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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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(Qploidy) > > test_check("Qploidy") `geom_line()`: Each group consists of only one observation. i Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. i Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. i Do you need to adjust the group aesthetic? `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `geom_smooth()` using formula = 'y ~ s(x, bs = "cs")' Saving 7 x 7 in image `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `geom_smooth()` using formula = 'y ~ s(x, bs = "cs")' Saving 7 x 7 in image `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. Saving 7 x 7 in image File written to: D:\temp\2025_04_25_21_10_16_2377\RtmpOuy25S\file247c05c403fec.txt File written to: D:\temp\2025_04_25_21_10_16_2377\RtmpOuy25S\file247c013643f36.txt Rows: 5000 Columns: 9 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): SNP Name, Sample ID dbl (7): GC Score, Theta, X, Y, X Raw, Y Raw, Log R Ratio 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. Rows: 3000 Columns: 9 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): SNP Name, Sample ID dbl (7): GC Score, Theta, X, Y, X Raw, Y Raw, Log R Ratio 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. Rows: 100 Columns: 51 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (1): probeset_id dbl (50): Sample1, Sample2, Sample3, Sample4, Sample5, Sample6, Sample7, Sam... 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. Rows: 50 Columns: 2 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): Plate_Name, Sample_Name 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. Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Generating standardize BAFs... [1] "Percentage of genotypes turned into missing data because of low genotype probability:0" [1] "Markers remove because of excess of missing data:0" Going to parallel mode... Back to single core usage [1] "Markers remove because of smaller number of clusters than set threshold:0" Going to parallel mode... Back to single core usage BAFs ready! Generating z scores... Z scores ready! Merging results into qploidy_standardization object... Writting Qploidy app input file:D:\temp\2025_04_25_21_10_16_2377\RtmpOuy25S\file247c07c784d80Done! This is on object of class 'ploidy_standardization' -------------------------------------------------------------------- Parameters 1 standardization type: counts 2 Ploidy: 2 3 Minimum number of heterozygous classes (clusters) present: 2 4 Maximum number of missing genotype by marker: 0 5 Minimum genotype probability: 0.5 -------------------------------------------------------------------- Filters 1 Number of markers at raw data: 10 2 Percentage of filtered genotypes by probability threshold: - 3 Number of markers filtered by missing data: 0 4 Number of markers filtered for not having the minimum number of clusters: 0 5 Number of markers filtered for not having genomic information: 0 6 Number of markers with estimated BAF: 10 1 (100%) 2 (0 %) 3 (0 %) 4 (0 %) 5 (0 %) 6 (100 %) Rows: 1 Columns: 6 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): out_filename, type dbl (4): threshold.missing.geno, threshold.geno.prob, ploidy.standardization... 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. Rows: 1 Columns: 6 -- Column specification -------------------------------------------------------- Delimiter: "\t" dbl (6): n.markers.start, geno.prob.rm, miss.rm, clusters.rm, no.geno.info.r... 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. Rows: 50 Columns: 11 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (2): MarkerName, SampleName dbl (9): X, Y, R, ratio, geno, baf, Chr, Position, z 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. This is on object of class 'ploidy_standardization' -------------------------------------------------------------------- Parameters 1 standardization type: counts 2 Ploidy: 2 3 Minimum number of heterozygous classes (clusters) present: 2 4 Maximum number of missing genotype by marker: 0 5 Minimum genotype probability: 0.5 -------------------------------------------------------------------- Filters 1 Number of markers at raw data: 10 2 Percentage of filtered genotypes by probability threshold: - 3 Number of markers filtered by missing data: 0 4 Number of markers filtered for not having the minimum number of clusters: 0 5 Number of markers filtered for not having genomic information: 0 6 Number of markers with estimated BAF: 10 1 (100%) 2 (0 %) 3 (0 %) 4 (0 %) 5 (0 %) 6 (100 %) | *.#,% ||| *******/ ||||||| (**..#**. */ **/ ||||||||| */****************************/*% ||| &****..,*.************************/ ||| (....,,,*,...****%********/(****** ||| ,,****%////,,,,./.****/ ||| /**// .*///.... ||| .*/*/%# .,/ ., ||| , **/ #% .* .. ||| ,,,* Working on it...Loading required package: foreach Loading required package: rngtools done![ FAIL 0 | WARN 0 | SKIP 0 | PASS 69 ] > > proc.time() user system elapsed 13.84 1.57 30.34