* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/demulticoder.Rcheck’
* using R Under development (unstable) (2025-12-20 r89211)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘demulticoder/DESCRIPTION’ ... OK
* this is package ‘demulticoder’ version ‘0.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘metacoder’
* 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 ‘demulticoder’ can be installed ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... 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 ... OK
* checking examples with --run-donttest ... [16s/16s] ERROR
Running examples in ‘demulticoder-Ex.R’ failed
The error most likely occurred in:

> ### Name: assign_tax
> ### Title: Assign taxonomy functions
> ### Aliases: assign_tax
> 
> ### ** Examples
> 
> ## No test: 
> # Assign taxonomies to ASVs on by metabarcode
> analysis_setup <- prepare_reads(
+   data_directory = system.file("extdata", package = "demulticoder"),
+   output_directory = tempdir(),
+   overwrite_existing = TRUE
+ )
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/RtmpD1GpB8/working_dir/RtmpdJCAyh/demulticoder_run/prefiltered_sequences
Warning: stack imbalance in '<-', 2 then 4
> cut_trim(
+ analysis_setup,
+ cutadapt_path="/usr/bin/cutadapt",
+ overwrite_existing = TRUE
+ )
Error in `<current-expression>` : error in running command
Calls: cut_trim ... tryCatchList -> tryCatchOne -> doTryCatch -> system2
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [15s/15s]
 [16s/16s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/demulticoder.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:16.02, 59.71 + 15.67