Test failures with latest R

[rekado]

As of Guix commit 3a37e3ecd8ae0bcc0e5d00393fa9365d611bcb71 pigx-sars-cov-2 fails its test suite. The run_deconvolution step fails.

Here's an excerpt from the Test2_se_deconvolution.log file:

Script running with parameters:

deconvolution_functions = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/scripts/deconvolution_funs.R",
sample_name = "Test2_se",
mutation_sheet = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/sample_data/mutation_sheet_211006_covidCG_NT_location.csv",
sample_sheet = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/sample_sheet.csv",
vep_file = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/output/variants/Test2_se_vep_sarscov2_parsed.txt",
snv_file = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/output/variants/Test2_se_snv.csv",
mutation_depth_threshold = "100",
sigmut_output_file = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/output/mutations/Test2_se_sigmuts.csv",
non_sigmut_output_file = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/output/mutations/Test2_se_non_sigmuts.csv",
variants_output_file = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/output/variants/Test2_se_variant_abundance.csv",
variants_with_meta_output_file = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/output/variants/Test2_se_variants_with_meta.csv",
mutation_output_file = "/tmp/guix-build-pigx-sars-cov-2-0.0.8.drv-0/pigx_sars-cov-2-0.0.8/tests/output/mutations/Test2_se_mutations.csv",
deconvolution_method = "weighted_rlm"

Error in `dplyr::na_if()`:
! Can't convert `y` <character> to match type of `x` <data.table>.
Backtrace:
     ▆
  1. ├─... %>% dplyr::select(variant = name, mutation = value)
  2. ├─dplyr::select(., variant = name, mutation = value)
  3. ├─tidyr::pivot_longer(., everything(), values_drop_na = TRUE)
  4. ├─dplyr::na_if(., "")
  5. │ └─vctrs::vec_cast(x = y, to = x, x_arg = "y", to_arg = "x")
  6. └─vctrs (local) `<fn>`()
  7.   └─vctrs::vec_default_cast(...)
  8.     ├─base::withRestarts(...)
  9.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
 10.     │   └─base (local) doWithOneRestart(return(expr), restart)
 11.     └─vctrs::stop_incompatible_cast(...)
 12.       └─vctrs::stop_incompatible_type(...)
 13.         └─vctrs:::stop_incompatible(...)
 14.           └─vctrs:::stop_vctrs(...)
 15.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted