Running ‘spelling.R’
  Running ‘testthat.R’ [206s/207s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tidypopgen)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: tibble
  > 
  > test_check("tidypopgen")
  Adding missing grouping variables: `population`
  which: no admixture in (/data/gannet/ripley/bin:/usr/local/bin:/usr/local/texbin:/usr/sbin:/usr/lib64/qt-3.3/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/lib64/openmpi/bin)
  which: no admixture in (/data/gannet/ripley/bin:/usr/local/bin:/usr/local/texbin:/usr/sbin:/usr/lib64/qt-3.3/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/lib64/openmpi/bin)
  Saving _problems/test_gt_as_plink-162.R
  [ FAIL 1 | WARN 4 | SKIP 5 | PASS 1019 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • (system2("which", args = "admixture", stdout = NULL) != 0) &&
    !requireNamespace("tidygenclust", quietly = TRUE) is TRUE (2):
    'test_gt_admix_methods.R:2:1', 'test_gt_admixture.R:2:1'
  • On CRAN (1): 'test_gt_pca.R:415:1'
  • {LEA} is not installed (1): 'test_gt_snmf.R:1:1'
  • {admixtools} is not installed (1): 'test_gt_extract_f2.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_gt_as_plink.R:162:5'): family.ID equals sample.ID from vcf ─────
  Error in `file(file, "rt")`: cannot open the connection
  Backtrace:
      ▆
   1. └─utils::read.table(fam_path, header = FALSE, stringsAsFactors = FALSE) at test_gt_as_plink.R:162:5
   2.   └─base::file(file, "rt")
  
  [ FAIL 1 | WARN 4 | SKIP 5 | PASS 1019 ]
  Error:
  ! Test failures.
  Execution halted