[R-pkg-team] Bug#983027: r-bioc-mutationalpatterns: autopkgtest regression in testing: no package called ‘BSgenome.Hsapiens.UCSC.hg19’

[Paul Gevers]

Source: r-bioc-mutationalpatterns
Version: 2.0.0-2
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

With a recent (October 2020) change somewhere outside of your package
the autopkgtest of your package started to fail. I copied some of the
output at the bottom of this report. Can you please investigate the
situation and fix it?

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

Paul

https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-mutationalpatterns/10546520/log.gz

══ Failed tests
════════════════════════════════════════════════════════════════
── Error (test-bin_mutation_density.R:11:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-bin_mutation_density.R:11:0
── Error (test-calculate_lesion_segretation.R:5:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-calculate_lesion_segretation.R:5:0
── Error (test-context_potential_damage_analysis.R:13:1): (code run
outside of `test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-context_potential_damage_analysis.R:13:0
── Error (test-extract_signatures.R:19:1): (code run outside of
`test_that()`) ──
Error: Package 'ccfindR' is needed for variational_bayes to work. Please
either install it or use the regular NMF.
Backtrace:
    â–ˆ
 1. └─MutationalPatterns::extract_signatures(...)
test-extract_signatures.R:19:0
── Error (test-get_indel_context.R:10:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-get_indel_context.R:10:0
── Error (test-mut_context.R:10:1): (code run outside of `test_that()`)
────────
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-mut_context.R:10:0
── Error (test-mut_matrix_stranded.R:6:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-mut_matrix_stranded.R:6:0
── Error (test-mut_matrix.R:5:1): (code run outside of `test_that()`)
──────────
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE) test-mut_matrix.R:5:0
── Error (test-mut_type_occurrences.R:10:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-mut_type_occurrences.R:10:0
── Error (test-plot_spectrum_region.R:10:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-plot_spectrum_region.R:10:0
── Error (test-plot_spectrum.R:11:1): (code run outside of
`test_that()`) ──────
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-plot_spectrum.R:11:0
── Error (test-plot_strand.R:10:1): (code run outside of `test_that()`)
────────
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-plot_strand.R:10:0
── Error (test-read_vcfs_as_granges.R:5:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-read_vcfs_as_granges.R:5:0
── Error (test-strand_occurrences.R:10:1): (code run outside of
`test_that()`) ──
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-strand_occurrences.R:10:0
── Error (test-type_context.R:10:1): (code run outside of `test_that()`)
───────
Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
    â–ˆ
 1. └─base::library(ref_genome, character.only = TRUE)
test-type_context.R:10:0

[ FAIL 15 | WARN 0 | SKIP 0 | PASS 264 ]

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