Last updated on 2026-09-11 08:50:38 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.16.8 | 37.77 | 782.95 | 820.72 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.16.8 | 26.27 | 504.60 | 530.87 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.16.8 | 42.00 | 609.40 | 651.40 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 0.16.8 | 39.00 | 598.35 | 637.35 | NOTE | |
| r-devel-windows-x86_64 | 0.16.8 | 56.00 | 806.00 | 862.00 | OK | |
| r-patched-linux-x86_64 | 0.16.8 | 41.09 | 615.20 | 656.29 | OK | |
| r-release-linux-x86_64 | 0.16.8 | 39.01 | 623.99 | 663.00 | 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 | 64.00 | 886.00 | 950.00 | OK |
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc
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: =
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> test_data_manipulation.R: =
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> 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: =
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> 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