[R-pkg-team] Bug#961572: r-bioc-mutationalpatterns: autopkgtest regression

[Graham Inggs]

Source: r-bioc-mutationalpatterns
Version: 2.0.0-1
Severity: serious
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: regression

Hi Maintainer

Since the upload of 2.0.0-1, r-bioc-mutationalpatterns has been
failing its own autopkgtests [1].   This now prevents the migration of
r-base.
I've copied what I hope is the relevant part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/r/r-bioc-mutationalpatterns/testing/amd64/


> test_check("MutationalPatterns")
── 1. Error: (unknown) (@test_mut_matrix_stranded.R#3)  ────────────────────────
there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Backtrace:
 1. base::library("TxDb.Hsapiens.UCSC.hg19.knownGene")

── 2. Error: (unknown) (@test_mut_matrix.R#5)  ─────────────────────────────────
there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
 1. base::library(ref_genome, character.only = TRUE)

── 3. Error: (unknown) (@test_read_vcfs_as_granges.R#5)  ───────────────────────
there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
 1. base::library(ref_genome, character.only = TRUE)

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Error: (unknown) (@test_mut_matrix_stranded.R#3)
2. Error: (unknown) (@test_mut_matrix.R#5)
3. Error: (unknown) (@test_read_vcfs_as_granges.R#5)

Error: testthat unit tests failed
Execution halted
autopkgtest [09:41:10]: test pkg-r-autopkgtest: -----------------------]
autopkgtest [09:41:10]: test pkg-r-autopkgtest:  - - - - - - - - - -
results - - - - - - - - - -
pkg-r-autopkgtest    FAIL non-zero exit status 1