Last updated on 2026-01-24 01:49:25 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| pastclim | 13 | ||
| tidypopgen | 1 | 3 | 9 |
| tidysdm | 3 | 10 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 3, OK: 9
Version: 0.4.2
Check: tests
Result: ERROR
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.4.2
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'admixtools', 'LEA'
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.4.2
Check: installed package size
Result: NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
doc 1.8Mb
extdata 1.2Mb
libs 5.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.4.2
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘LEA’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.4.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'admixtools'
Flavor: r-oldrel-windows-x86_64
Current CRAN status: NOTE: 3, OK: 10
Version: 1.0.4
Check: installed package size
Result: NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 2.2Mb
doc 2.2Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64