R Under development (unstable) (2024-09-28 r87201 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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(ALLSPICE) Warning messages: 1: replacing previous import 'stats::filter' by 'dplyr::filter' when loading 'ALLSPICE' 2: replacing previous import 'stats::lag' by 'dplyr::lag' when loading 'ALLSPICE' 3: replacing previous import 'magrittr::set_names' by 'purrr::set_names' when loading 'ALLSPICE' > > test_check("ALLSPICE") n_ind n_var c r pi sigma 1.000000e+04 1.000000e+02 6.000000e-01 5.000000e-01 5.000000e-01 1.000000e+00 c_hat lambda pvalue 6.029111e-01 8.832747e+01 7.702687e-01 n_ind n_var c r pi 1.000000e+04 1.000000e+02 6.000000e-01 5.000000e-01 5.000000e-01 sigma c_hat lambda pvalue 1.000000e+00 -6.290681e-01 1.256086e+03 1.106218e-199 Rows: 418 Columns: 9 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (4): locus, alleles, gene, annotation dbl (5): pop_AF, BETA_30600, BETA_30680, Pvalue_30600, Pvalue_30680 ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. # A tibble: 6 × 9 locus alleles pop_AF gene annotation BETA_30600 BETA_30680 Pvalue_30600 1 chr4:7340… "[\"G\… 1.27e-6 ALB pLoF -2.42 -0.980 1.13e- 2 2 chr4:7340… "[\"CA… 5.07e-5 ALB pLoF -2.65 -1.54 1.58e-57 3 chr4:7340… "[\"CA… 6.33e-6 ALB pLoF -2.72 -1.49 1.71e-10 4 chr4:7340… "[\"TG… 1.27e-6 ALB pLoF -2.90 -1.57 2.36e- 3 5 chr4:7340… "[\"C\… 1.27e-6 ALB pLoF -2.56 -0.512 7.36e- 3 6 chr4:7340… "[\"C\… 8.86e-6 ALB pLoF -2.76 -1.31 2.09e-14 # ℹ 1 more variable: Pvalue_30680 [1] "locus" "alleles" "pop_AF" "gene" "annotation" [6] "BETA_30600" "BETA_30680" "Pvalue_30600" "Pvalue_30680" pheno1 pheno2 gene c_hat lambda pvalue n_var 1 Albumin Calcium ALB-pLoF 1.94723 27.37874 0.5512789 30 [1] "locus" "alleles" "pop_AF" "gene" "annotation" [6] "BETA_30600" "BETA_30680" "Pvalue_30600" "Pvalue_30680" pheno1 pheno2 gene c_hat lambda pvalue n_var 1 Albumin Calcium ALB-missense -75.51293 631.1371 0 268 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 6.43 0.50 9.65