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

[Andreas Tille]

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-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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