Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 828/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicPlot 1.4.0 (landing page) Shuye Pu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GenomicPlot package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicPlot.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GenomicPlot |
Version: 1.4.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicPlot.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomicPlot_1.4.0.tar.gz |
StartedAt: 2024-12-20 01:54:59 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:34:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 2350.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicPlot.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicPlot.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomicPlot_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GenomicPlot.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GenomicPlot/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GenomicPlot' version '1.4.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'GenomicPlot' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE get_targeted_genes: no visible binding for global variable '5'UTR' get_targeted_genes: no visible binding for global variable '3'UTR' handle_bam: no visible global function definition for 'seqlevelsStyle' handle_bam: no visible global function definition for 'seqlevelsStyle<-' handle_bed: no visible global function definition for 'seqlevelsStyle' handle_bed: no visible global function definition for 'seqlevelsStyle<-' handle_bedGraph: no visible global function definition for 'seqlevelsStyle' handle_bedGraph: no visible global function definition for 'seqlevelsStyle<-' handle_bw: no visible global function definition for 'seqlevelsStyle' handle_bw: no visible global function definition for 'seqlevelsStyle<-' plot_bam_correlation: no visible binding for global variable '.' plot_peak_annotation: no visible binding for global variable '.' Undefined global functions or variables: . 3'UTR 5'UTR seqlevelsStyle seqlevelsStyle<- * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_start_end_with_random 17.33 0.61 216.83 plot_start_end 12.72 0.27 109.78 plot_locus 10.65 0.27 82.30 plot_5parts_metagene 10.14 0.53 174.48 plot_peak_annotation 9.90 0.14 10.08 get_targeted_genes 8.25 0.16 8.41 get_txdb_features 7.73 0.12 7.86 plot_region 6.80 0.19 107.12 plot_locus_with_random 6.82 0.14 75.28 prepare_5parts_genomic_features 6.77 0.11 6.89 plot_bam_correlation 1.05 0.11 22.63 effective_size 0.73 0.01 22.34 parallel_countOverlaps 0.41 0.08 22.98 parallel_scoreMatrixBin 0.42 0.03 17.08 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test-plotFunctions.R' Running 'test-shortFunctions.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/GenomicPlot.Rcheck/00check.log' for details.
GenomicPlot.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GenomicPlot ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GenomicPlot' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' ** testing if installed package keeps a record of temporary installation path * DONE (GenomicPlot)
GenomicPlot.Rcheck/tests/test-plotFunctions.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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. > library(GenomicPlot) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Warning message: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' > library(testthat) > > Sys.setenv("R_TESTS" = "") > > data(gf5_meta) > data(gf5_genomic) > > gtffile <- system.file("extdata", "gencode.v19.annotation_chr19.gtf", + package = "GenomicPlot") > txdb <- custom_TxDb_from_GTF(gtffile, genome = "hg19") [custom_TxDb_from_GTF] [set_seqinfo] Reading existing granges.rds object from F:/biocbuild/bbs-3.20-bioc/R/library/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds Keeping standard chromosomes only File F:/biocbuild/bbs-3.20-bioc/R/library/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds already exists. Use overwriteObjectAsRds = TRUE to overwrite the file Warning message: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. > > bedQueryFiles <- c( + system.file("extdata", "test_chip_peak_chr19.narrowPeak", + package = "GenomicPlot"), + system.file("extdata", "test_chip_peak_chr19.bed", package = "GenomicPlot"), + system.file("extdata", "test_clip_peak_chr19.bed", package = "GenomicPlot") + ) > names(bedQueryFiles) <- c("NarrowPeak", "SummitPeak", "iCLIPPeak") > > bedImportParams <- setImportParams( + offset = 0, fix_width = 100, fix_point = "center", norm = FALSE, + useScore = FALSE, outRle = TRUE, useSizeFactor = FALSE, genome = "hg19" + ) > > bamQueryFiles <- system.file("extdata", "treat_chr19.bam", + package = "GenomicPlot") > names(bamQueryFiles) <- "clip_bam" > bamInputFiles <- system.file("extdata", "input_chr19.bam", + package = "GenomicPlot") > names(bamInputFiles) <- "clip_input" > > bamImportParams <- setImportParams( + offset = -1, fix_width = 0, fix_point = "start", norm = TRUE, + useScore = FALSE, outRle = TRUE, useSizeFactor = FALSE, genome = "hg19" + ) > > chipQueryFiles <- system.file("extdata", "chip_treat_chr19.bam", + package = "GenomicPlot") > names(chipQueryFiles) <- "chip_bam" > chipInputFiles <- system.file("extdata", "chip_input_chr19.bam", + package = "GenomicPlot") > names(chipInputFiles) <- "chip_input" > > chipImportParams <- setImportParams( + offset = 0, fix_width = 150, fix_point = "start", norm = TRUE, + useScore = FALSE, outRle = TRUE, useSizeFactor = FALSE, genome = "hg19" + ) > > > test_that("testing parallel_countOverlaps", { + importParams <- setImportParams(fix_width = 100, outRle = FALSE) + out_list <- handle_input( + inputFiles = bedQueryFiles, + importParams = importParams, verbose = FALSE, nc = 2 + ) + + chromInfo <- circlize::read.chromInfo(species = "hg19")$df + seqi <- Seqinfo(seqnames = chromInfo$chr, seqlengths = chromInfo$end, + isCircular = rep(FALSE, nrow(chromInfo)), + genome = "hg19") + grange_list <- lapply(out_list, function(x) x$query) + tilewidth <- 100000 + tileBins <- tileGenome(seqi, tilewidth = tilewidth, + cut.last.tile.in.chrom = TRUE) + + score_list1 <- parallel_countOverlaps(grange_list, tileBins, nc = 2) + }) ── Skip: testing parallel_countOverlaps ──────────────────────────────────────── Reason: empty test > > test_that("testing parallel_scoreMatrixBin", { + + queryRegion <- handle_input(chipQueryFiles, chipImportParams, + verbose = TRUE)[[1]]$query + + importParams <- setImportParams(outRle = FALSE) + + windowRegion <- handle_bed(bedQueryFiles[1], importParams, verbose = TRUE)$query + + out <- parallel_scoreMatrixBin( + queryRegions = queryRegion, + windowRs = windowRegion, + bin_num = 50, + bin_op = "mean", + weight_col = "score", + stranded = TRUE, + nc = 2 + ) + }) ── Skip: testing parallel_scoreMatrixBin ─────────────────────────────────────── Reason: empty test > > test_that("testing handle_bed", { + out <- handle_bed(bedQueryFiles[1], bedImportParams, verbose = TRUE) + }) ── Skip: testing handle_bed ──────────────────────────────────────────────────── Reason: empty test > > test_that("testing effective_size", { + importParams <- setImportParams(outRle = FALSE) + out_list <- handle_input( + inputFiles = c(chipQueryFiles, chipInputFiles), + importParams = importParams, verbose = TRUE, nc = 2 + ) + + out <- effective_size(out_list, outRle = TRUE) + }) ── Skip: testing effective_size ──────────────────────────────────────────────── Reason: empty test > > test_that("testing handle_input", { + + queryFiles2 <- system.file("extdata", "test_wig_chr19_+.wig", + package = "GenomicPlot") + names(queryFiles2) <- "test_wig" + + queryFiles3 <- system.file("extdata", "test_wig_chr19_+.bw", + package = "GenomicPlot") + names(queryFiles3) <- "test_bw" + + importParams <- setImportParams() + + out <- handle_input(c(bamQueryFiles, queryFiles2, queryFiles3), + importParams, verbose = TRUE) + }) ── Skip: testing handle_input ────────────────────────────────────────────────── Reason: empty test > > test_that("testing plot_bam_correlation", { + + importParams <- setImportParams(fix_width = 150, outRle = FALSE) + + plot_bam_correlation( + bamFiles = c(chipQueryFiles, chipInputFiles), binSize = 100000, + outPrefix = NULL, importParams = importParams, nc = 2, verbose = FALSE + ) + }) ── Skip: testing plot_bam_correlation ────────────────────────────────────────── Reason: empty test > > test_that("testing plot_overlap_bed", { + importParams <- setImportParams(fix_width = 100, outRle = FALSE) + plot_overlap_bed( + bedList = bedQueryFiles, importParams = importParams, pairOnly = FALSE, + stranded = FALSE, outPrefix = NULL + ) + }) ── Skip: testing plot_overlap_bed ────────────────────────────────────────────── Reason: empty test > > test_that("testing plot_argument_list", { + + alist <- list( + "txdb" = txdb, "treat" = bamQueryFiles, "control" = bamInputFiles, + "feature" = gf5_meta, "param" = bamImportParams + ) + + p <- GenomicPlot:::plot_named_list(alist) + }) ── Skip: testing plot_argument_list ──────────────────────────────────────────── Reason: empty test > > > test_that("testing plot_peak_annotation", { + plot_peak_annotation( + peakFile = bedQueryFiles[2], gtfFile = gtffile, importParams = bedImportParams, + fiveP = -2000, dsTSS = 200, threeP = 2000, simple = FALSE + ) + }) ── Warning: testing plot_peak_annotation ─────────────────────────────────────── The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. Backtrace: ▆ 1. └─GenomicPlot::plot_peak_annotation(...) 2. └─txdbmaker::makeTxDbFromGRanges(gff) 3. └─txdbmaker:::.get_cds_IDX(mcols0$type, mcols0$phase) ── Skip: testing plot_peak_annotation ────────────────────────────────────────── Reason: empty test > > > test_that("testing plot_overlap_genes", { + testfile1 <- system.file("extdata", "test_file1.txt", + package = "GenomicPlot") + testfile2 <- system.file("extdata", "test_file2.txt", + package = "GenomicPlot") + testfile3 <- system.file("extdata", "test_file3.txt", + package = "GenomicPlot") + testfile4 <- system.file("extdata", "test_file4.txt", + package = "GenomicPlot") + testfiles <- c(testfile1, testfile2, testfile3, testfile4) + names(testfiles) <- c("test1", "test2", "test3", "test4") + + plot_overlap_genes(testfiles, c(3,2,1,1), pairOnly = FALSE) + }) ── Skip: testing plot_overlap_genes ──────────────────────────────────────────── Reason: empty test > > test_that("testing plot_5parts_metagene", { + plot_5parts_metagene( + queryFiles = bedQueryFiles, + gFeatures_list = list("metagene" = gf5_meta), + inputFiles = NULL, + importParams = bedImportParams, + verbose = FALSE, + smooth = TRUE, + scale = FALSE, + stranded = TRUE, + outPrefix = NULL, + transform = NA, + heatmap = TRUE, + rmOutlier = 0, + heatRange = NULL, + nc = 2 + ) + }) ── Skip: testing plot_5parts_metagene ────────────────────────────────────────── Reason: empty test > > test_that("testing plot_locus", { + plot_locus( + queryFiles = bedQueryFiles[c(1,3)], + centerFiles = bedQueryFiles[2], + ext = c(-500, 500), + hl = c(-100, 100), + inputFiles = NULL, + importParams = bedImportParams, + shade = TRUE, + binSize = 10, + refPoint = "center", + Xlab = "Summit", + verbose = FALSE, + smooth = TRUE, + scale = FALSE, + stranded = TRUE, + outPrefix = NULL, + transform = NA, + heatmap = TRUE, + heatRange = NULL, + rmOutlier = 0, + Ylab = "Coverage/base/peak", + nc = 2 + ) + + plot_locus( + queryFiles = chipQueryFiles, + centerFiles = bedQueryFiles[2], + ext = c(-500, 500), + hl = c(-100, 100), + inputFiles = chipInputFiles, + importParams = chipImportParams, + shade = TRUE, + binSize = 10, + refPoint = "center", + Xlab = "Summit", + verbose = FALSE, + smooth = TRUE, + scale = FALSE, + stranded = TRUE, + outPrefix = NULL, + transform = NA, + heatmap = TRUE, + heatRange = NULL, + rmOutlier = 0, + Ylab = "Coverage/base/peak", + nc = 2 + ) + }) ── Skip: testing plot_locus ──────────────────────────────────────────────────── Reason: empty test > > test_that("testing plot_region", { + plot_region( + queryFiles = chipQueryFiles, + centerFiles = bedQueryFiles[1], + inputFiles = chipInputFiles, + nbins = 100, + heatmap = TRUE, + scale = FALSE, + regionName = "narrowPeak", + importParams = chipImportParams, + verbose = FALSE, + fiveP = -200, + threeP = 200, + smooth = TRUE, + transform = "log2", + stranded = TRUE, + Ylab = "Coverage/base/peak", + outPrefix = NULL, + rmOutlier = 0, + nc = 2 + ) + }) ── Skip: testing plot_region ─────────────────────────────────────────────────── Reason: empty test > > test_that("testing plot_start_end", { + plot_start_end( + queryFiles = bamQueryFiles, + inputFiles = bamInputFiles, + txdb = txdb, + centerFiles = "intron", + binSize = 10, + importParams = bamImportParams, + ext = c(-100, 100, -100, 100), + hl = c(-50, 50, -50, 50), + insert = 100, + stranded = TRUE, + scale = FALSE, + smooth = TRUE, + transform = "log2", + outPrefix = NULL, + nc = 2 + ) + }) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 1 row containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 1 row containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end ───────────────────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Skip: testing plot_start_end ──────────────────────────────────────────────── Reason: empty test > > test_that("testing plot_start_end_with_random", { + + plot_start_end_with_random( + queryFiles = bamQueryFiles, + inputFiles = bamInputFiles, + txdb = txdb, + centerFile = "intron", + binSize = 10, + importParams = bamImportParams, + ext = c(-100, 100, -100, 100), + hl = c(-20, 20, -20, 20), + insert = 100, + stranded = TRUE, + scale = FALSE, + smooth = TRUE, + transform = "log2", + outPrefix = NULL, + randomize = TRUE, + nc = 2 + ) + }) ── Warning: testing plot_start_end_with_random ───────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end_with_random(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end_with_random ───────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end_with_random(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end_with_random ───────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end_with_random(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end_with_random ───────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end_with_random(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end_with_random ───────────────────────────────── Removed 1 row containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end_with_random(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end_with_random ───────────────────────────────── Removed 3 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end_with_random(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Warning: testing plot_start_end_with_random ───────────────────────────────── Removed 2 rows containing missing values or values outside the scale range (`geom_line()`). Backtrace: ▆ 1. └─GenomicPlot::plot_start_end_with_random(...) 2. └─GenomicPlot::draw_stacked_profile(...) 3. └─cowplot::plot_grid(...) 4. └─cowplot::align_plots(...) 5. └─base::lapply(...) 6. └─cowplot (local) FUN(X[[i]], ...) 7. ├─cowplot::as_gtable(x) 8. └─cowplot:::as_gtable.default(x) 9. ├─cowplot::as_grob(plot) 10. └─cowplot:::as_grob.ggplot(plot) 11. └─ggplot2::ggplotGrob(plot) 12. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 13. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 14. └─ggplot2:::by_layer(...) 15. ├─rlang::try_fetch(...) 16. │ ├─base::tryCatch(...) 17. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ └─base::withCallingHandlers(...) 21. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 22. └─l$draw_geom(d, layout) 23. └─ggplot2 (local) draw_geom(..., self = self) 24. └─self$geom$handle_na(data, self$computed_geom_params) 25. └─ggplot2 (local) handle_na(..., self = self) 26. └─cli::cli_warn(...) ── Skip: testing plot_start_end_with_random ──────────────────────────────────── Reason: empty test > > test_that("testing plot_locus_with_random", { + plot_locus_with_random( + queryFiles = bamQueryFiles, + centerFiles = bedQueryFiles[3], + txdb = txdb, + ext = c(-200, 200), + hl = c(-100, 100), + shade = FALSE, + importParams = bamImportParams, + verbose = FALSE, + smooth = FALSE, + transform = NA, + binSize = 10, + refPoint = "center", + Xlab = "Center", + Ylab = "Coverage/base/peak", + inputFiles = bamInputFiles, + stranded = TRUE, + scale = FALSE, + outPrefix = NULL, + rmOutlier = 0, + n_random = 1, + hw = c(8, 8), + detailed = FALSE, + statsMethod = "wilcox.test", + nc = 2) + }) ── Skip: testing plot_locus_with_random ──────────────────────────────────────── Reason: empty test > > proc.time() user system elapsed 97.87 5.06 1011.81
GenomicPlot.Rcheck/tests/test-shortFunctions.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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. > library(GenomicPlot) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Warning message: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' > library(testthat) > > Sys.setenv("R_TESTS" = "") > > test_that("testing start and stop of cluster", { + cl <- start_parallel(2L) + stop_parallel(cl) + }) ── Skip: testing start and stop of cluster ───────────────────────────────────── Reason: empty test > > test_that("testing inspect_matrix", { + fullMatrix <- matrix(rnorm(100), ncol = 10) + for (i in 5:6) { + fullMatrix[i, 4:7] <- NaN + fullMatrix[i+1, 4:7] <- NA + fullMatrix[i+2, 4:7] <- -Inf + fullMatrix[i-1, 4:7] <- 0 + fullMatrix[i-2, 1:3] <- Inf + } + + GenomicPlot:::inspect_matrix(fullMatrix, verbose = TRUE) + }) n_invalid fraction_invalid infinite 10 0.10 NA 8 0.08 NaN 4 0.04 zero 8 0.08 negative 36 0.36 ── Skip: testing inspect_matrix ──────────────────────────────────────────────── Reason: empty test > > test_that("testing impute_hm", { + fullMatrix <- matrix(rlnorm(100), ncol = 10) + for (i in 5:6) { + fullMatrix[i-1, 4:7] <- 0 + } + + imp <- GenomicPlot:::impute_hm(fullMatrix, verbose = TRUE) + }) ── Skip: testing impute_hm ───────────────────────────────────────────────────── Reason: empty test > > test_that("testing ratio_over_input", { + IP <- matrix(rlnorm(100), ncol = 10) + Input <- matrix(runif(100), ncol = 10) + + ratio <- GenomicPlot:::ratio_over_input(IP, Input, verbose = TRUE) + }) ── Skip: testing ratio_over_input ────────────────────────────────────────────── Reason: empty test > > test_that("testing gr2df", { + gr2 <- GenomicRanges::GRanges(c("chr1", "chr1"), IRanges::IRanges(c(7, 13), + width = 3), + strand = c("+", "-") + ) + GenomicRanges::mcols(gr2) <- data.frame(score = c(0.3, 0.9), + cat = c(TRUE, FALSE)) + df2 <- gr2df(gr2) + }) ── Skip: testing gr2df ───────────────────────────────────────────────────────── Reason: empty test > > test_that("testing aov_TukeyHSD", { + stat_df <- data.frame( + Feature = rep(c("A", "B"), c(20, 30)), + Intensity = c(rnorm(20, 2), rnorm(30, 3)) + ) + + out <- aov_TukeyHSD(stat_df, xc="Feature") + }) ── Skip: testing aov_TukeyHSD ────────────────────────────────────────────────── Reason: empty test > > test_that("testing rm_outlier", { + fullmatrix <- matrix(rnorm(100), ncol = 10) + maxm <- max(fullmatrix) + fullmatrix[3, 9] <- maxm + 1000 + fullmatrix[8, 1] <- maxm + 500 + rm_outlier(fullmatrix, verbose = TRUE, multiplier = 100) + rm_outlier(fullmatrix, verbose = TRUE, multiplier = 1000) + }) ── Skip: testing rm_outlier ──────────────────────────────────────────────────── Reason: empty test > > test_that("testing process_scoreMatrix", { + fullMatrix <- matrix(rlnorm(100), ncol = 10) + for (i in 5:6) { + fullMatrix[i, 4:7] <- NaN + fullMatrix[i+1, 4:7] <- NA + fullMatrix[i+2, 4:7] <- -Inf + fullMatrix[i-1, 4:7] <- 0 + fullMatrix[i-2, 1:3] <- Inf + } + fullMatrix[9, 4:7] <- runif(4) + 90 + + wo <- process_scoreMatrix(fullMatrix, rmOutlier = 3, verbose = TRUE) + tf <- process_scoreMatrix(fullMatrix, + rmOutlier = 0, transform = "log2", verbose = TRUE + ) + scaled <- process_scoreMatrix(fullMatrix, scale = TRUE, verbose = TRUE) + }) n_invalid fraction_invalid infinite 10 0.10 NA 8 0.08 NaN 4 0.04 zero 8 0.08 negative 4 0.04 n_invalid fraction_invalid infinite 10 0.10 NA 8 0.08 NaN 4 0.04 zero 8 0.08 negative 4 0.04 n_invalid fraction_invalid infinite 10 0.10 NA 8 0.08 NaN 4 0.04 zero 8 0.08 negative 4 0.04 ── Skip: testing process_scoreMatrix ─────────────────────────────────────────── Reason: empty test > > test_that("testing rank_rows", { + fullMatrix <- matrix(rnorm(100), ncol = 10) + for (i in 5:8) { + fullMatrix[i, 4:7] <- runif(4) + i + } + apply(fullMatrix, 1, sum) + ranked <- rank_rows(fullMatrix, ranking = "Sum") + }) ── Skip: testing rank_rows ───────────────────────────────────────────────────── Reason: empty test > > test_that("testing overlap_quad", { + test_list <- list(A = c(1, 2, 3, 4, 5), B = c(4, 5, 7), C = c(1, 3), D = 6) + overlap_quad(test_list, intersect) + + ## GRanges overlap + query1 <- GRanges("chr19", + IRanges(rep(c(10, 15), 2), width=c(1, 20, 40, 50)), + strand=c("+", "+", "-", "-") + ) + + query2 <- GRanges("chr19", + IRanges(rep(c(1, 15), 2), width=c(1, 20, 40, 50)), + strand=c("+", "+", "-", "-") + ) + + subject1 <- GRanges("chr19", + IRanges(rep(c(13, 150), 2), width=c(10, 14, 20, 28)), + strand=c("+", "-", "-", "+") + ) + + subject2 <- GRanges("chr19", + IRanges(rep(c(13, 50), 2), width=c(10, 14, 20, 21)), + strand=c("+", "-", "-", "+") + ) + + p <- overlap_quad(list(subject1 = subject1, subject2 = subject2, + query1 = query1, + query2 = query2), filter_by_overlaps_stranded + ) + }) ── Skip: testing overlap_quad ────────────────────────────────────────────────── Reason: empty test > > test_that("testing overlap_triple", { + test_list <- list(A = c(1, 2, 3, 4, 5), B = c(4, 5, 7), C = c(1, 3)) + overlap_triple(test_list, intersect) + + ## GRanges overlap + query <- GRanges("chr19", + IRanges(rep(c(10, 15), 2), width=c(1, 20, 40, 50)), + strand=c("+", "+", "-", "-") + ) + + subject1 <- GRanges("chr19", + IRanges(rep(c(13, 150), 2), width=c(10, 14, 20, 28)), + strand=c("+", "-", "-", "+") + ) + + subject2 <- GRanges("chr19", + IRanges(rep(c(13, 50), 2), width=c(10, 14, 20, 21)), + strand=c("+", "-", "-", "+") + ) + + p <- overlap_triple(list(subject1 = subject1, subject2 = subject2, + query = query), filter_by_overlaps_stranded) + }) ── Skip: testing overlap_triple ──────────────────────────────────────────────── Reason: empty test > > test_that("testing overlap_pair", { + test_list <- list(A = c(1, 2, 3, 4, 5), B = c(4, 5, 7)) + overlap_pair(test_list, intersect) + + ## GRanges overlap + query <- GRanges("chr19", + IRanges(rep(c(10, 15), 2), width=c(1, 20, 40, 50)), + strand=c("+", "+", "-", "-") + ) + + subject <- GRanges("chr19", + IRanges(rep(c(13, 150), 2), width=c(10, 14, 20, 28)), + strand=c("+", "-", "-", "+") + ) + + p <- overlap_pair(list(query = query, subject = subject), + filter_by_overlaps_stranded) + }) ── Skip: testing overlap_pair ────────────────────────────────────────────────── Reason: empty test > > test_that("testing draw_combo_plot", { + stat_df <- data.frame( + Feature = rep(c("A", "B"), c(200, 300)), + Intensity = c(rnorm(200, 2, 5), rnorm(300, 3, 5)), + Height = c(rnorm(200, 5, 5), rnorm(300, 1, 5)) + ) + stat_df_long <- tidyr::pivot_longer(stat_df, + cols = c(Intensity, Height), + names_to = "type", values_to = "value" + ) + + p <- draw_combo_plot(stat_df_long, + xc = "Feature", yc = "value", fc = "type", + Ylab = "value", comp = list(c(1, 2), c(3, 4), c(1, 3), c(2, 4)), nf = 2 + ) + }) ── Skip: testing draw_combo_plot ─────────────────────────────────────────────── Reason: empty test > > test_that("testing draw_rank_plot", { + stat_df <- data.frame( + Feature = rep(c("A", "B"), c(20, 30)), + Intensity = c(rlnorm(20, 5, 5), rlnorm(30, 1, 5)) + ) + stat_df1 <- data.frame( + Feature = rep(c("A", "B"), c(20, 30)), + Height = c(rnorm(20, 5, 5), rnorm(30, 1, 5)) + ) + + p1 <- draw_rank_plot(stat_df, xc = "Feature", yc = "Intensity", + Ylab = "Intensity") + p2 <- draw_rank_plot(stat_df1, xc = "Feature", yc = "Height", + Ylab = "Height") + }) ── Skip: testing draw_rank_plot ──────────────────────────────────────────────── Reason: empty test > > test_that("testing draw_quantile_plot", { + stat_df <- data.frame( + Feature = rep(c("A", "B"), c(20, 30)), + Intensity = c(rnorm(20, 2, 5), rnorm(30, 3, 5)), + Height = c(rnorm(20, 5, 5), rnorm(30, 1, 5)) + ) + stat_df_long <- tidyr::pivot_longer(stat_df, + cols = c(Intensity, Height), names_to = "type", + values_to = "value" + ) + + p1 <- draw_quantile_plot(stat_df, xc = "Feature", yc = "Intensity") + p2 <- draw_quantile_plot(stat_df, xc = "Feature", yc = "Height") + p3 <- draw_quantile_plot(stat_df_long, xc = "Feature", yc = "value", + fc = "type", Ylab = "value") + }) ── Skip: testing draw_quantile_plot ──────────────────────────────────────────── Reason: empty test > > test_that("testing draw_mean_se_barplot", { + stat_df <- data.frame( + Feature = rep(c("A", "B"), c(20, 30)), + Intensity = c(rnorm(20, 2), rnorm(30, 3)) + ) + p <- draw_mean_se_barplot(stat_df, xc = "Feature", yc = "Intensity", + Ylab = "Intensity") + }) ── Skip: testing draw_mean_se_barplot ────────────────────────────────────────── Reason: empty test > > test_that("testing draw_boxplot_wo_outlier", { + stat_df <- data.frame(Feature = rep(c("A", "B"), c(20, 30)), + Intensity = c(rnorm(20, 2), rnorm(30, 3))) + p <- draw_boxplot_wo_outlier(stat_df, + xc = "Feature", yc = "Intensity", + Ylab = "Signal Intensity" + ) + }) ── Skip: testing draw_boxplot_wo_outlier ─────────────────────────────────────── Reason: empty test > > test_that("testing draw_boxplot_by_factor", { + stat_df <- data.frame( + Feature = rep(c("A", "B"), c(20, 30)), + Intensity = c(rnorm(20, 2, 0.5), rnorm(30, 3, 0.6)) + ) + p <- draw_boxplot_by_factor(stat_df, + xc = "Feature", yc = "Intensity", + Ylab = "Signal Intensity" + ) + + }) ── Skip: testing draw_boxplot_by_factor ──────────────────────────────────────── Reason: empty test > > test_that("testing draw_locus_profile", { + library(dplyr) + Reference <- rep(rep(c("Ref1", "Ref2"), each = 100), 2) + Query <- rep(c("Query1", "Query2"), each = 200) + Position <- rep(seq(-50, 49), 4) + Intensity <- rlnorm(400) + se <- runif(400) + df <- data.frame(Intensity, se, Position, Query, Reference) %>% + mutate(lower = Intensity - se, upper = Intensity + se) %>% + mutate(Group = paste(Query, Reference, sep = ":")) + + p <- draw_locus_profile(df, cn = "Group", shade = TRUE, hl = c(-10, 20)) + }) ── Skip: testing draw_locus_profile ──────────────────────────────────────────── Reason: empty test > > test_that("testing draw_region_profile", { + library(dplyr) + Reference <- rep(rep(c("Ref1", "Ref2"), each = 100), 2) + Query <- rep(c("Query1", "Query2"), each = 200) + Position <- rep(seq_len(100), 4) + Intensity <- rlnorm(400) + se <- runif(400) + df <- data.frame(Intensity, se, Position, Query, Reference) %>% + mutate(lower = Intensity - se, upper = Intensity + se) %>% + mutate(Group = paste(Query, Reference, sep = ":")) + vx <- c(1, 23, 70) + + p <- draw_region_profile(df, cn = "Group", vx = vx) + }) ── Skip: testing draw_region_profile ─────────────────────────────────────────── Reason: empty test > > test_that("testing draw_region_name", { + fn <- c("5'UTR", "CDS", "3'UTR") + bins <- c(5, 15, 5) + xmax <- 25 + + p <- draw_region_name(featureNames = fn, scaled_bins = bins, xmax = xmax) + }) ── Skip: testing draw_region_name ────────────────────────────────────────────── Reason: empty test > > test_that("testing draw_region_landmark", { + fn <- c("5'UTR", "CDS", "3'UTR") + mark <- c(1, 5, 20) + xmax <- 25 + + p <- draw_region_landmark(featureNames = fn, vx = mark, xmax = xmax) + }) ── Skip: testing draw_region_landmark ────────────────────────────────────────── Reason: empty test > > test_that("testing draw_matrix_heatmap", { + fullMatrix <- matrix(rnorm(10000), ncol = 100) + for (i in seq_len(80)) { + fullMatrix[i, 16:75] <- runif(60) + i + } + labels_col <- as.character(seq_len(100)) + levels_col <- c("start", "center", "end") + names(labels_col) <- rep(levels_col, c(15, 60, 25)) + + p <- draw_matrix_heatmap(fullMatrix, dataName = "test", labels_col, + levels_col) + }) ── Skip: testing draw_matrix_heatmap ─────────────────────────────────────────── Reason: empty test > > test_that("testing draw_stacked_profile", { + Reference <- rep(rep(c("Ref1", "Ref2"), each = 100), 2) + Query <- rep(c("Query1", "Query2"), each = 200) + Position <- rep(seq(-50, 49), 4) + Intensity <- rlnorm(400) + se <- runif(400) + start_df <- data.frame(Intensity, se, Position, Query, Reference) %>% + mutate(lower = Intensity - se, upper = Intensity + se) %>% + mutate(Group = paste(Query, Reference, sep = ":")) %>% + mutate(Location = rep("Start", 400)) %>% + mutate(Interval = sample.int(1000, 400)) + Intensity <- rlnorm(400, meanlog = 1.5) + se <- runif(400) + center_df <- data.frame(Intensity, se, Position, Query, Reference) %>% + mutate(lower = Intensity - se, upper = Intensity + se) %>% + mutate(Group = paste(Query, Reference, sep = ":")) %>% + mutate(Location = rep("Center", 400)) %>% + mutate(Interval = sample.int(600, 400)) + Intensity <- rlnorm(400, meanlog = 2) + se <- runif(400) + end_df <- data.frame(Intensity, se, Position, Query, Reference) %>% + mutate(lower = Intensity - se, upper = Intensity + se) %>% + mutate(Group = paste(Query, Reference, sep = ":")) %>% + mutate(Location = rep("End", 400)) %>% + mutate(Interval = sample.int(2000, 400)) + + df <- rbind(start_df, center_df, end_df) + p <- draw_stacked_profile(df, cn = "Group", shade = TRUE, + ext = c(-50, 50, -50, 50), + hl = c(-20, 20, -25, 25), insert = 100) + }) ── Skip: testing draw_stacked_profile ────────────────────────────────────────── Reason: empty test > > proc.time() user system elapsed 27.42 2.59 32.93
GenomicPlot.Rcheck/GenomicPlot-Ex.timings
name | user | system | elapsed | |
aov_TukeyHSD | 0.16 | 0.00 | 0.16 | |
check_constraints | 0.11 | 0.01 | 3.97 | |
custom_TxDb_from_GTF | 2.36 | 0.14 | 2.50 | |
draw_boxplot_by_factor | 0.52 | 0.08 | 0.59 | |
draw_boxplot_wo_outlier | 0.28 | 0.03 | 0.31 | |
draw_combo_plot | 2.30 | 0.10 | 2.39 | |
draw_locus_profile | 0.48 | 0.00 | 0.48 | |
draw_matrix_heatmap | 2.03 | 0.92 | 1.66 | |
draw_mean_se_barplot | 0.45 | 0.07 | 0.50 | |
draw_quantile_plot | 0.65 | 0.01 | 0.66 | |
draw_rank_plot | 0.42 | 0.00 | 0.42 | |
draw_region_landmark | 0.01 | 0.00 | 0.02 | |
draw_region_name | 0 | 0 | 0 | |
draw_region_profile | 0.36 | 0.00 | 0.36 | |
draw_stacked_profile | 2.11 | 0.02 | 2.13 | |
effective_size | 0.73 | 0.01 | 22.34 | |
extract_longest_tx | 1.39 | 0.11 | 1.50 | |
filter_by_nonoverlaps_stranded | 0.39 | 0.00 | 0.39 | |
filter_by_overlaps_nonstranded | 0.1 | 0.0 | 0.1 | |
filter_by_overlaps_stranded | 0.31 | 0.00 | 0.31 | |
find_mate | 0.01 | 0.00 | 0.01 | |
gene2tx | 0.27 | 0.02 | 0.29 | |
get_genomic_feature_coordinates | 2.36 | 0.03 | 2.39 | |
get_targeted_genes | 8.25 | 0.16 | 8.41 | |
get_txdb_features | 7.73 | 0.12 | 7.86 | |
gr2df | 0.05 | 0.00 | 0.04 | |
handle_bam | 0.20 | 0.00 | 0.21 | |
handle_bed | 0.16 | 0.00 | 0.15 | |
handle_bedGraph | 0.10 | 0.00 | 0.09 | |
handle_bw | 0.4 | 0.0 | 3.6 | |
handle_input | 1.17 | 0.05 | 2.39 | |
handle_wig | 0.25 | 0.01 | 0.31 | |
impute_hm | 0 | 0 | 0 | |
inspect_matrix | 0.02 | 0.00 | 0.02 | |
make_subTxDb_from_GTF | 0.73 | 0.10 | 1.92 | |
overlap_pair | 0.35 | 0.00 | 0.50 | |
overlap_quad | 3.03 | 0.03 | 3.06 | |
overlap_triple | 1.06 | 0.01 | 1.08 | |
parallel_countOverlaps | 0.41 | 0.08 | 22.98 | |
parallel_scoreMatrixBin | 0.42 | 0.03 | 17.08 | |
plot_5parts_metagene | 10.14 | 0.53 | 174.48 | |
plot_bam_correlation | 1.05 | 0.11 | 22.63 | |
plot_locus | 10.65 | 0.27 | 82.30 | |
plot_locus_with_random | 6.82 | 0.14 | 75.28 | |
plot_named_list | 0.89 | 0.06 | 0.95 | |
plot_overlap_bed | 1.42 | 0.08 | 1.50 | |
plot_overlap_genes | 1.22 | 0.09 | 1.36 | |
plot_peak_annotation | 9.90 | 0.14 | 10.08 | |
plot_region | 6.80 | 0.19 | 107.12 | |
plot_start_end | 12.72 | 0.27 | 109.78 | |
plot_start_end_with_random | 17.33 | 0.61 | 216.83 | |
prepare_3parts_genomic_features | 1.87 | 0.01 | 1.89 | |
prepare_5parts_genomic_features | 6.77 | 0.11 | 6.89 | |
process_scoreMatrix | 0.01 | 0.00 | 0.02 | |
rank_rows | 0.02 | 0.00 | 0.02 | |
ratio_over_input | 0 | 0 | 0 | |
rm_outlier | 0 | 0 | 0 | |
setImportParams | 0 | 0 | 0 | |
set_seqinfo | 0 | 0 | 0 | |
start_parallel | 0.00 | 0.02 | 0.32 | |
stop_parallel | 0.0 | 0.0 | 0.3 | |