* using log directory 'd:/Rcompile/CRANpkg/local/4.7/MiscMetabar.Rcheck' * using R Under development (unstable) (2026-05-09 r90031 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-05-10 07:16:29 UTC * checking for file 'MiscMetabar/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MiscMetabar' version '0.14.4' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'gghalves' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'MiscMetabar' can be installed ... OK * 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 ... [15s] OK * checking whether the package can be loaded with stated dependencies ... [14s] OK * checking whether the package can be unloaded cleanly ... [14s] OK * checking whether the namespace can be loaded with stated dependencies ... [13s] OK * checking whether the namespace can be unloaded cleanly ... [16s] OK * checking loading without being on the library search path ... [15s] OK * checking use of S3 registration ... 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 ... [40s] OK * checking Rd files ... [3s] 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 ... [12s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking namespace references in data files ... WARNING 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. * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [83s] ERROR Running examples in 'MiscMetabar-Ex.R' failed The error most likely occurred in: > ### Name: hill_curves_pq > ### Title: Hill Diversities and Corresponding Accumulation Curves for > ### phyloseq > ### Aliases: hill_curves_pq > > ### ** Examples > > if (requireNamespace("vegan")) { + hill_curves_pq(data_fungi_mini, merge_sample_by = "Time") + hill_curves_pq(data_fungi_mini, color_fac = "Time", plot_legend = FALSE) + hill_curves_pq(data_fungi_mini, + color_fac = "Time", plot_legend = FALSE, + nperm = 9, size_point = 1, linewidth = 0.5 + ) + + hill_curves_pq(data_fungi_mini, + nperm = 9, plot_legend = FALSE, size_point = 1, + linewidth = 0.5 + ) + hill_curves_pq(data_fungi_mini, "Height", + hill_scales = c(0, 1, 2, 8), plot_legend = FALSE + ) + hill_curves_pq(data_fungi_mini, "Height", + hill_scales = c(0, 0.5, 1, 2, 4, 8), + nperm = 9 + ) + hill_curves_pq(data_fungi_mini, "Height", nperm = 9, wrap_factor = FALSE) + + data_fungi_mini@sam_data$H_T <- paste0( + data_fungi_mini@sam_data$Height, + "_", data_fungi_mini@sam_data$Time + ) + merge_samples2(data_fungi_mini, "H_T") + hill_curves_pq(data_fungi_mini, "H_T", color_fac = "Time", nperm = 9) + } 17 were discarded due to NA in variables present in formula. At least one sample name start with a zero. That can be a problem for some phyloseq functions such as plot_bar and psmelt. Error in (function (cl, name, valueClass) : assignment of an object of class "numeric" is not valid for @'.Data' in an object of class "otu_table"; is(value, "matrix") is not TRUE Calls: hill_curves_pq ... renyi -> as.matrix -> apply -> FUN -> FUN -> Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [62s] ERROR Running 'spelling.R' [0s] Running 'testthat.R' [61s] 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_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: Taxa are now in rows. > 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_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: 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_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_deseq2_edgeR.R: Loading required namespace: DESeq2 > 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_deseq2_edgeR.R: converting counts to integer mode > test_figures_alpha_div.R: 80OTUs 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: 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: 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 > test_figures_beta_div.R: 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 > test_figures_beta_div.R: 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 b=108 > test_figures_beta_div.R: 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_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 > test_figures_beta_div.R: 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 > test_figures_beta_div.R: 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 > test_figures_beta_div.R: 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 b=291 > test_figures_beta_div.R: 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 > test_figures_beta_div.R: r=4 > test_figures_beta_div.R: r=5 r=6 > test_figures_beta_div.R: r=7 > test_figures_beta_div.R: r=8 > test_figures_beta_div.R: 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 > test_figures_beta_div.R: r=14 > test_figures_beta_div.R: r=15 > test_figures_beta_div.R: 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 r=23 > test_figures_beta_div.R: 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 > test_figures_beta_div.R: r=30 > test_figures_beta_div.R: r=31 r=32 > test_figures_beta_div.R: r=33 > test_figures_beta_div.R: r=34 > test_figures_beta_div.R: r=35 > test_figures_beta_div.R: r=36 > test_figures_beta_div.R: r=37 r=38 > test_figures_beta_div.R: r=39 r=40 > test_figures_beta_div.R: r=41 r=42 > test_figures_beta_div.R: r=43 > test_figures_beta_div.R: r=44 > test_figures_beta_div.R: r=45 > test_figures_beta_div.R: Loading required namespace: phyloseqGraphTest > test_deseq2_edgeR.R: fitting model and testing > 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: networkD3 > 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: 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_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_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_krona.R: Error in system("ktImportText 2>&1", intern = TRUE) : > test_krona.R: 'ktImportText' not found > 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_10_01_50_00_3017/Rtmp6PXvMA/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: 1018OTUs 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_biplot.R:14:3', 'test_figures_biplot.R:52:3', '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: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_summary_plot.R:9:3', 'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3', '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_krona.R:7:3', '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_misc.R:10:3', 'test_figures_misc.R:18:3', 'test_figures_beta_div.R:208:3', 'test_figures_beta_div.R:401:3', 'test_figures_beta_div.R:413:3', '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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [21s] OK * checking PDF version of manual ... [27s] OK * checking HTML version of manual ... [40s] OK * DONE Status: 2 ERRORs, 1 WARNING