[R-pkg-team] Bug#1111761: r-cran-bold: autopkgtest regression: operator is invalid for atomic vectors

[Paul Gevers]

Source: r-cran-bold
Version: 1.3.0-1
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

Your package has an autopkgtest, great. However, it fails. Can you 
please investigate the situation and fix it? I copied some of the output 
at the bottom of this report.

The release team has announced [1] that failing autopkgtest on amd64 and 
arm64 are considered RC in testing.

More information about this bug and the reason for filing it can be 
found on 
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://lists.debian.org/debian-devel-announce/2019/07/msg00002.html

https://ci.debian.net/packages/r/r-cran-bold/testing/amd64/62856313/

  41s autopkgtest [00:04:53]: test run-unit-test: [-----------------------
  41s
  41s R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
  41s Copyright (C) 2025 The R Foundation for Statistical Computing
  41s Platform: x86_64-pc-linux-gnu
  41s
  41s R is free software and comes with ABSOLUTELY NO WARRANTY.
  41s You are welcome to redistribute it under certain conditions.
  41s Type 'license()' or 'licence()' for distribution details.
  41s
  41s R is a collaborative project with many contributors.
  41s Type 'contributors()' for more information and
  41s 'citation()' on how to cite R or R packages in publications.
  41s
  41s Type 'demo()' for some demos, 'help()' for on-line help, or
  41s 'help.start()' for an HTML browser interface to help.
  41s Type 'q()' to quit R.
  41s
  41s > library(testthat)
  41s > test_check('bold')
  41s Loading required package: bold
  47s [ FAIL 2 | WARN 22 | SKIP 59 | PASS 111 ]
  47s
  47s == Skipped tests (59) 
==========================================================
  48s * On CRAN (59): 'test-bold_get_attr.R:2:3', 
'test-bold_identify.R:4:3',
  48s   'test-bold_identify.R:14:3', 'test-bold_identify.R:25:3',
  48s   'test-bold_identify.R:39:3', 'test-bold_seq.R:5:3', 
'test-bold_seq.R:18:3',
  48s   'test-bold_seq.R:30:3', 'test-bold_seqspec.R:4:3',
  48s   'test-bold_seqspec.R:14:3', 'test-bold_seqspec.R:25:3',
  48s   'test-bold_seqspec.R:36:3', 'test-bold_seqspec.R:47:3',
  48s   'test-bold_specimens.R:4:3', 'test-bold_specimens.R:14:3',
  48s   'test-bold_specimens.R:24:3', 'test-bold_specimens.R:34:3',
  48s   'test-bold_stats.R:4:3', 'test-bold_stats.R:16:3', 
'test-bold_stats.R:30:3',
  48s   'test-bold_stats.R:40:3', 'test-bold_stats.R:50:3', 
'test-bold_tax_id.R:4:3',
  48s   'test-bold_tax_id.R:16:3', 'test-bold_tax_id.R:25:3',
  48s   'test-bold_tax_id.R:35:3', 'test-bold_tax_id.R:44:3',
  48s   'test-bold_tax_id.R:57:3', 'test-bold_tax_id.R:65:3',
  48s   'test-bold_tax_id.R:73:3', 'test-bold_tax_id.R:82:3',
  48s   'test-bold_tax_id.R:90:3', 'test-bold_tax_id.R:98:3',
  48s   'test-bold_tax_id.R:106:3', 'test-bold_tax_id.R:114:3',
  48s   'test-bold_tax_id2.R:4:3', 'test-bold_tax_id2.R:16:3',
  48s   'test-bold_tax_id2.R:25:3', 'test-bold_tax_id2.R:41:3',
  48s   'test-bold_tax_id2.R:56:3', 'test-bold_tax_id2.R:64:3',
  48s   'test-bold_tax_id2.R:72:3', 'test-bold_tax_id2.R:81:3',
  48s   'test-bold_tax_id2.R:90:3', 'test-bold_tax_id2.R:102:3',
  48s   'test-bold_tax_id2.R:114:3', 'test-bold_tax_id2.R:126:3',
  48s   'test-bold_tax_id2.R:134:3', 'test-bold_tax_name.R:4:3',
  48s   'test-bold_tax_name.R:13:3', 'test-bold_tax_name.R:22:3',
  48s   'test-bold_tax_name.R:43:3', 'test-bold_tax_name.R:53:3',
  48s   'test-bold_tax_name.R:68:3', 'test-bold_tax_name.R:79:3',
  48s   'test-bold_trace.R:4:3', 'test-bold_trace.R:17:3', 
'test-bold_trace.R:30:3',
  48s   'test-bold_trace.R:42:3'
  48s
  48s == Failed tests 
================================================================
  48s -- Failure ('test-bold_filter.R:26:3'): bold_filter works as 
expected ----------
  48s `test` inherits from `'matrix'/'array'` not `'character'`.
  48s -- Error ('test-bold_filter.R:29:3'): bold_filter works as 
expected ------------
  48s Error in `test$species_name`: $ operator is invalid for atomic vectors
  48s Backtrace:
  48s     x
  48s  1. +-testthat::expect_equal(length(unique(test$species_name)), 
NROW(test)) at test-bold_filter.R:29:3
  48s  2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
  48s  3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
  48s  4. \-base::unique(test$species_name)
  48s
  48s [ FAIL 2 | WARN 22 | SKIP 59 | PASS 111 ]
  48s Error: Test failures
  48s Execution halted
  48s Ran 12/12 deferred expressions
  48s autopkgtest [00:05:00]: test run-unit-test: -----------------------]
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature.asc
Type: application/pgp-signature
Size: 585 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/r-pkg-team/attachments/20250821/a343e2e9/attachment.sig>