Hi folks, I think this is a consequence of running autopkgtest-pkg-r blindly for all bioc packages since we are adding
Testsuite: autopkgtest-pkg-r automatically to all packages. The "manual" test is prevented by simply renaming the debian/tests/control file to https://salsa.debian.org/r-pkg-team/r-bioc-mutationalpatterns/-/blob/master/debian/tests/control_needs_large_data and thus documenting the issue. The easiest cure would be to simply remove the Testsuite field from debian/control. However, routine-update would re-add this (which I think is a sensible thing to do) and if we use a comment to prevent routine-update to add this field this in turn is removed again by dh-update-R (called by run-unit-test). This is all not so elegant. I'm currently thinking about some file debian/tests/autopkgtest-pkg-r.hook which will be executed after https://salsa.debian.org/r-pkg-team/dh-r/-/blob/master/scripts/pkg-r-autopkgtest#L28 This could exclude or tweak some test files and in the case below simply remove those tests that are trying to load not yet packaged stuff (which is for a reason since these are just big data files). What do you think? Kind regards Andreas. On Thu, Feb 18, 2021 at 12:33:47PM +0100, Paul Gevers wrote: > 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 ] > > _______________________________________________ > R-pkg-team mailing list > r-pkg-t...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team -- http://fam-tille.de
