Last updated on 2026-05-05 15:51:44 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.14.4 | 60.55 | 764.03 | 824.58 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.14.4 | 40.90 | 541.79 | 582.69 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.14.4 | 58.00 | 731.54 | 789.54 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.14.4 | 99.00 | 662.64 | 761.64 | ERROR | |
| r-devel-windows-x86_64 | 0.14.4 | 63.00 | 748.00 | 811.00 | WARN | |
| r-patched-linux-x86_64 | 0.14.4 | 52.53 | 702.03 | 754.56 | OK | |
| r-release-linux-x86_64 | 0.14.4 | 0.31 | 2.19 | 2.50 | ERROR | |
| r-release-macos-arm64 | 0.14.4 | 17.00 | 166.00 | 183.00 | OK | |
| r-release-macos-x86_64 | 0.14.4 | 42.00 | 674.00 | 716.00 | OK | |
| r-release-windows-x86_64 | 0.14.4 | 66.00 | 706.00 | 772.00 | OK | |
| r-oldrel-macos-arm64 | 0.14.4 | OK | ||||
| r-oldrel-macos-x86_64 | 0.14.4 | 41.00 | 662.00 | 703.00 | OK | |
| r-oldrel-windows-x86_64 | 0.14.4 | 87.00 | 994.00 | 1081.00 | OK |
Version: 0.14.4
Check: namespace references in data files
Result: WARN
Data files with namespace references not in the recursive strong
package dependencies:
data/data_fungi.rda: XVector
data/data_fungi_mini.rda: XVector
data/data_fungi_sp_known.rda: XVector
See section 'Data in packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 0.14.4
Check: examples
Result: ERROR
Running examples in ‘MiscMetabar-Ex.R’ failed
The error most likely occurred in:
> ### Name: read_pq
> ### Title: Read phyloseq object from multiple csv tables and a phylogenetic
> ### tree in Newick format.
> ### Aliases: read_pq
>
> ### ** Examples
>
> write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
Error in .local(x, row.names, optional, ...) :
unused argument (validRN = FALSE)
Calls: write_pq ... as.data.frame.Vector -> as.data.frame -> as.data.frame
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.14.4
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [117s/70s]
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_clean_pq.R: Change the samples names in refseq slot
> 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: Loading required package: BiocGenerics
> test_controls.R: Loading required package: generics
> test_clean_pq.R: Change the taxa names in tax_table slot
> 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_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: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_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_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
> test_clean_pq.R: Change the taxa names in tax_table slot
> 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: 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_deseq2_edgeR.R: Loading required namespace: edgeR
> 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: 75OTUs 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: Conversion to edgeR format
> test_deseq2_edgeR.R: calcNormFactors has been renamed to normLibSizes
> test_deseq2_edgeR.R: Loading required namespace: DESeq2
> test_figures_beta_div.R: B=300
> test_figures_beta_div.R: b=3 b=6 b=9 b=12 b=15
> test_figures_beta_div.R: b=18 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 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 b=90
> test_figures_beta_div.R: b=93 b=96 b=99 b=102 b=105
> test_figures_beta_div.R: b=108 b=111 b=114 b=117 b=120
> test_figures_beta_div.R: b=123 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 b=162 b=165 b=168 b=171 b=174 b=177 b=180
> test_figures_beta_div.R: b=183
> test_figures_beta_div.R: b=186 b=189 b=192 b=195 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 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
> test_figures_beta_div.R: b=267 b=270
> test_figures_beta_div.R: b=273 b=276 b=279 b=282 b=285 b=288 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
> test_figures_beta_div.R: r=5 r=6
> test_figures_beta_div.R: r=7 r=8 r=9
> test_figures_beta_div.R: r=10
> test_figures_beta_div.R: r=11 r=12
> test_figures_beta_div.R: r=13 r=14 r=15
> test_figures_beta_div.R: r=16 r=17 r=18
> test_figures_beta_div.R: r=19
> test_figures_beta_div.R: r=20
> test_figures_beta_div.R: r=21 r=22
> test_figures_beta_div.R: r=23 r=24 r=25
> test_figures_beta_div.R: r=26 r=27 r=28
> test_figures_beta_div.R: r=29 r=30
> test_figures_beta_div.R: r=31
> test_figures_beta_div.R: r=32 r=33
> test_figures_beta_div.R: r=34 r=35 r=36
> test_figures_beta_div.R: r=37 r=38 r=39
> test_figures_beta_div.R: r=40
> test_figures_beta_div.R: r=41 r=42
> test_figures_beta_div.R: r=43 r=44
> test_figures_beta_div.R: r=45
> test_deseq2_edgeR.R: converting counts to integer mode
> test_figures_beta_div.R: Loading required namespace: phyloseqGraphTest
> 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_deseq2_edgeR.R: mean-dispersion relationship
> test_deseq2_edgeR.R: final dispersion estimates
> test_figures_beta_div.R: Loading required namespace: networkD3
> 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_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_deseq2_edgeR.R: Cleaning suppress 157 taxa and 0 samples.
> test_figures_beta_div.R: Loading required namespace: tidyr
> test_figures_beta_div.R: Loading required namespace: ComplexUpset
> 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_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_krona.R: Error in system("ktImportText 2>&1", intern = TRUE) :
> test_krona.R: error in running command
> test_figures_taxo.R: Loading required namespace: ggh4x
> test_figures_taxo.R: Loading required namespace: ggridges
> 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: sh: line 1: mumu: command not found
> 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 2
> test_targets.R:
> test_targets.R: selfConsist step 3
> test_targets.R:
> test_targets.R: selfConsist step 4
> test_targets.R:
> test_targets.R: selfConsist step 5
> test_targets.R:
> test_targets.R: Convergence after 5 rounds.
> test_targets.R: Loading required namespace: pbapply
> test_targets.R: Compute the number of sequences
> test_targets.R: Start object of class: otu_table
> test_targets.R: Start object of class: derep
> test_targets.R: Start object of class: list
> test_targets.R: Start object of class: character
> test_targets.R: Start object of class: dada
> test_targets.R: Compute the number of clusters
> test_targets.R: Start object of class: otu_table
> test_targets.R: Start object of class: derep
> test_targets.R: Start object of class: list
> test_targets.R: Start object of class: character
> test_targets.R: Start object of class: dada
> test_targets.R: Compute the number of samples
> test_targets.R: Start object of class: otu_table
> test_targets.R: Start object of class: derep
> test_targets.R: Start object of class: list
> test_targets.R: Start object of class: character
> test_targets.R: Start object of class: dada
> test_targets.R: Creating output directory:/tmp/RtmpssrkmG/working_dir/Rtmp7I3B6m/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: 1025OTUs 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 77 | PASS 81 ]
══ Skipped tests (77) ══════════════════════════════════════════════════════════
• On CRAN (72): '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_biplot.R:14:3',
'test_figures_biplot.R:52:3', '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:209:3', '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_beta_div.R:402:3',
'test_figures_beta_div.R:414:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', '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_figures_taxo.R:414:3',
'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',
'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:39:3',
'test_subset.R:7:3', 'test_subset.R:18:3', 'test_table_functions.R:6:3',
'test_table_functions.R:19:3', '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:84:3', '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'
• 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 77 | PASS 81 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.14.4
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [99s/59s]
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_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: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_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 samples names in refseq slot
> test_clean_pq.R: Cleaning suppress 2 taxa and 1 samples.
> test_clean_pq.R: Change the samples names in refseq slot
> 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_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_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: 75OTUs 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: DESeq2
> test_deseq2_edgeR.R: converting counts to integer mode
> test_deseq2_edgeR.R: Calculation of Deseq2 results.
> test_figures_beta_div.R: B=300
> test_figures_beta_div.R: b=3 b=6 b=9 b=12
> test_figures_beta_div.R: b=15 b=18 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 b=54 b=57 b=60
> test_figures_beta_div.R: b=63 b=66 b=69
> test_figures_beta_div.R: b=72 b=75 b=78 b=81 b=84 b=87 b=90
> test_figures_beta_div.R: b=93 b=96 b=99 b=102
> test_figures_beta_div.R: b=105 b=108 b=111 b=114 b=117 b=120
> test_figures_beta_div.R: b=123 b=126 b=129 b=132 b=135 b=138 b=141 b=144
> test_deseq2_edgeR.R: estimating size factors
> test_figures_beta_div.R: b=147 b=150
> test_figures_beta_div.R: b=153 b=156 b=159 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 b=198 b=201 b=204
> test_figures_beta_div.R: b=207 b=210
> test_figures_beta_div.R: b=213 b=216 b=219 b=222 b=225 b=228 b=231 b=234 b=237 b=240
> test_figures_beta_div.R: b=243 b=246
> test_figures_beta_div.R: 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
> test_figures_beta_div.R: b=288 b=291 b=294 b=297 b=300
> test_figures_beta_div.R: r=1
> test_figures_beta_div.R: r=2
> test_figures_beta_div.R: r=3 r=4
> test_figures_beta_div.R: r=5
> test_figures_beta_div.R: r=6 r=7
> test_figures_beta_div.R: r=8
> test_figures_beta_div.R: r=9 r=10
> test_figures_beta_div.R: r=11
> test_figures_beta_div.R: r=12 r=13
> test_figures_beta_div.R: r=14
> test_figures_beta_div.R: r=15 r=16
> test_figures_beta_div.R: r=17 r=18
> test_figures_beta_div.R: r=19
> test_figures_beta_div.R: r=20
> test_figures_beta_div.R: r=21
> test_figures_beta_div.R: r=22
> test_figures_beta_div.R: r=23 r=24
> test_figures_beta_div.R: r=25
> test_figures_beta_div.R: r=26 r=27
> test_figures_beta_div.R: r=28
> test_figures_beta_div.R: r=29 r=30
> test_figures_beta_div.R: r=31
> test_figures_beta_div.R: r=32 r=33
> test_figures_beta_div.R: r=34
> test_figures_beta_div.R: r=35 r=36
> test_figures_beta_div.R: r=37
> test_figures_beta_div.R: r=38 r=39
> test_figures_beta_div.R: r=40
> test_figures_beta_div.R: r=41
> test_figures_beta_div.R: r=42
> test_figures_beta_div.R: r=43 r=44
> test_figures_beta_div.R: r=45
> test_figures_beta_div.R: Loading required namespace: phyloseqGraphTest
> test_deseq2_edgeR.R: estimating dispersions
> test_deseq2_edgeR.R: gene-wise dispersion estimates
> 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: networkD3
> 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_deseq2_edgeR.R: Cleaning suppress 157 taxa and 0 samples.
> test_figures_beta_div.R: Loading required namespace: ggVennDiagram
> test_figures_beta_div.R: Taxa are now in columns.
> 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_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_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_figures_taxo.R: Loading required namespace: ggh4x
> test_krona.R: Error in system("ktImportText 2>&1", intern = TRUE) :
> test_krona.R: error in running command
> test_figures_taxo.R: Loading required namespace: ggridges
> 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: sh: line 1: mumu: command not found
> 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 2
> test_targets.R:
> test_targets.R: selfConsist step 3
> test_targets.R:
> test_targets.R: selfConsist step 4
> test_targets.R:
> test_targets.R: selfConsist step 5
> test_targets.R:
> test_targets.R: Convergence after 5 rounds.
> test_targets.R: Loading required namespace: pbapply
> test_targets.R: Compute the number of sequences
> test_targets.R: Start object of class: otu_table
> test_targets.R: Start object of class: derep
> test_targets.R: Start object of class: list
> test_targets.R: Start object of class: character
> test_targets.R: Start object of class: dada
> test_targets.R: Compute the number of clusters
> test_targets.R: Start object of class: otu_table
> test_targets.R: Start object of class: derep
> test_targets.R: Start object of class: list
> test_targets.R: Start object of class: character
> test_targets.R: Start object of class: dada
> test_targets.R: Compute the number of samples
> test_targets.R: Start object of class: otu_table
> test_targets.R: Start object of class: derep
> test_targets.R: Start object of class: list
> test_targets.R: Start object of class: character
> test_targets.R: Start object of class: dada
> test_targets.R: Creating output directory:/tmp/RtmpvkipAK/working_dir/Rtmpqz8kg2/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: 1019OTUs 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 77 | PASS 81 ]
══ Skipped tests (77) ══════════════════════════════════════════════════════════
• On CRAN (72): '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_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', '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:209:3', '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_beta_div.R:402:3',
'test_figures_beta_div.R:414:3', '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_figures_taxo.R:414:3',
'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',
'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:39:3',
'test_subset.R:7:3', 'test_subset.R:18:3', 'test_table_functions.R:6:3',
'test_table_functions.R:19:3', '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:84:3', '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'
• 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 77 | PASS 81 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.14.4
Check: package dependencies
Result: ERROR
Package required but not available: ‘dada2’
Packages suggested but not available for checking:
'DESeq2', 'gghalves', 'mia', 'SummarizedExperiment'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-release-linux-x86_64