• using R Under development (unstable) (2026-01-25 r89330)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-12) 15.2.0     GNU Fortran (Debian 15.2.0-12) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘glyparse/DESCRIPTION’ ... OK
• this is package ‘glyparse’ version ‘0.5.3’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• 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 ‘glyparse’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ 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 ... [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 ... [4s/6s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [11s/14s] ERROR   Running ‘testthat.R’ [11s/13s] 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(glyparse)   >   > test_check("glyparse")   Saving _problems/test-auto-parse-49.R   [ FAIL 1 | WARN 0 | SKIP 12 | PASS 291 ]      ══ Skipped tests (12) ══════════════════════════════════════════════════════════   • On CRAN (12): 'test-parse-iupac-condensed.R:1:1',     'test-parse-iupac-extended.R:74:1', 'test-parse-iupac-short.R:74:1',     'test-parse-pglyco.R:1:1', 'test-parse-pglyco.R:8:1',     'test-parse-pglyco.R:15:1', 'test-parse-pglyco.R:22:1',     'test-parse-strucgp.R:1:1', 'test-parse-strucgp.R:8:1',     'test-parse-wurcs.R:456:1', 'test-parse-wurcs.R:463:1',     'test-parse-wurcs.R:470:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-auto-parse.R:49:3'): auto_parse works with mixed format vector ──   Error in `validate_glycan_structure_vector(reordered_graphs)`: All structures must have the same monosaccharide type.   x Found 2 concrete and 1 generic structure(s) in the same vector.   i Use `convert_to_generic()` to convert concrete structures to generic type.   Backtrace:        ▆     1. └─glyparse::auto_parse(mixed_input) at test-auto-parse.R:49:3     2. └─glyparse:::struc_parser_wrapper(x, do_auto_parse)     3. └─glyrepr::as_glycan_structure(unique_graphs)     4. └─vctrs::vec_cast(x, glycan_structure())     5. └─vctrs (local) `<fn>`()     6. └─glyrepr:::vec_cast.glyrepr_structure.list(...)     7. ├─base::do.call(glycan_structure, x)     8. └─glyrepr (local) `<fn>`(`<igraph>`, `<igraph>`, `<igraph>`)     9. └─glyrepr:::validate_glycan_structure_vector(reordered_graphs)    10. └─cli::cli_abort(...)    11. └─rlang::abort(...)      [ FAIL 1 | WARN 0 | SKIP 12 | PASS 291 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [3s/4s] OK
• checking PDF version of manual ... [4s/5s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR