[R-pkg-team] Bug#1150390: r-bioc-ballgown: autopkgtest fails with testthat 3.3.2: could not find function "is_true"

[Sebastien Bacher]

Source: r-bioc-ballgown
Version: 2.43.0+dfsg-2
Severity: normal
Tags: patch
X-Debbugs-Cc: seb128 at ubuntu.com
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu  ubuntu-patch

Hi,

The package builds fine, but its autopkgtest fails with testthat 3.3.2,
which removed the long-deprecated is_true() expectation. This blocks
migration to testing:

  > test_check('ballgown')
  Saving _problems/test-annotation-42.R
  [ FAIL 1 | WARN 32 | SKIP 0 | PASS 127 ]

  ══ Failed tests ══
  ── Error ('test-annotation.R:41:5'): splitting attribute fields works ──
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at test-annotation.R:41:5

Ubuntu sees the same failure.

Upstream fixed this by replacing both is_true() calls in
tests/testthat/test-annotation.R with equals(TRUE):

  https://github.com/alyssafrazee/ballgown/commit/0ccd85f97c942de7e93a3f9b341fe688a6b4bb88

The attached patch is that commit as a quilt patch, unchanged. It only
touches the test file. We are applying it in Ubuntu as
2.43.0+dfsg-2ubuntu1.

Cheers,
Sebastien


-- System Information:
Debian Release: forky/sid
  APT prefers resolute-updates
  APT policy: (500, 'resolute-updates'), (500, 'resolute-security'), (500, 'resolute'), (100, 'resolute-backports')
Architecture: amd64 (x86_64)

Kernel: Linux 7.0.0-38-generic (SMP w/16 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-------------- next part --------------
Description: Replace is_true() removed from testthat
 testthat 3.3.2 removed the long-deprecated is_true() expectation, so
 test-annotation.R fails with 'could not find function "is_true"'.
 Use equals(TRUE) instead.
Origin: upstream, https://github.com/alyssafrazee/ballgown/commit/0ccd85f97c942de7e93a3f9b341fe688a6b4bb88
Last-Update: 2026-10-09
---
Index: r-bioc-ballgown-2.43.0+dfsg/tests/testthat/test-annotation.R
===================================================================
--- r-bioc-ballgown-2.43.0+dfsg.orig/tests/testthat/test-annotation.R
+++ r-bioc-ballgown-2.43.0+dfsg/tests/testthat/test-annotation.R
@@ -39,14 +39,14 @@ test_that('splitting attribute fields wo
     expect_that(getAttributeField(x$attributes, 'transcript_id'), 
         not(throws_error()))
     expect_that(all(is.na(getAttributeField(x$seqname, 'transcript_id'))), 
-        is_true())
+        equals(TRUE))
     transcripts = getAttributeField(x$attributes, 'transcript_id')
     expect_that(transcripts, is_a('character'))
     expect_that(length(transcripts), equals(13732))
     expect_that(transcripts[192], equals('ENST00000444520'))
     expect_that(all(is.na(getAttributeField(x$attributes, 'transcript_id', 
         attrsep=','))), 
-        is_true())
+        equals(TRUE))
 })