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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(wingen) > > test_check("wingen") Loading required package: sp Loading required package: vcfR ***** *** vcfR *** ***** This is vcfR 1.15.0 browseVignettes('vcfR') # Documentation citation('vcfR') # Citation ***** ***** ***** ***** Loading required namespace: adegenet Attaching package: 'purrr' The following object is masked from 'package:testthat': is_null terra 1.7.71 Attaching package: 'terra' The following objects are masked from 'package:testthat': compare, describe Simple feature collection with 1 feature and 3 fields Geometry type: POINT Dimension: XY Bounding box: xmin: 85 ymin: -65 xmax: 85 ymax: -65 CRS: NA layer geometry x y 4 0.3231611 POINT (85 -65) 85 -65 [using ordinary kriging] Simple feature collection with 1 feature and 3 fields Geometry type: POINT Dimension: XY Bounding box: xmin: 85 ymin: -65 xmax: 85 ymax: -65 CRS: NA layer geometry x y 4 0.3231611 POINT (85 -65) 85 -65 [using ordinary kriging] Simple feature collection with 1 feature and 3 fields Geometry type: POINT Dimension: XY Bounding box: xmin: 85 ymin: -65 xmax: 85 ymax: -65 Projected CRS: PROJCRS["unknown", BASEGEOGCRS["unknown", DATUM["Unknown based on WGS 84 ellipsoid", ELLIPSOID["WGS 84",6378137,298.257223563, LENGTHUNIT["metre",1], ID["EPSG",7030]]], PRIMEM["Greenwich",0, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8901]]], CONVERSION["unknown", METHOD["Lambert Conic Conformal (2SP)", ID["EPSG",9802]], PARAMETER["Latitude of false origin",0, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8821]], PARAMETER["Longitude of false origin",-100, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8822]], PARAMETER["Latitude of 1st standard parallel",48, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8823]], PARAMETER["Latitude of 2nd standard parallel",33, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8824]], PARAMETER["Easting at false origin",0, LENGTHUNIT["metre",1], ID["EPSG",8826]], PARAMETER["Northing at false origin",0, LENGTHUNIT["metre",1], ID["EPSG",8827]]], CS[Cartesian,2], AXIS["(E)",east, ORDER[1], LENGTHUNIT["metre",1, ID["EPSG",9001]]], AXIS["(N)",north, ORDER[2], LENGTHUNIT["metre",1, ID["EPSG",9001]]]] layer geometry x y 4 0.3231611 POINT (85 -65) 85 -65 [using ordinary kriging] Simple feature collection with 1 feature and 3 fields Geometry type: POINT Dimension: XY Bounding box: xmin: 85 ymin: -65 xmax: 85 ymax: -65 Projected CRS: PROJCRS["unknown", BASEGEOGCRS["unknown", DATUM["Unknown based on WGS 84 ellipsoid", ELLIPSOID["WGS 84",6378137,298.257223563, LENGTHUNIT["metre",1], ID["EPSG",7030]]], PRIMEM["Greenwich",0, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8901]]], CONVERSION["unknown", METHOD["Lambert Conic Conformal (2SP)", ID["EPSG",9802]], PARAMETER["Latitude of false origin",0, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8821]], PARAMETER["Longitude of false origin",-100, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8822]], PARAMETER["Latitude of 1st standard parallel",48, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8823]], PARAMETER["Latitude of 2nd standard parallel",33, ANGLEUNIT["degree",0.0174532925199433], ID["EPSG",8824]], PARAMETER["Easting at false origin",0, LENGTHUNIT["metre",1], ID["EPSG",8826]], PARAMETER["Northing at false origin",0, LENGTHUNIT["metre",1], ID["EPSG",8827]]], CS[Cartesian,2], AXIS["(E)",east, ORDER[1], LENGTHUNIT["metre",1, ID["EPSG",9001]]], AXIS["(N)",north, ORDER[2], LENGTHUNIT["metre",1, ID["EPSG",9001]]]] layer geometry x y 4 0.3231611 POINT (85 -65) 85 -65 [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE Scanning file to determine attributes. File attributes: meta lines: 3 header_line: 4 variant count: 10 column count: 19 Meta line 3 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 10 Character matrix gt cols: 19 skip: 0 nrows: 10 row_num: 0 Processed variant: 10 All variants processed Scanning file to determine attributes. File attributes: meta lines: 3 header_line: 4 variant count: 10 column count: 19 Meta line 3 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 10 Character matrix gt cols: 19 skip: 0 nrows: 10 row_num: 0 Processed variant: 10 All variants processed [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] Simple feature collection with 1 feature and 3 fields Geometry type: POINT Dimension: XY Bounding box: xmin: 85 ymin: -65 xmax: 85 ymax: -65 CRS: NA layer geometry x y 4 0.3231611 POINT (85 -65) 85 -65 [using ordinary kriging] Simple feature collection with 1 feature and 3 fields Geometry type: POINT Dimension: XY Bounding box: xmin: 85 ymin: -65 xmax: 85 ymax: -65 CRS: NA layer geometry x y 4 0.3231611 POINT (85 -65) 85 -65 [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] [using ordinary kriging] -------------- middle earth example -------------- Objects loaded: *lotr_vcf* vcfR object (100 variants x 100 samples) *lotr_coords* dataframe with x and y coordinates *lotr_lyr* middle earth RasterLayer (100 x 100) *lotr_range* SpatialPolygonsDataFrame of spp range -------------------------------------------------- ---------- mini middle earth example ---------- Objects loaded: *mini_vcf* vcfR object (10 variants x 10 samples) and no missing data *mini_vcf_NA* vcfR object (10 variants x 10 samples) and missing data *mini_coords* dataframe with x and y coordinates *mini_lyr* middle earth RasterLayer (10 x 10) -----------------------------------------------Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:terra': blocks, compare, union The following objects are masked from 'package:purrr': compose, simplify The following object is masked from 'package:raster': union The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: Matrix Attaching package: 'gdistance' The following object is masked from 'package:igraph': normalize Progress: ───────────────────────────────── 100% Progress: ────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: ────────────────────────────────────────────────── 100% Progress: ───────────────────────────────────────────────────── 100% Progress: ───────────────────────────────────── 100% Progress: ───────────────────────────────────── 100% Progress: ──────────────────────────────────────────── 100% Progress: ────────────────────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────────── 100% Progress: ───────────────── 100% Progress: ───────────────────── 100% Progress: ─────────────────────────── 100% Progress: ───────────────────────────────── 100% Progress: ───────────────────────────────────── 100% Progress: ─────────────────────────────────────────── 100% Progress: ─────────────────────────────────────────────────── 100% Progress: ───────────────────────────────── 100% Progress: ──────────────────────────────────────────────── 100% Progress: ──────────────────────────────────────────────────────────────── 100% Progress: ────────────────────────────────────────────────── 100% ---------- mini middle earth example ---------- Objects loaded: *mini_vcf* vcfR object (10 variants x 10 samples) and no missing data *mini_vcf_NA* vcfR object (10 variants x 10 samples) and missing data *mini_coords* dataframe with x and y coordinates *mini_lyr* middle earth RasterLayer (10 x 10) ----------------------------------------------- ---------- mini middle earth example ---------- Objects loaded: *mini_vcf* vcfR object (10 variants x 10 samples) and no missing data *mini_vcf_NA* vcfR object (10 variants x 10 samples) and missing data *mini_coords* dataframe with x and y coordinates *mini_lyr* middle earth RasterLayer (10 x 10) ----------------------------------------------- ---------- mini middle earth example ---------- Objects loaded: *mini_vcf* vcfR object (10 variants x 10 samples) and no missing data *mini_vcf_NA* vcfR object (10 variants x 10 samples) and missing data *mini_coords* dataframe with x and y coordinates *mini_lyr* middle earth RasterLayer (10 x 10) ----------------------------------------------- ---------- mini middle earth example ---------- Objects loaded: *mini_vcf* vcfR object (10 variants x 10 samples) and no missing data *mini_vcf_NA* vcfR object (10 variants x 10 samples) and missing data *mini_coords* dataframe with x and y coordinates *mini_lyr* middle earth RasterLayer (10 x 10) ----------------------------------------------- Scanning file to determine attributes. File attributes: meta lines: 3 header_line: 4 variant count: 10 column count: 19 Meta line 3 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 10 Character matrix gt cols: 19 skip: 0 nrows: 10 row_num: 0 Processed variant: 10 All variants processed [ FAIL 0 | WARN 0 | SKIP 0 | PASS 240 ] > > proc.time() user system elapsed 92.15 3.89 127.34