Source: r-bioc-mutationalpatterns Version: 2.0.0-2 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 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: █ 1. └─base::library(ref_genome, character.only = TRUE) test-type_context.R:10:0 [ FAIL 15 | WARN 0 | SKIP 0 | PASS 264 ]
OpenPGP_signature
Description: OpenPGP digital signature
