From cb11a1df099e636c601ab65eb38e29322decb3f9 Mon Sep 17 00:00:00 2001 From: Andrea Manica Date: Sat, 19 Oct 2024 11:41:28 +0100 Subject: [PATCH] fix tests --- .github/workflows/vcf-check.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/vcf-check.yaml b/.github/workflows/vcf-check.yaml index 1a612d01..f4eee4d3 100644 --- a/.github/workflows/vcf-check.yaml +++ b/.github/workflows/vcf-check.yaml @@ -44,7 +44,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::rcmdcheck - devtools + any::devtools needs: check # - uses: r-lib/actions/check-r-package@v2 @@ -58,9 +58,8 @@ jobs: vcf_path <- system.file("extdata/pop_b.vcf", package = "tidypopgen") pop_b_vcf_gt <- gen_tibble(vcf_path, quiet=TRUE,backingfile = tempfile(), parser="vcfR") - all.equal(show_genotypes(pop_b_gt),show_genotypes(pop_b_vcf_gt)) # reload it in chunks - pop_b_vcf_gt2 <- gen_tibble(vcf_path, quiet=TRUE,backingfile = tempfile(), - chunk_size = 2, parser = "vcfR") - all.equal(show_genotypes(pop_b_vcf_gt2),show_genotypes(pop_b_vcf_gt)) + pop_b_vcf_fast_gt <- gen_tibble(vcf_path, quiet=TRUE,backingfile = tempfile(), + chunk_size = 2, parser = "cpp") + all.equal(show_genotypes(pop_b_vcf_fast_gt),show_genotypes(pop_b_vcf_gt)) shell: Rscript {0}