CRAN Package Check Results for Package MiscMetabar

Last updated on 2026-09-21 17:50:54 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.16.8	41.30	799.64	840.94	NOTE
r-devel-linux-x86_64-debian-gcc	0.16.8	29.44	534.77	564.21	NOTE
r-devel-linux-x86_64-fedora-clang	0.16.8	42.00	617.73	659.73	NOTE
r-devel-linux-x86_64-fedora-gcc	0.16.8	40.00	612.58	652.58	NOTE
r-devel-windows-x86_64	0.16.8	59.00	847.00	906.00	NOTE
r-patched-linux-x86_64	0.16.8	40.87	617.77	658.64	OK
r-release-linux-x86_64	0.16.8	40.08	638.96	679.04	OK
r-release-macos-arm64	0.16.8	10.00	151.00	161.00	OK
r-release-macos-x86_64	0.16.8	29.00	592.00	621.00	OK
r-release-windows-x86_64	0.16.8	55.00	739.00	794.00	ERROR
r-oldrel-macos-arm64	0.16.8			9.00	ERROR
r-oldrel-macos-x86_64	0.16.8	29.00	523.00	552.00	OK
r-oldrel-windows-x86_64	0.16.8	63.00	807.00	870.00	ERROR

Additional issues

donttest

Check Details

Version: 0.16.8
Check: dependencies in R code
Result: NOTE Base package in Suggests/Enhances imported in NAMESPACE: ‘grDevices’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Version: 0.16.8
Check: tests
Result: ERROR Running 'spelling.R' [0s] Running 'testthat.R' [93s] 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: 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 > > test_check("MiscMetabar") Starting 2 test processes. > test_blast.R: Loading required package: Rcpp > 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_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_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_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:grDevices': > test_controls.R: > test_controls.R: windows > 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: 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_dada_phyloseq.R: Loading required package: Rcpp > test_data_manipulation.R: > test_data_manipulation.R: Attaching package: 'divent' > test_data_manipulation.R: > test_data_manipulation.R: The following object is masked from 'package:Biostrings': > test_data_manipulation.R: > test_data_manipulation.R: coverage > test_data_manipulation.R: > test_data_manipulation.R: The following object is masked from 'package:IRanges': > test_data_manipulation.R: > test_data_manipulation.R: coverage > test_data_manipulation.R: > test_dada_phyloseq.R: Taxa are now in columns. > test_dada_phyloseq.R: Cleaning suppress 3 taxa and 0 samples. > test_dada_phyloseq.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_dada_phyloseq.R: Number of non-matching ASV 0 > test_dada_phyloseq.R: Number of matching ASV 42 > test_dada_phyloseq.R: Number of filtered-out ASV 35 > test_dada_phyloseq.R: Number of kept ASV 7 > test_dada_phyloseq.R: Number of kept samples 3 > test_dada_phyloseq.R: Cleaning suppress 3 taxa and 0 samples. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: Joining with `by = join_by(Sample)` > test_dada_phyloseq.R: `set.seed(123)` was used to initialize repeatable random subsampling. > test_dada_phyloseq.R: Please record this for your records so others can reproduce. > test_dada_phyloseq.R: Try `set.seed(123); .Random.seed` for the full vector > test_dada_phyloseq.R: Cleaning suppress 0 taxa ( ) and 1 sample(s) ( N23-002-M_S132_MERGED.fastq.gz ). > test_dada_phyloseq.R: Number of non-matching ASV 0 > test_dada_phyloseq.R: Number of matching ASV 1420 > test_dada_phyloseq.R: Number of filtered-out ASV 771 > test_dada_phyloseq.R: Number of kept ASV 649 > test_dada_phyloseq.R: Number of kept samples 184 > test_dada_phyloseq.R: You filtered out 771 taxa, leading to a phyloseq object including 649 taxa without NA in the taxonomic ranks: 1 2 3 4 5 6 7 8 9 10 11 12. > 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_data_manipulation.R: Taxa are now in rows. > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 32 > test_filtering.R: Number of kept ASV 1388 > test_filtering.R: Number of kept samples 185 > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 206 > test_filtering.R: Number of kept ASV 1214 > test_filtering.R: Number of kept samples 185 > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 212 > test_filtering.R: Number of kept ASV 1208 > test_filtering.R: Number of kept samples 185 > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 159 > test_filtering.R: Number of kept ASV 1261 > test_filtering.R: Number of kept samples 185 > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 93 > test_filtering.R: Number of kept ASV 1327 > test_filtering.R: Number of kept samples 185 > test_filtering.R: You filtered out 93 taxa, leading to a phyloseq object including 1327 taxa without NA in the taxonomic ranks: Class. > test_filtering.R: Taxa are now in rows. > test_krona.R: Error in system("ktImportText 2>&1", intern = TRUE) : > test_krona.R: 'ktImportText' not found > test_data_manipulation.R: Joining with `by = join_by(Sample)` > test_data_manipulation.R: `set.seed(42)` was used to initialize repeatable random subsampling. > test_data_manipulation.R: Please record this for your records so others can reproduce. > test_data_manipulation.R: Try `set.seed(42); .Random.seed` for the full vector > test_data_manipulation.R: Cleaning suppress 0 taxa ( ) and 4 sample(s) ( DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz ). > test_data_manipulation.R: Number of non-matching ASV 0 > test_data_manipulation.R: Number of matching ASV 1420 > test_data_manipulation.R: Number of filtered-out ASV 1159 > test_data_manipulation.R: Number of kept ASV 261 > test_data_manipulation.R: Number of kept samples 181 > test_data_manipulation.R: Partitioning sequences by 5-mer similarity: > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: === > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: == > test_data_manipulation.R: === > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: > test_data_manipulation.R: > test_data_manipulation.R: Time difference of 0.14 secs > test_data_manipulation.R: > test_data_manipulation.R: Sorting by relatedness within 116 groups: > test_data_manipulation.R: iteration 1 of up to 7 (100.0% stability) > test_data_manipulation.R: > test_data_manipulation.R: Time difference of 0.09 secs > test_data_manipulation.R: > test_data_manipulation.R: Clustering sequences by 9-mer similarity: > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: > test_data_manipulation.R: > test_data_manipulation.R: Time difference of 0.33 secs > test_data_manipulation.R: > test_data_manipulation.R: Clusters via relatedness sorting: 100% (0% exclusively) > test_data_manipulation.R: Clusters via rare 5-mers: 100% (0% exclusively) > test_data_manipulation.R: Estimated clustering effectiveness: 100% > test_data_manipulation.R: > test_normalize_pq.R: Taxa are now in columns. > test_normalize_pq.R: Default value being used. > test_normalize_pq.R: calcNormFactors has been renamed to normLibSizes > test_normalize_pq.R: converting counts to integer mode > test_normalize_pq.R: -- note: fitType='parametric', but the dispersion trend was not well captured by the > test_normalize_pq.R: function: y = a/x + b, and a local regression fit was automatically substituted. > test_normalize_pq.R: specify fitType='local' or 'mean' to avoid this message next time. > 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 > test_misc.R: All modality were undoubtedly rarefy in the physeq object. > test_plot_utilities.R: Loading required namespace: ggridges > test_plot_utilities.R: Loading required namespace: treemapify > test_plot_utilities.R: 47 were discarded due to NA in variables present in formula. > test_plot_utilities.R: Cleaning suppress 3 taxa and 0 samples. > test_plot_utilities.R: 17 were discarded due to NA in variables present in formula. > test_plot_utilities.R: At least one sample name start with a zero. > test_plot_utilities.R: That can be a problem for some phyloseq functions such as > test_plot_utilities.R: plot_bar and psmelt. > 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_taxonomy_utils.R: Taxa are now in rows. > test_taxonomy_utils.R: Cleaning suppress 144 taxa and 0 samples. > test_taxonomy_utils.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_taxonomy_utils.R: Number of non-matching ASV 0 > test_taxonomy_utils.R: Number of matching ASV 1276 > test_taxonomy_utils.R: Number of filtered-out ASV 953 > test_taxonomy_utils.R: Number of kept ASV 323 > test_taxonomy_utils.R: Number of kept samples 3 > test_taxonomy_utils.R: Cleaning suppress 199 taxa and 0 samples. > test_plot_funcs.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_plot_funcs.R: Number of non-matching ASV 0 > test_plot_funcs.R: Number of matching ASV 1420 > test_plot_funcs.R: Number of filtered-out ASV 1 > test_plot_funcs.R: Number of kept ASV 1419 > test_plot_funcs.R: Number of kept samples 185 > test_taxonomy_utils.R: New names: > test_taxonomy_utils.R: * `` -> `...1` > test_taxonomy_utils.R: * `` -> `...2` > test_utils.R: D:\temp\2026_09_09_01_50_00_18435\RtmpIPUvLU/script_cutadapt.sh: line 1: /c/Users/CRAN/Documents/miniconda3/etc/profile.d/conda.sh: No such file or directory > test_visualization.R: Please load ggalluvial with: library(ggalluvial) > test_visualization.R: `set.seed(207706)` was used to initialize repeatable random subsampling. > test_visualization.R: Please record this for your records so others can reproduce. > test_visualization.R: Try `set.seed(207706); .Random.seed` for the full vector > test_visualization.R: ... > test_visualization.R: Taxa are now in rows. > test_plot_funcs.R: `set.seed(1)` was used to initialize repeatable random subsampling. > test_plot_funcs.R: Please record this for your records so others can reproduce. > test_plot_funcs.R: Try `set.seed(1); .Random.seed` for the full vector > test_plot_funcs.R: | | | 0% > test_plot_funcs.R: | |====== | 11% > test_visualization.R: Joining with `by = join_by(Sample)` > test_plot_funcs.R: | |=========== | 22% > test_plot_funcs.R: | |================= | 33% > test_visualization.R: Joining with `by = join_by(Sample)` > test_plot_funcs.R: | |====================== | 44% > test_plot_funcs.R: | |============================ | 56% > test_visualization.R: Taxa are now in rows. > test_plot_funcs.R: | |================================= | 67% > test_plot_funcs.R: | |======================================= | 78% > test_plot_funcs.R: | |============================================ | 89% > test_plot_funcs.R: | |==================================================| 100% > test_vsearch.R: Error: ! testthat subprocess exited in file 'test_vsearch.R'. Caused by error: ! R session crashed with exit code -1073741819 Backtrace: ▆ 1. └─testthat::test_check("MiscMetabar") 2. └─testthat::test_dir(...) 3. └─testthat:::test_files(...) 4. └─testthat:::test_files_parallel(...) 5. ├─withr::with_dir(...) 6. │ └─base::force(code) 7. ├─testthat::with_reporter(...) 8. │ └─base::tryCatch(...) 9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".") 13. └─queue$poll(Inf) 14. └─base::lapply(...) 15. └─testthat (local) FUN(X[[i]], ...) 16. └─private$handle_error(msg, i) 17. └─cli::cli_abort(...) 18. └─rlang::abort(...) Execution halted Flavor: r-release-windows-x86_64

Version: 0.16.8
Check: package dependencies
Result: ERROR Package required but not available: ‘dada2’ Packages suggested but not available for checking: 'ALDEx2', 'ANCOMBC', 'DECIPHER', 'lefser', 'mia', 'metagenomeSeq' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-oldrel-macos-arm64

Version: 0.16.8
Check: tests
Result: ERROR Running 'spelling.R' [0s] Running 'testthat.R' [74s] 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: 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 > > test_check("MiscMetabar") Starting 2 test processes. > test_blast.R: Loading required package: Rcpp > 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_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_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:grDevices': > test_controls.R: > test_controls.R: windows > 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: 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_dada_phyloseq.R: Loading required package: Rcpp > test_dada_phyloseq.R: > test_dada_phyloseq.R: Attaching package: 'divent' > test_dada_phyloseq.R: > test_dada_phyloseq.R: The following object is masked from 'package:Biostrings': > test_dada_phyloseq.R: > test_dada_phyloseq.R: coverage > test_dada_phyloseq.R: > test_dada_phyloseq.R: The following object is masked from 'package:IRanges': > test_dada_phyloseq.R: > test_dada_phyloseq.R: coverage > test_dada_phyloseq.R: > test_dada_phyloseq.R: Taxa are now in columns. > test_dada_phyloseq.R: Cleaning suppress 3 taxa and 0 samples. > test_dada_phyloseq.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_dada_phyloseq.R: Number of non-matching ASV 0 > test_dada_phyloseq.R: Number of matching ASV 42 > test_dada_phyloseq.R: Number of filtered-out ASV 35 > test_dada_phyloseq.R: Number of kept ASV 7 > test_dada_phyloseq.R: Number of kept samples 3 > test_dada_phyloseq.R: Cleaning suppress 3 taxa and 0 samples. > 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_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: ! Sample coverage is 0, most estimators will return `NaN`. > test_dada_phyloseq.R: Joining with `by = join_by(Sample)` > test_dada_phyloseq.R: `set.seed(123)` was used to initialize repeatable random subsampling. > test_dada_phyloseq.R: Please record this for your records so others can reproduce. > test_dada_phyloseq.R: Try `set.seed(123); .Random.seed` for the full vector > test_dada_phyloseq.R: Cleaning suppress 0 taxa ( ) and 1 sample(s) ( N23-002-M_S132_MERGED.fastq.gz ). > test_dada_phyloseq.R: Number of non-matching ASV 0 > test_dada_phyloseq.R: Number of matching ASV 1420 > test_dada_phyloseq.R: Number of filtered-out ASV 771 > test_dada_phyloseq.R: Number of kept ASV 649 > test_dada_phyloseq.R: Number of kept samples 184 > test_dada_phyloseq.R: You filtered out 771 taxa, leading to a phyloseq object including 649 taxa without NA in the taxonomic ranks: 1 2 3 4 5 6 7 8 9 10 11 12. > 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_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 32 > test_filtering.R: Number of kept ASV 1388 > test_filtering.R: Number of kept samples 185 > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 206 > test_filtering.R: Number of kept ASV 1214 > test_filtering.R: Number of kept samples 185 > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 212 > test_filtering.R: Number of kept ASV 1208 > test_filtering.R: Number of kept samples 185 > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 159 > test_filtering.R: Number of kept ASV 1261 > test_filtering.R: Number of kept samples 185 > test_data_manipulation.R: Taxa are now in rows. > test_filtering.R: Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). > test_filtering.R: Number of non-matching ASV 0 > test_filtering.R: Number of matching ASV 1420 > test_filtering.R: Number of filtered-out ASV 93 > test_filtering.R: Number of kept ASV 1327 > test_filtering.R: Number of kept samples 185 > test_filtering.R: You filtered out 93 taxa, leading to a phyloseq object including 1327 taxa without NA in the taxonomic ranks: Class. > test_filtering.R: Taxa are now in rows. > test_krona.R: Error in system("ktImportText 2>&1", intern = TRUE) : > test_krona.R: 'ktImportText' not found > test_data_manipulation.R: Joining with `by = join_by(Sample)` > test_data_manipulation.R: `set.seed(42)` was used to initialize repeatable random subsampling. > test_data_manipulation.R: Please record this for your records so others can reproduce. > test_data_manipulation.R: Try `set.seed(42); .Random.seed` for the full vector > test_data_manipulation.R: Cleaning suppress 0 taxa ( ) and 4 sample(s) ( DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz ). > test_data_manipulation.R: Number of non-matching ASV 0 > test_data_manipulation.R: Number of matching ASV 1420 > test_data_manipulation.R: Number of filtered-out ASV 1159 > test_data_manipulation.R: Number of kept ASV 261 > test_data_manipulation.R: Number of kept samples 181 > test_data_manipulation.R: Partitioning sequences by 5-mer similarity: > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: == > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: > test_data_manipulation.R: > test_data_manipulation.R: Time difference of 0.23 secs > test_data_manipulation.R: > test_data_manipulation.R: Sorting by relatedness within 116 groups: > test_data_manipulation.R: iteration 1 of up to 7 (100.0% stability) > test_data_manipulation.R: > test_data_manipulation.R: Time difference of 0.12 secs > test_data_manipulation.R: > test_data_manipulation.R: Clustering sequences by 9-mer similarity: > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: = > test_data_manipulation.R: > test_data_manipulation.R: > test_data_manipulation.R: Time difference of 0.53 secs > test_data_manipulation.R: > test_data_manipulation.R: Clusters via relatedness sorting: 100% (0% exclusively) > test_data_manipulation.R: Clusters via rare 5-mers: 100% (0% exclusively) > test_data_manipulation.R: Estimated clustering effectiveness: 100% > test_data_manipulation.R: > test_normalize_pq.R: Taxa are now in columns. > test_normalize_pq.R: Default value being used. > test_normalize_pq.R: converting counts to integer mode > test_normalize_pq.R: -- note: fitType='parametric', but the dispersion trend was not well captured by the > test_normalize_pq.R: function: y = a/x + b, and a local regression fit was automatically substituted. > test_normalize_pq.R: specify fitType='local' or 'mean' to avoid this message next time. > 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 > test_misc.R: All modality were undoubtedly rarefy in the physeq object. > test_plot_utilities.R: Loading required namespace: ggridges > test_plot_utilities.R: Loading required namespace: treemapify > test_plot_utilities.R: 47 were discarded due to NA in variables present in formula. > test_plot_utilities.R: Cleaning suppress 3 taxa and 0 samples. > test_plot_utilities.R: 17 were discarded due to NA in variables present in formula. > test_plot_utilities.R: At least one sample name start with a zero. > test_plot_utilities.R: That can be a problem for some phyloseq functions such as > test_plot_utilities.R: plot_bar and psmelt. > 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: Error: ! testthat subprocess exited in file 'test_swarm.R'. Caused by error: ! R session crashed with exit code -1073741819 Backtrace: ▆ 1. └─testthat::test_check("MiscMetabar") 2. └─testthat::test_dir(...) 3. └─testthat:::test_files(...) 4. └─testthat:::test_files_parallel(...) 5. ├─withr::with_dir(...) 6. │ └─base::force(code) 7. ├─testthat::with_reporter(...) 8. │ └─base::tryCatch(...) 9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".") 13. └─queue$poll(Inf) 14. └─base::lapply(...) 15. └─testthat (local) FUN(X[[i]], ...) 16. └─private$handle_error(msg, i) 17. └─cli::cli_abort(...) 18. └─rlang::abort(...) Execution halted Flavor: r-oldrel-windows-x86_64