* using log directory ‘/srv/hornik/tmp/CRAN_pretest/Rsearch.Rcheck’ * using R Under development (unstable) (2025-09-18 r88857) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘Rsearch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rsearch’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Cassandra Hjortdahl ’ New submission License components with restrictions and base license permitting such: GPL (>= 3) + file LICENSE File 'LICENSE': Rsearch Copyright (C) 2024, Cassandra Hjortdahl All rights reserved. Contact: Cassandra Hjortdahl Possibly misspelled words in DESCRIPTION: VSEARCH (12:59) amplicon (3:33) Found the following (possibly) invalid URLs: URL: https://cassandrahjo.github.io/Rsearch (moved to https://cassandrahjo.github.io/Rsearch/) From: DESCRIPTION man/Rsearch-package.Rd Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. Found the following (possibly) invalid DOIs: DOI: x From: inst/CITATION Message: Invalid DOI The Title field should be in title case. Current version is: ‘Processing and analyzing amplicon sequence data’ In title case that is: ‘Processing and Analyzing Amplicon Sequence Data’ Size of tarball: 14646592 bytes * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rsearch’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking whether startup messages can be suppressed ... [0s/0s] 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 ... [5s/5s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [24s/24s] ERROR Running ‘testthat.R’ [23s/23s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(Rsearch) > > test_check("Rsearch") sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not 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found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found sh: 1: vsearch: not found [ FAIL 199 | WARN 0 | SKIP 0 | PASS 124 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plot_base_quality.R:105:3'): plot_base_quality returns ggplot with overlap box ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::plot_base_quality(fastq_input = R1, reverse = R2, show_overlap_box = TRUE) at test-plot_base_quality.R:105:3 2. └─Rsearch::vs_merging_lengths(fastq.tbl, reverse.tbl, tmpdir = tmpdir) 3. └─Rsearch::vs_fastq_mergepairs(...) 4. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-plot_base_quality.R:125:3'): plot_base_quality downsamples if more than 10 000 reads ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::plot_base_quality(...) at test-plot_base_quality.R:125:3 2. └─Rsearch::vs_merging_lengths(fastq.tbl, reverse.tbl, tmpdir = tmpdir) 3. └─Rsearch::vs_fastq_mergepairs(...) 4. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:8:3'): error when wrong strand ─── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:8:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:22:3'): error when lca_cutoff value is out of range ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:22:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:37:3'): error when wrong columns in fastx_input fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:37:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:52:3'): error when wrong columns in db fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:52:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:68:3'): error when wrong columns in fastx_input fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:68:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:84:3'): error when wrong columns in db fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:84:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:97:3'): error when fastx_input does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:97:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:109:3'): error when db does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_alignment_classification.R:109:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_alignment_classification(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:122:3'): allignment with default values with fasta files as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_alignment_classification(...) at test-vs_alignment_classification.R:122:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:146:3'): allignment with default values with fasta tables as input, and table as output ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_alignment_classification(...) at test-vs_alignment_classification.R:146:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:161:3'): alignment returns tibble with top_hits_only = TRUE ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_alignment_classification(...) at test-vs_alignment_classification.R:161:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:179:3'): alignment runs with strand = 'both' ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_alignment_classification(...) at test-vs_alignment_classification.R:179:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:198:3'): character FASTQ input path is handled and joined back to sequences ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_alignment_classification(...) at test-vs_alignment_classification.R:198:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:215:3'): non-NULL tmpdir is accepted and used ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_alignment_classification(...) at test-vs_alignment_classification.R:215:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_alignment_classification.R:232:3'): alignment accepts FASTQ tibble as database (covers writeFastq branch) ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_alignment_classification(...) at test-vs_alignment_classification.R:232:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:7:3'): error when wrong strand ─────────────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_cluster_size.R:7:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_size(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:17:3'): error when input fasta_input does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_cluster_size.R:17:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_size(fasta_input = fasta_input) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:27:3'): error when both outputs are specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_cluster_size.R:27:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_size(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:38:3'): cluster sequences from fasta file, and return fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_size(...) at test-vs_cluster_size.R:38:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:54:3'): cluster sequences from fasta file, and return fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_size(...) at test-vs_cluster_size.R:54:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:69:3'): cluster sequences from fasta file, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_size(...) at test-vs_cluster_size.R:69:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:83:3'): cluster sequences from fasta tibble, and return fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_size(...) at test-vs_cluster_size.R:83:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:101:3'): cluster sequences from fasta tibble, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_size(...) at test-vs_cluster_size.R:101:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:114:3'): vs_cluster_size returns OTU table tibble when otutabout = TRUE ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_size(...) at test-vs_cluster_size.R:114:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:132:3'): vs_cluster_size writes OTU table to file when otutabout is path ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_size(...) at test-vs_cluster_size.R:132:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_size.R:151:3'): cluster sequences from empty fasta tibble, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-vs_cluster_size.R:151:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_size(fasta_input = fasta_input) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_subseq.R:2:3'): throws error if input FASTA file doesn't exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_cluster_subseq.R:2:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_subseq("nonexistent_file.fasta") 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_subseq.R:10:3'): throws error for invalid strand input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_cluster_subseq.R:10:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_subseq(dummy_fasta, strand = "invalid_strand") 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_subseq.R:21:3'): returns a tibble with expected columns ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_subseq(fasta_input) at test-vs_cluster_subseq.R:21:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_subseq.R:34:3'): writes output to file if centroids is specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_subseq(...) at test-vs_cluster_subseq.R:34:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_subseq.R:47:3'): respects sizein = FALSE ──────────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_subseq(fasta_input, sizein = FALSE) at test-vs_cluster_subseq.R:47:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_unoise.R:5:3'): error when input fasta_input does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_cluster_unoise.R:5:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_unoise(fasta_input = fasta_input) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_unoise.R:15:3'): cluster sequences from fasta file, and return file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_unoise(...) at test-vs_cluster_unoise.R:15:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_unoise.R:31:3'): cluster sequences from fasta file, and return tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_unoise(...) at test-vs_cluster_unoise.R:31:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_unoise.R:47:3'): cluster sequences from fasta tibble, and return file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_cluster_unoise(...) at test-vs_cluster_unoise.R:47:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_cluster_unoise.R:65:3'): vs_cluster_unoise returns NULL and warning when no clusters found ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-vs_cluster_unoise.R:65:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_cluster_unoise(fasta_input = fasta_input, minsize = 20) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:7:3'): error when wrong output_format ────────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_join.R:7:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_join(fastq_input = R1, reverse = R2, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:20:3'): error when output_format is 'fasta', and fastqout is defined ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_join.R:20:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_join(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:34:3'): error when output_format is 'fastq', and fastaout is defined ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_join.R:34:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_join(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:50:3'): error when fastq_input has incorrect columns if input is tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_join.R:50:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_join(fastq_input = R1, reverse = R2, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:65:3'): error when reverse has incorrect columns if input is tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_join.R:65:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_join(fastq_input = R1, reverse = R2, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:77:3'): error when input file does not exist ─── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_join.R:77:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_join(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:89:3'): error when reverse file does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_join.R:89:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_join(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:102:3'): fastq_input and reverse can be joined when files, and results written to fastq file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:102:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:123:3'): fastq_input and reverse can be joined when files, and results written to fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:123:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:141:3'): fastq_input and reverse can be joined when files, and results given as fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:141:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:157:3'): fastq_input and reverse can be joined when files, and results given as fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:157:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:173:3'): fastq_input and reverse can be joined when tibbles, and results written to fastq file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:173:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:191:3'): fastq_input and reverse can be joined when tibbles, and results given as tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:191:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:208:3'): log file exists when specified ──────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:208:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:226:3'): fastq_input and reverse can be joined when files, and results given as fastq tibble with vsearch_options ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(...) at test-vs_fastq_join.R:226:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_join.R:240:3'): join fastq sequences from a pe_df data frame ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_join(fastq_input = fastq_input) at test-vs_fastq_join.R:240:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:7:3'): error when wrong output_format ──── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:7:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:20:3'): error when output_format is 'fasta', and fastqout is defined ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:20:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:34:3'): error when output_format is 'fastq', and fastaout is defined ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:34:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:50:3'): error when fastq_input has incorrect columns if input is tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:50:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:65:3'): error when reverse has incorrect columns if input is tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:65:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:77:3'): error when input file does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:77:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:89:3'): error when reverse file does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:89:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:102:3'): fastq_input and reverse can be merged when files, and results written to fastq file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:102:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:120:3'): fastq_input and reverse can be merged when files, and results written to fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:120:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:137:3'): fastq_input and reverse can be merged when files, and results given as fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:137:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:152:3'): fastq_input and reverse can be merged when files, and results given as fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:152:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:168:3'): fastq_input and reverse can be merged when tibbles, and results written to fastq file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:168:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:185:3'): fastq_input and reverse can be merged when tibbles, and results given as tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:185:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:201:3'): log file exists when specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:201:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:219:3'): fastq_input and reverse can be merged when files, and results given as fastq tibble with vsearch_options ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(...) at test-vs_fastq_mergepairs.R:219:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:234:3'): merge read pairs from a pe_df data frame ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastq_mergepairs(fastq_input = fastq_input, output_format = output_format) at test-vs_fastq_mergepairs.R:234:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:248:3'): error when no reverse reads provided and fastq_input is not pe_df ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:248:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(fastq_input = fastq_input) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastq_mergepairs.R:258:3'): error when output file is empty and no reads were merged ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastq_mergepairs.R:258:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastq_mergepairs(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:7:3'): error when wrong output_format ───── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_subsample.R:7:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_subsample(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:19:3'): error when input is fasta and output_format is fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_subsample.R:19:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_subsample(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:32:3'): error if neither sample_size or sample_pct is specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_subsample.R:32:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_subsample(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:46:3'): error if both sample_size and sample_pct are specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_subsample.R:46:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_subsample(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:61:3'): error when fastx_input has incorrect columns if input is fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_subsample.R:61:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_subsample(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:75:3'): error when fastx_input has incorrect columns if input is fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_subsample.R:75:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_subsample(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:86:3'): error when input file does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_subsample.R:86:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_subsample(fastx_input = fastx_input, sample_size = sample_size) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:99:3'): subsample fastq file with size, and return fastq file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:99:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:120:3'): subsample fastq file with size, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:120:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:139:3'): subsample fasta file with pct, and return fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:139:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:160:3'): subsample fasta file with pct, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:160:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:180:3'): subsample fastq file with size, and return fastq file with relabeling ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:180:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:203:3'): subsample fastq file with size, and return fastq file with sha1 relabeling ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:203:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:225:3'): subsample fastq tibble with size, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:225:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:244:3'): subsample fasta tibble with size, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:244:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_subsample.R:265:3'): subsample fastq file with size, and return fastq tibble with vsearch_options ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_subsample(...) at test-vs_fastx_subsample.R:265:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:7:3'): error when wrong output_format ───── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:7:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(fastx_input = R1, reverse = R2, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:21:3'): error when output_format is fastq, and fastaout and fastaout_rev are defined ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:21:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:34:3'): error when input is fasta and output_format is fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:34:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(fastx_input = fastx_input, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:47:3'): error when output_format is 'fasta', and fastqout and fastqout_rev are defined ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:47:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:63:3'): error when reverse is specified, but output files are not both NULL or both character strings ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:63:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:79:3'): error when reverse is specified, but output files are not both NULL or both character strings ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:79:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:94:3'): error when fastx_input has incorrect columns if input is fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:94:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(fastx_input = R1, reverse = R2) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:105:3'): error when reverse has incorrect columns if input is fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:105:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(fastx_input = R1, reverse = R2) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:118:3'): error when fastx_input has incorrect columns if input is fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:118:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(fastx_input = R1, reverse = R2, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:133:3'): error when reverse has incorrect columns if input is fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:133:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:147:3'): error when input file does not exist when output_format is fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:147:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:159:3'): error when reverse file does not exist when output_format is fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:159:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:171:3'): error when input file does not exist when output_format is fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:171:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:183:3'): error when reverse file does not exist when output_format is fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:183:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:197:3'): error if reverse input is of type fasta and output_format is fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_trim_filt.R:197:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_trim_filt(fastx_input = R1, reverse = R2, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:215:3'): trim/filter fastq sequences from two files, and return two fastq files ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:215:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:244:3'): trim/filter fastq sequences from two files, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:244:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:262:3'): trim/filter fastq sequences from one file, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:262:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:278:3'): trim/filter fastq sequences from two tibbles, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:278:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:300:3'): trim/filter fasta sequences from two files, and return two fasta files ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:300:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:332:3'): trim/filter fasta sequences from two tibbles, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:332:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:354:3'): trim/filter fastq sequences from two files, and return fastq tibble with stripping ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:354:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:375:3'): trim/filter fastq sequences from one file with size values, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(...) at test-vs_fastx_trim_filt.R:375:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:390:3'): trim/filter fastq sequences from pe_df data frame ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_trim_filt(fastx_input = fastx_input) at test-vs_fastx_trim_filt.R:390:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_trim_filt.R:410:3'): trim/filter fasta sequences with wrong parameters ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::capture_warnings(...) at test-vs_fastx_trim_filt.R:410:3 2. │ └─base::withCallingHandlers(...) 3. └─Rsearch::vs_fastx_trim_filt(...) 4. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:6:3'): error when wrong output_format ─────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_uniques.R:6:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_uniques(fastx_input = fastx_input, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:16:3'): error when input is fasta and output_format is fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_uniques.R:16:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_uniques(fastx_input = fastx_input, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:26:3'): error when wrong strand ───────────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_uniques.R:26:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_uniques(fastx_input = fastx_input, strand = strand) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:36:3'): error when fastx_input has incorrect columns if input is fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_uniques.R:36:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_uniques(fastx_input = fastx_input) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:47:3'): error when fastx_input has incorrect columns if input is fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_uniques.R:47:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_uniques(fastx_input = fastx_input, output_format = output_format) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:56:3'): error when input file does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_fastx_uniques.R:56:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_fastx_uniques(fastx_input = fastx_input) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:66:3'): dereplicate fastq file, and return fastq file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:66:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:82:3'): dereplicate fastq file, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:82:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:96:3'): dereplicate fastq tibble, and return fastq file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:96:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:112:3'): dereplicate fastq tibble, and return fastq tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:112:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:126:3'): dereplicate fasta file, and return fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:126:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:142:3'): dereplicate fasta file, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:142:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:156:3'): dereplicate fasta tibble, and return fasta file ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:156:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:172:3'): dereplicate fasta tibble, and return fasta tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:172:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:187:3'): dereplicate fastq file, and return fastq file with relabeling ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:187:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:205:3'): dereplicate fastq file, and return fastq file with relbeling sha1 ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:205:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:223:3'): dereplicate fastq file, and return fastq file with fastq_qout_max ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:223:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_fastx_uniques.R:242:3'): dereplicate fastq file, and return fastq tibble with vsearch_options ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_fastx_uniques(...) at test-vs_fastx_uniques.R:242:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_merging_lengths.R:30:3'): get merging lengths from merging two fastq files ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_merging_lengths(fastq_input = fastq_input, reverse = reverse) at test-vs_merging_lengths.R:30:3 2. └─Rsearch::vs_fastq_mergepairs(...) 3. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_merging_lengths.R:52:3'): get merging lengths from merging two fastq tibbles ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_merging_lengths(...) at test-vs_merging_lengths.R:52:3 2. └─Rsearch::vs_fastq_mergepairs(...) 3. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_merging_lengths.R:84:5'): vs_merging_lengths creates histograms when R1 and R2 lengths vary ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-vs_merging_lengths.R:83:3 2. │ └─base::withCallingHandlers(...) 3. └─Rsearch::vs_merging_lengths(fastq_input = fastq_input, reverse = reverse) at test-vs_merging_lengths.R:84:5 4. └─Rsearch::vs_fastq_mergepairs(...) 5. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_merging_lengths.R:101:3'): pe_df tibble can be merged ─────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_merging_lengths(fastq_input = fastq_input) at test-vs_merging_lengths.R:101:3 2. └─Rsearch::vs_fastq_mergepairs(...) 3. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncee_rate.R:6:3'): optimizing truncee_rate with default values and files as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncee_rate(...) at test-vs_optimize_truncee_rate.R:6:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncee_rate.R:26:3'): optimizing truncee_rate with tibbles as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncee_rate(...) at test-vs_optimize_truncee_rate.R:26:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncee_rate.R:46:3'): optimizing truncee_rate with pe_df tibble as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncee_rate(...) at test-vs_optimize_truncee_rate.R:46:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncee_rate.R:68:3'): vs_optimize_truncee_rate handles vs_fastq_mergepairs failure gracefully ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncee_rate(...) at test-vs_optimize_truncee_rate.R:68:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncqual.R:6:3'): optimizing truncqual with default values and files as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncqual(fastq_input = fastq_input, reverse = reverse) at test-vs_optimize_truncqual.R:6:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncqual.R:26:3'): optimizing truncqual with tibbles as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncqual(...) at test-vs_optimize_truncqual.R:26:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncqual.R:45:3'): optimizing truncqual with pe_df tibble as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncqual(...) at test-vs_optimize_truncqual.R:45:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_optimize_truncqual.R:67:3'): vs_optimize_truncqual handles vs_fastq_mergepairs failure gracefully ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_optimize_truncqual(...) at test-vs_optimize_truncqual.R:67:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:8:3'): error when wrong strand ─────────────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:8:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:22:3'): error when both outputs are specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:22:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:37:3'): error when wrong columns in fastx_input fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:37:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:52:3'): error when wrong columns in db fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:52:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:68:3'): error when wrong columns in fastx_input fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:68:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:84:3'): error when wrong columns in db fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:84:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:97:3'): error when fastx_input does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:97:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:109:3'): error when db does not exist ──────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_search_exact.R:109:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_search_exact(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:122:3'): search with default values with fastq tibbles as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_search_exact(...) at test-vs_search_exact.R:122:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:148:3'): search with default values with fasta files as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_search_exact(...) at test-vs_search_exact.R:148:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:174:3'): search with default values with fasta file and tibble as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_search_exact(...) at test-vs_search_exact.R:174:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:200:3'): vs_search_exact returns OTU table tibble when otutabout = TRUE ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_search_exact(...) at test-vs_search_exact.R:200:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:218:3'): vs_search_exact writes OTU table to file when otutabout is path ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_search_exact(...) at test-vs_search_exact.R:218:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_search_exact.R:236:3'): vs_search_exact returns alignment tibble with default userfields ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_search_exact(fastx_input = fasta_input, database = db) at test-vs_search_exact.R:236:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:5:3'): vs_sintax fails with invalid strand ───────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_sintax.R:5:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_sintax(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:16:3'): vs_sintax errors if input fasta file does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_sintax.R:16:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_sintax(fasta_input = fake_fasta, database = db_file) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:28:3'): vs_sintax errors if input database file does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_sintax.R:28:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_sintax(fasta_input = fasta_input, database = fake_db) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:37:3'): vs_sintax returns expected columns in classification ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_sintax(fasta_input = fasta_file, database = db_file) at test-vs_sintax.R:37:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:49:3'): vs_sintax writes output to file if outfile is specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_sintax(...) at test-vs_sintax.R:49:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:64:3'): vs_sintax creates logfile if specified ───── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_sintax(...) at test-vs_sintax.R:64:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:73:3'): vs_sintax accepts additional vsearch_options ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_sintax(...) at test-vs_sintax.R:73:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:88:3'): vs_sintax errors when database tibble lacks required columns ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_sintax.R:88:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_sintax(fasta_input = fasta_input, database = fake_db) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:185:3'): vs_sintax returns empty data.frame when no classification match ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_sintax(fasta_input = fasta_input, database = db_file) at test-vs_sintax.R:185:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:198:3'): vs_sintax works with database as tibble ─── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_sintax(fasta_input = fasta_input, database = database) at test-vs_sintax.R:198:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_sintax.R:208:3'): vs_sintax includes randseed argument ────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_sintax(...) at test-vs_sintax.R:208:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:7:3'): vs_uchime_denovo errors if only one output file is given ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_uchime_denovo.R:7:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_uchime_denovo(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:15:3'): error when input file is missing ──── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_uchime_denovo.R:15:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_uchime_denovo(fasta_input = "some_fasta_file.fa") 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:23:3'): vs_uchime_denovo returns tibble with chimeras and stats ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_denovo(fasta_input = R1) at test-vs_uchime_denovo.R:23:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:38:3'): vs_uchime_denovo works with tibble input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_denovo(fasta_input = R1) at test-vs_uchime_denovo.R:38:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:56:3'): vs_uchime_denovo writes output files when paths are specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-vs_uchime_denovo.R:56:3 2. │ └─base::withVisible(call) 3. └─Rsearch::vs_uchime_denovo(...) 4. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:70:3'): vs_uchime_denovo handles optional arguments ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_denovo(...) at test-vs_uchime_denovo.R:70:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:92:3'): vs_uchime_denovo joins otu_id when present in input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_denovo(fasta_input = fasta_input) at test-vs_uchime_denovo.R:92:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:100:3'): vs_uchime_denovo returns empty chimera table when none found ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_denovo(fasta_input = fasta_input) at test-vs_uchime_denovo.R:100:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_denovo.R:113:3'): vs_uchime_denovo preserves all extra columns from input tibble ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_denovo(fasta_input = fasta_input) at test-vs_uchime_denovo.R:113:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_ref.R:3:3'): error when input file does not exist ──── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_uchime_ref.R:3:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_uchime_ref(fasta_input = "missing_file.fa", database = "db.fa") 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_ref.R:12:3'): error when only one of nonchimeras/chimeras is provided ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_uchime_ref.R:12:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_uchime_ref(fasta_input = fasta, database = db, nonchimeras = "nonchim.fa") 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_ref.R:23:3'): vs_uchime_ref returns nonchimeras tibble with attributes ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_ref(fasta_input = fasta, database = db) at test-vs_uchime_ref.R:23:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_ref.R:38:3'): vs_uchime_ref writes files with relabel and log ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-vs_uchime_ref.R:38:3 2. │ └─base::withVisible(call) 3. └─Rsearch::vs_uchime_ref(...) 4. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_ref.R:56:3'): vs_uchime_ref works with FASTA tibble as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_ref(...) at test-vs_uchime_ref.R:56:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_uchime_ref.R:71:3'): vs_uchime_ref returns empty data frame for chimeras if none found ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_uchime_ref(fasta_input = fasta, database = db, sample = "sample1") at test-vs_uchime_ref.R:71:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:8:3'): error when wrong strand ───────────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:8:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:22:3'): error when both outputs are specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:22:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:37:3'): error when wrong columns in fastx_input fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:37:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:52:3'): error when wrong columns in db fastq ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:52:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:68:3'): error when wrong columns in fastx_input fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:68:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:84:3'): error when wrong columns in db fasta ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:84:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:97:3'): error when fastx_input does not exist ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:97:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:109:3'): error when db does not exist ────── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-vs_usearch_global.R:109:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─Rsearch::vs_usearch_global(...) 8. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:122:3'): allignment with default values with fastq tibbles as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(...) at test-vs_usearch_global.R:122:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:148:3'): allignment with default values with fasta files as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(...) at test-vs_usearch_global.R:148:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:174:3'): allignment with default values with fasta file and tibble as input ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(...) at test-vs_usearch_global.R:174:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:201:3'): vs_usearch_global returns OTU table tibble when otutabout = TRUE ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(...) at test-vs_usearch_global.R:201:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:221:3'): vs_usearch_global writes OTU table to file when otutabout is path ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(...) at test-vs_usearch_global.R:221:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:238:3'): vs_usearch_global returns tibble with default userfields when no output file is specified ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(fastx_input = fastx_input, database = db) at test-vs_usearch_global.R:238:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:254:3'): vs_usearch_global respects custom userfields ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(...) at test-vs_usearch_global.R:254:3 2. └─Rsearch:::vsearch_available(vsearch_executable) ── Error ('test-vs_usearch_global.R:269:3'): vs_usearch_global runs when strand is 'both' (without maxaccepts) ── Error in `vsearch_available(vsearch_executable)`: Cannot run vsearch from R, use set_vsearch_executable() to set proper command to invoke vsearch Backtrace: ▆ 1. └─Rsearch::vs_usearch_global(...) at test-vs_usearch_global.R:269:3 2. └─Rsearch:::vsearch_available(vsearch_executable) [ FAIL 199 | WARN 0 | SKIP 0 | PASS 124 ] Error: Test failures Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE