R Under development (unstable) (2025-05-11 r88197 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 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. > library(testthat) > library(BIGr) > > test_check("BIGr") No repeated ids found. Ids found as male and female parent: id 1 grandfather2 2 grandfather3 Missing parents found: id sire dam 1 grandmother1 0 0 2 grandfather2 0 0 3 grandfather3 0 0 4 grandfather4 0 0 5 grandmother4 0 0 6 grandfather5 0 0 7 grandmother5 0 0 8 grandfather6 0 0 9 grandmother6 0 0 10 grandfather7 0 0 11 grandmother7 0 0 12 grandfather8 0 0 13 grandmother8 0 0 Dependencies found: Cycle detected involving nodes: off1 -> sire1 Cycle detected involving nodes: sire1 -> off1 Reading input files Converting dosages to genotype format Formatting VCF and generating output file Filtering by DP Filtering by MPP Filtering by OD Filtering by BIAS Filtering by PMC Filtering by SNP missing data Filtering by Sample missing data Filtering by MAF Exporting VCF Ratio of missing data = 0.02174667 The Ref_0001 sequence had to be added for: 0 tags The Alt_0002 sequence had to be added for: 1 tags Tags discarded due to lack of Ref_0001 sequence: 0 tags Tags discarded due to lack of Alt_0002 sequence: 0 tags Number of tags removed because of low alignment score: 0 tags Number of tags removed because of N in the alternative sequence: 0 tags [1] "SNP removed because presented more than one allele: 0" The Ref_0001 sequence had to be added for: 0 tags The Alt_0002 sequence had to be added for: 1 tags Tags discarded due to lack of Ref_0001 sequence: 0 tags Tags discarded due to lack of Alt_0002 sequence: 0 tags Number of tags removed because of low alignment score: 0 tags Number of tags removed because of N in the alternative sequence: 0 tags [1] "SNP removed because presented more than one allele: 1" Scanning file to determine attributes. File attributes: meta lines: 9 header_line: 10 variant count: 33 column count: 19 Meta line 9 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 33 Character matrix gt cols: 19 skip: 0 nrows: 33 row_num: 0 Processed variant: 33 All variants processed Scanning file to determine attributes. File attributes: meta lines: 9 header_line: 10 variant count: 32 column count: 19 Meta line 9 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 32 Character matrix gt cols: 19 skip: 0 nrows: 32 row_num: 0 Processed variant: 32 All variants processed The Ref_0001 sequence had to be added for: 0 tags The Alt_0002 sequence had to be added for: 0 tags Tags discarded due to lack of Ref_0001 sequence: 0 tags Tags discarded due to lack of Alt_0002 sequence: 1 tags Number of tags removed because of low alignment score: 0 tags Number of tags removed because of N in the alternative sequence: 0 tags [1] "SNP removed because presented more than one allele: 0" Scanning file to determine attributes. File attributes: meta lines: 9 header_line: 10 variant count: 28 column count: 19 Meta line 9 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 28 Character matrix gt cols: 19 skip: 0 nrows: 28 row_num: 0 Processed variant: 28 All variants processed Ratio of missing data = 0.1 Ratio of missing data = 0.1 Number of combinations tested: 11175 Number of combinations tested: 45 Number of combinations tested: 450 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 61 ] > > proc.time() user system elapsed 26.26 5.39 102.92