Package: prevR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘intro_prevR.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/prevR.Rcheck/vign_test/prevR/vignettes/intro_prevR_files/figure-html/unnamed-chunk-4-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10971 bytes Input file size = 11841 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9476 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9476 Output IDAT size = 9476 bytes (1495 bytes decrease) Output file size = 9554 bytes (2287 bytes = 19.31% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/prevR.Rcheck/vign_test/prevR/vignettes/intro_prevR_files/figure-html/unnamed-chunk-4-2.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27189 bytes Input file size = 27303 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21891 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21891 Output IDAT size = 21891 bytes (5298 bytes decrease) Output file size = 21969 bytes (5334 bytes = 19.54% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/prevR.Rcheck/vign_test/prevR/vignettes/intro_prevR_files/figure-html/unnamed-chunk-4-3.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28546 bytes Input file size = 28660 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23010 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23010 Output IDAT size = 23010 bytes (5536 bytes decrease) Output file size = 23088 bytes (5572 bytes = 19.44% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/prevR.Rcheck/vign_test/prevR/vignettes/intro_prevR_files/figure-html/unnamed-chunk-4-4.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 31726 bytes Input file size = 31840 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25601 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25601 Output IDAT size = 25601 bytes (6125 bytes decrease) Output file size = 25679 bytes (6161 bytes = 19.35% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/prevR.Rcheck/vign_test/prevR/vignettes/intro_prevR_files/figure-html/unnamed-chunk-5-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 12779 bytes Input file size = 13649 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11188 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11180 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11180 Output IDAT size = 11180 bytes (1599 bytes decrease) Output file size = 11258 bytes (2391 bytes = 17.52% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/prevR.Rcheck/vign_test/prevR/vignettes/intro_prevR_files/figure-html/unnamed-chunk-5-2.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11667 bytes Input file size = 12537 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10478 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10478 Output IDAT size = 10478 bytes (1189 bytes decrease) Output file size = 10556 bytes (1981 bytes = 15.80% decrease) Quitting from lines 96-103 [unnamed-chunk-6] (intro_prevR.Rmd) Error: processing vignette 'intro_prevR.Rmd' failed with diagnostics: arguments imply differing number of rows: 1, 64614, 0 --- failed re-building ‘intro_prevR.Rmd’ SUMMARY: processing the following file failed: ‘intro_prevR.Rmd’ Error: Vignette re-building failed. Execution halted Package: qlcVisualize Check: examples New result: ERROR Running examples in ‘qlcVisualize-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: addContour > ### Title: Add contourlines to a map > ### Aliases: addContour > > ### ** Examples > > data(hessen) > > # continuous variable between 0 and 1 > data <- hessen$data[,1:3] > heights <- round(data[,1]/rowSums(data), digits = 1) > cols <- heat.colors(11) > names(cols) <- names(table(heights)) > > # boundary as sf > w <- sf::st_as_sf(hessen$boundary) > sf::st_crs(w) <- 4326 > w <- sf::st_transform(w, 2397) > > # points as sf > p <- sf::st_as_sf(hessen$villages, coords = c("longitude", "latitude")) > sf::st_crs(p) <- 4326 > p <- sf::st_transform(p, 2397) > > # plot map > plot(p, col = cols[as.character(heights)], border = NA, pch = 19) > plot(w, add = TRUE, border = "grey") > > # add boundary > addContour(heights, points = p, window = w, crs = 2397, grid = 1000, + levels = c(0.25, 0.35, 0.45), col = "blue") Error in if (prod(dim(x))%%length(value) != 0) { : missing value where TRUE/FALSE needed Calls: addContour -> $<- -> $<-.stars -> [[<- -> [[<-.stars Execution halted Package: slendr Check: tests New result: ERROR Running ‘testthat.R’ [33s/35s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(slendr) The 'slim' binary could not be found in your $PATH. Most of the functionality of slendr will work without any issues but you will not be able to simulate data with the `slim()` function. If you want to run SLiM simulations, make sure to modify the $PATH variable so that it points to the directory containing the slim command-line program. One easy way to do this is to add this: PATH="path/to/directory/with/slim/binary" to your ~/.Renviron file. Alternatively, use the `slim_path` argument of the `slim()` function. -------------------- A slendr Python (3.12) environment with the necessary versions of msprime (1.3.1), tskit (0.5.6), pyslim (1.0.4), and tspop (0.0.2) has not been found. You can setup a pre-configured environment with all of slendr's Python dependencies automatically by running the function `setup_env()`. > > test_check("slendr") [ FAIL 1 | WARN 0 | SKIP 32 | PASS 178 ] ══ Skipped tests (32) ══════════════════════════════════════════════════════════ • !is_slendr_env_present() is TRUE (32): 'test-compilation.R:65:1', 'test-engines.R:1:1', 'test-geneflow.R:50:3', 'test-ibd-squashing.R:1:1', 'test-ibd.R:1:1', 'test-interaction-changes.R:49:3', 'test-manual-ts.R:1:1', 'test-msprime-geneflow.R:5:1', 'test-msprime-metadata.R:1:1', 'test-msprime.R:23:1', 'test-nonserialized.R:1:1', 'test-population.R:43:3', 'test-population.R:60:3', 'test-population.R:142:3', 'test-pure-msprime-vs-slendr.R:4:1', 'test-pure-slim-vs-slendr.R:4:1', 'test-resizes-locked.R:1:1', 'test-resizes.R:1:1', 'test-runners.R:1:1', 'test-sampling.R:70:3', 'test-sampling.R:127:3', 'test-sampling.R:228:3', 'test-sampling.R:254:3', 'test-sampling.R:287:3', 'test-simulation-runs.R:1:1', 'test-time-direction.R:1:1', 'test-trees.R:1:1', 'test-ts-ancestors-descendants.R:1:1', 'test-ts-pure-nonspatial.R:1:1', 'test-ts-pure-spatial.R:1:1', 'test-ts.R:1:1', 'test-tspop.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-compilation.R:48:3'): invalid blank maps are prevented ─────── `compile_model(...)` did not throw the expected error. [ FAIL 1 | WARN 0 | SKIP 32 | PASS 178 ] Error: Test failures Execution halted