > test_controls.R:     first, rename
  > test_controls.R: 
  > test_controls.R: The following objects are masked from 'package:base':
  > test_controls.R: 
  > test_controls.R:     I, expand.grid, unname
  > test_controls.R: 
  > test_controls.R: Loading required package: IRanges
  > test_controls.R: 
  > test_controls.R: Attaching package: 'IRanges'
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:grDevices':
  > test_controls.R: 
  > test_controls.R:     windows
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:purrr':
  > test_controls.R: 
  > test_controls.R:     reduce
  > test_controls.R: 
  > test_controls.R: The following objects are masked from 'package:dplyr':
  > test_controls.R: 
  > test_controls.R:     collapse, desc, slice
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:phyloseq':
  > test_controls.R: 
  > test_controls.R:     distance
  > test_controls.R: 
  > test_controls.R: Loading required package: XVector
  > test_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
  > test_clean_pq.R: Change the samples names in refseq slot
  > test_controls.R: 
  > test_controls.R: Attaching package: 'XVector'
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:purrr':
  > test_controls.R: 
  > test_controls.R:     compact
  > test_controls.R: 
  > test_controls.R: Loading required package: Seqinfo
  > test_controls.R: 
  > test_controls.R: Attaching package: 'Biostrings'
  > test_controls.R: 
  > test_controls.R: The following object is masked from 'package:base':
  > test_controls.R: 
  > test_controls.R:     strsplit
  > test_controls.R: 
  > test_clean_pq.R: Change the taxa names in tax_table slot
  > test_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
  > test_clean_pq.R: Change the taxa names in tax_table slot
  > test_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
  > test_clean_pq.R: At least one sample name start with a zero.
  > test_clean_pq.R:     That can be a problem for some phyloseq functions such as
  > test_clean_pq.R:     plot_bar and psmelt.
  > test_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
  > test_figures_alpha_div.R: You set `rngseed` to FALSE. Make sure you've set & recorded
  > test_figures_alpha_div.R:  the random seed of your session for reproducibility.
  > test_figures_alpha_div.R: See `?set.seed`
  > test_figures_alpha_div.R: 
  > test_figures_alpha_div.R: ...
  > test_figures_alpha_div.R: 73OTUs were removed because they are no longer 
  > test_figures_alpha_div.R: present in any sample after random subsampling
  > test_figures_alpha_div.R: 
  > test_figures_alpha_div.R: ...
  > test_deseq2_edgeR.R: Loading required namespace: edgeR
  > test_deseq2_edgeR.R: Conversion to edgeR format
  > test_deseq2_edgeR.R: calcNormFactors has been renamed to normLibSizes
  > test_figures_beta_div.R: B=300
  > test_figures_beta_div.R: b=3	b=6	b=9	b=12	b=15	b=18	
  > test_figures_beta_div.R: b=21	b=24	b=27	b=30	
  > test_figures_beta_div.R: b=33	b=36	b=39	b=42	b=45	b=48	b=51	
  > test_figures_beta_div.R: b=54	b=57	b=60	
  > test_figures_beta_div.R: b=63	b=66	b=69	b=72	b=75	b=78	b=81	b=84	b=87	
  > test_figures_beta_div.R: b=90	
  > test_figures_beta_div.R: b=93	b=96	b=99	b=102	b=105	b=108	b=111	b=114	b=117	b=120	
  > test_figures_beta_div.R: b=123	
  > test_figures_beta_div.R: b=126	b=129	b=132	b=135	b=138	b=141	b=144	b=147	b=150	
  > test_figures_beta_div.R: b=153	b=156	b=159	
  > test_figures_beta_div.R: b=162	b=165	b=168	b=171	b=174	b=177	b=180	
  > test_figures_beta_div.R: b=183	b=186	b=189	b=192	b=195	
  > test_figures_beta_div.R: b=198	b=201	b=204	b=207	b=210	
  > test_figures_beta_div.R: b=213	b=216	b=219	b=222	b=225	b=228	
  > test_figures_beta_div.R: b=231	b=234	b=237	b=240	
  > test_figures_beta_div.R: b=243	b=246	b=249	b=252	b=255	b=258	b=261	b=264	b=267	b=270	
  > test_figures_beta_div.R: b=273	b=276	b=279	b=282	b=285	b=288	
  > test_figures_beta_div.R: b=291	b=294	b=297	b=300	
  > test_figures_beta_div.R: r=1	
  > test_figures_beta_div.R: r=2	r=3	r=4	r=5	r=6	r=7	r=8	r=9	
  > test_figures_beta_div.R: r=10	
  > test_figures_beta_div.R: r=11	r=12	r=13	r=14	r=15	r=16	r=17	
  > test_figures_beta_div.R: r=18	
  > test_figures_beta_div.R: r=19	r=20	
  > test_figures_beta_div.R: r=21	r=22	
  > test_figures_beta_div.R: r=23	
  > test_figures_beta_div.R: r=24	
  > test_figures_beta_div.R: r=25	
  > test_figures_beta_div.R: r=26	
  > test_figures_beta_div.R: r=27	
  > test_figures_beta_div.R: r=28	
  > test_figures_beta_div.R: r=29	
  > test_figures_beta_div.R: r=30	
  > test_figures_beta_div.R: r=31	
  > test_figures_beta_div.R: r=32	
  > test_figures_beta_div.R: r=33	
  > test_figures_beta_div.R: r=34	
  > test_figures_beta_div.R: r=35	r=36	r=37	r=38	r=39	r=40	
  > test_figures_beta_div.R: r=41	
  > test_figures_beta_div.R: r=42	r=43	r=44	r=45	
  > test_deseq2_edgeR.R: Loading required namespace: DESeq2
  > test_figures_beta_div.R: Loading required namespace: phyloseqGraphTest
  > test_deseq2_edgeR.R: converting counts to integer mode
  > test_deseq2_edgeR.R: Calculation of Deseq2 results.
  > test_deseq2_edgeR.R: estimating size factors
  > test_deseq2_edgeR.R: estimating dispersions
  > test_deseq2_edgeR.R: gene-wise dispersion estimates
  > test_figures_beta_div.R: Loading required namespace: networkD3
  > test_deseq2_edgeR.R: mean-dispersion relationship
  > test_deseq2_edgeR.R: final dispersion estimates
  > test_deseq2_edgeR.R: fitting model and testing
  > test_figures_beta_div.R: Loading required namespace: ggVennDiagram
  > test_figures_beta_div.R: Taxa are now in columns.
  > test_figures_beta_div.R: Cleaning suppress 11 taxa and 0 samples.
  > test_figures_beta_div.R: Cleaning suppress 11 taxa and 0 samples.
  > test_figures_beta_div.R: Cleaning suppress 11 taxa and 0 samples.
  > test_figures_beta_div.R: Loading required namespace: tidyr
  > test_figures_beta_div.R: Loading required namespace: ComplexUpset
  > test_deseq2_edgeR.R: None taxa present significant distribution pattern through
  > test_deseq2_edgeR.R:               contrast.
  > test_deseq2_edgeR.R: Taxa are now in columns.
  > test_figures_beta_div.R: Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
  > test_figures_beta_div.R: Number of non-matching ASV 0
  > test_figures_beta_div.R: Number of matching ASV 45
  > test_figures_beta_div.R: Number of filtered-out ASV 0
  > test_figures_beta_div.R: Number of kept ASV 45
  > test_figures_beta_div.R: Number of kept samples 137
  > test_deseq2_edgeR.R: Cleaning suppress 157 taxa and 0 samples.
  > test_figures_biplot.R: Cleaning suppress 0 taxa (  ) and 15 sample(s) ( BE9-006-B_S27_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / DJ2-008-B_S87_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-H_S101_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / O20-X-B_S139_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
  > test_figures_biplot.R: Number of non-matching ASV 0
  > test_figures_biplot.R: Number of matching ASV 1420
  > test_figures_biplot.R: Number of filtered-out ASV 1385
  > test_figures_biplot.R: Number of kept ASV 35
  > test_figures_biplot.R: Number of kept samples 170
  > test_figures_taxo.R: Loading required namespace: ggh4x
  > test_figures_taxo.R: Loading required namespace: ggridges
  > test_krona.R: Error in system("ktImportText 2>&1", intern = TRUE) : 
  > test_krona.R:   'ktImportText' not found
  > test_figures_taxo.R: Scale for x is already present.
  > test_figures_taxo.R: Adding another scale for x, which will replace the existing scale.
  > test_figures_taxo.R: Loading required namespace: treemapify
  > test_phyloseq_class.R: lulu_pq() can't be tested when vsearch is not installed
  > test_phyloseq_class.R: mumu_pq() can't be tested when mumu is not installed
  Saving _problems/test_rw-23.R
  > test_subset.R: Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
  > test_subset.R: Number of non-matching ASV 0
  > test_subset.R: Number of matching ASV 1420
  > test_subset.R: Number of filtered-out ASV 354
  > test_subset.R: Number of kept ASV 1066
  > test_subset.R: Number of kept samples 185
  > test_swarm.R: swarm_clustering() and asv2otu(..., method=swarm) can't be
  > test_swarm.R:     tested when swarm is not installed
  > test_table_functions.R: Cleaning suppress 256 taxa and 0 samples.
  > test_table_functions.R: Loading required namespace: gtsummary
  > test_targets.R: Taxa are now in rows.
  > test_targets.R: Initializing error rates to maximum possible estimate.
  > test_targets.R: selfConsist step 1 .
  > test_targets.R: 
  > test_targets.R:    selfConsist step
  > test_targets.R:  2
  > test_targets.R: 
  > test_targets.R:    selfConsist step
  > test_targets.R:  3
  > test_targets.R: 
  > test_targets.R:    selfConsist step
  > test_targets.R:  4
  > test_targets.R: 
  > test_targets.R:    selfConsist step
  > test_targets.R:  5
  > test_targets.R: 
  > test_targets.R: Convergence after  5  rounds.
  > test_targets.R: Creating output directory:D:/temp/2026_05_12_01_50_00_10253/RtmpolyooV/rev
  > test_vsearch.R: Cleaning suppress 0 taxa (  ) and 39 sample(s) ( A9-012_S5_MERGED.fastq.gz / BE9-006-B_S27_MERGED.fastq.gz / BE9-006-H_S28_MERGED.fastq.gz / BG7-010-B_S30_MERGED.fastq.gz / BG7-010-M_S32_MERGED.fastq.gz / BL7-006-B_S36_MERGED.fastq.gz / BL7-006-M_S38_MERGED.fastq.gz / C21-NV1-H_S63_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / CA12-024_S66_MERGED.fastq.gz / CA9-027_S67_MERGED.fastq.gz / CC8-003_S74_MERGED.fastq.gz / D18-003-H_S79_MERGED.fastq.gz / D9-027-B_S83_MERGED.fastq.gz / DJ2-008-M_S89_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-M_S102_MERGED.fastq.gz / M22-001_S125_MERGED.fastq.gz / N19X-B_S126_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / N23-002-M_S132_MERGED.fastq.gz / O20-X-B_S139_MERGED.fastq.gz / O21-007-B_S142_MERGED.fastq.gz / O21-007-H_S143_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / O24-003-H_S146_MERGED.fastq.gz / O24-003-M_S147_MERGED.fastq.gz / O26-004-H_S149_MERGED.fastq.gz / O26-004-M_S150_MERGED.fastq.gz / R28-008-B_S158_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / W26-001-H_S166_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / Y28-002-H_S179_MERGED.fastq.gz / Y29-007-B_S181_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
  > test_vsearch.R: Number of non-matching ASV 0
  > test_vsearch.R: Number of matching ASV 345
  > test_vsearch.R: Number of filtered-out ASV 231
  > test_vsearch.R: Number of kept ASV 114
  > test_vsearch.R: Number of kept samples 146
  > test_vsearch.R: vs_search_global() and asv2otu(..., method=vsearch) can't be tested when vsearch is not installed
  > test_misc.R: You set `rngseed` to FALSE. Make sure you've set & recorded
  > test_misc.R:  the random seed of your session for reproducibility.
  > test_misc.R: See `?set.seed`
  > test_misc.R: 
  > test_misc.R: ...
  > test_misc.R: 1040OTUs were removed because they are no longer 
  > test_misc.R: present in any sample after random subsampling
  > test_misc.R: 
  > test_misc.R: ...
  > test_misc.R: All modality were undoubtedly rarefy in the physeq object.
  [ FAIL 1 | WARN 0 | SKIP 78 | PASS 80 ]
  
  ══ Skipped tests (78) ══════════════════════════════════════════════════════════
  • On CRAN (61): 'test_adonis.R:1:1', 'test_controls.R:7:3',
    'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
    'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
    'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
    'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
    'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
    'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',
    'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
    'test_deseq2_edgeR.R:59:3', 'test_figures_beta_div.R:22:3',
    'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
    'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
    'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:289:5',
    'test_figures_beta_div.R:314:3', 'test_figures_beta_div.R:346:3',
    'test_figures_beta_div.R:355:3', 'test_figures_beta_div.R:387:3',
    'test_figures_biplot.R:14:3', 'test_figures_biplot.R:52:3',
    'test_figures_misc.R:26:3', 'test_figures_misc.R:35:3',
    'test_figures_summary_plot.R:9:3', 'test_figures_summary_plot.R:19:3',
    'test_figures_summary_plot.R:28:3', 'test_krona.R:7:3',
    'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
    'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
    'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
    'test_figures_taxo.R:379:3', 'test_phyloseq_class.R:10:3',
    'test_phyloseq_class.R:51:3', 'test_rw.R:8:3', 'test_subset.R:7:3',
    'test_subset.R:18:3', 'test_table_functions.R:34:5',
    'test_table_functions.R:47:5', 'test_targets.R:5:3', 'test_targets.R:56:3',
    'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
    'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
    'test_misc.R:30:3', 'test_misc.R:97:3'
  • On Windows (12): 'test_figures_beta_div.R:208:3',
    'test_figures_beta_div.R:401:3', 'test_figures_beta_div.R:413:3',
    'test_figures_misc.R:10:3', 'test_figures_misc.R:18:3',
    'test_figures_taxo.R:413:3', 'test_phyloseq_class.R:93:3', 'test_rw.R:38:3',
    'test_table_functions.R:5:3', 'test_table_functions.R:18:3',
    'test_targets.R:83:3', 'test_targets.R:128:3'
  • empty test (5): , , 'test_figures_beta_div.R:256:1', ,
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_rw.R:23:3'): write_pq function works fine with data_fungi dataset ──
  Error in `.local(x, row.names, optional, ...)`: unused argument (validRN = FALSE)
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test_rw.R:23:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─MiscMetabar::write_pq(data_fungi, path = testFolder, silent = TRUE)
   10.   └─utils::write.table(...)
   11.     └─base::data.frame(x)
   12.       ├─base::as.data.frame(x[[i]], optional = TRUE, validRN = FALSE)
   13.       └─S4Vectors::as.data.frame.Vector(x[[i]], optional = TRUE, validRN = FALSE)
   14.         ├─BiocGenerics::as.data.frame(...)
   15.         └─Biostrings::as.data.frame(...)
  
  [ FAIL 1 | WARN 0 | SKIP 78 | PASS 80 ]
  Error:
  ! Test failures.
  Execution halted