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Type 'q()' to quit R. > # 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(demulticoder) > > test_check("demulticoder") Existing files found in the output directory. Overwriting existing files. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 4 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): sample_name, primer_name, organism i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Creating output directory: D:/temp/2025_04_30_22_35_16_20738/RtmpEvKQP8/demulticoder_run/prefiltered_sequences Existing files found in the output directory. Overwriting existing files. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 4 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): sample_name, primer_name, organism i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Creating output directory: D:/temp/2025_04_30_22_35_16_20738/RtmpEvKQP8/demulticoder_run/prefiltered_sequences Existing files found in the output directory. Overwriting existing files. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 4 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): sample_name, primer_name, organism i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Creating output directory: D:/temp/2025_04_30_22_35_16_20738/RtmpEvKQP8/demulticoder_run/prefiltered_sequences Existing files found in the output directory. Overwriting existing files. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 4 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): sample_name, primer_name, organism i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Creating output directory: D:/temp/2025_04_30_22_35_16_20738/RtmpEvKQP8/demulticoder_run/prefiltered_sequences Existing files found in the output directory. Overwriting existing files. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 2 Columns: 25 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): primer_name, forward, reverse dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo... lgl (4): already_trimmed, count_all_samples, multithread, verbose i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Rows: 4 Columns: 3 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): sample_name, primer_name, organism i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. Creating output directory: D:/temp/2025_04_30_22_35_16_20738/RtmpEvKQP8/demulticoder_run/prefiltered_sequences [ FAIL 4 | WARN 0 | SKIP 0 | PASS 2 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_assign_tax.R:4:3'): assign_taxonomy works correctly ──────────── Error in `system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE)`: '"/usr/bin/cutadapt"' not found Backtrace: ▆ 1. └─demulticoder::cut_trim(...) at test_assign_tax.R:4:3 2. └─demulticoder:::run_cutadapt(...) 3. ├─base::tryCatch(...) 4. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 7. └─base::system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE) ── Error ('test_convert_matrix.R:4:3'): convert_asv_matrix works correctly ───── Error in `system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE)`: '"/usr/bin/cutadapt"' not found Backtrace: ▆ 1. └─demulticoder::cut_trim(...) at test_convert_matrix.R:4:3 2. └─demulticoder:::run_cutadapt(...) 3. ├─base::tryCatch(...) 4. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 7. └─base::system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE) ── Error ('test_cut_trim.R:4:3'): cut_trim works correctly ───────────────────── Error in `system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE)`: '"/usr/bin/cutadapt"' not found Backtrace: ▆ 1. └─demulticoder::cut_trim(...) at test_cut_trim.R:4:3 2. └─demulticoder:::run_cutadapt(...) 3. ├─base::tryCatch(...) 4. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 7. └─base::system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE) ── Error ('test_make_matrix.R:4:3'): make_asv_abund_matrix works correctly ───── Error in `system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE)`: '"/usr/bin/cutadapt"' not found Backtrace: ▆ 1. └─demulticoder::cut_trim(...) at test_make_matrix.R:4:3 2. └─demulticoder:::run_cutadapt(...) 3. ├─base::tryCatch(...) 4. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 7. └─base::system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE) [ FAIL 4 | WARN 0 | SKIP 0 | PASS 2 ] Error: Test failures Execution halted