* using log directory ‘/srv/hornik/tmp/CRAN_pretest/demulticoder.Rcheck’ * using R Under development (unstable) (2025-04-29 r88182) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘demulticoder/DESCRIPTION’ ... OK * this is package ‘demulticoder’ version ‘0.1.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/4s] NOTE Maintainer: ‘Martha A. Sudermann ’ New submission Possibly misspelled words in DESCRIPTION: ASV (5:224, 5:451) Metabarcodes (2:45) Sudermann (5:789) al (5:701, 5:802) amplicon (5:197) demulticoder (5:762) et (5:698, 5:799) metabarcode (5:85, 5:291, 5:422) metabarcodes (5:338) Found the following (possibly) invalid URLs: URL: https://apsjournals.apsnet.org/doi/10.1094/PHYTO-02-25-0043-FI From: README.md Status: 403 Message: Forbidden * 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 serialization versions ... OK * checking whether package ‘demulticoder’ 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 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 ... [3s/3s] 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 ... [0s/0s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [16s/15s] ERROR Running ‘testthat.R’ [15s/15s] 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(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: /tmp/RtmpPABoC4/working_dir/RtmplYEIdB/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: /tmp/RtmpPABoC4/working_dir/RtmplYEIdB/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: /tmp/RtmpPABoC4/working_dir/RtmplYEIdB/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: /tmp/RtmpPABoC4/working_dir/RtmplYEIdB/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: /tmp/RtmpPABoC4/working_dir/RtmplYEIdB/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)`: error in running command 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)`: error in running command 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)`: error in running command 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)`: error in running command 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 * checking PDF version of manual ... [3s/3s] 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