Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 822/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicPlot 1.5.2 (landing page) Shuye Pu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: GenomicPlot |
Version: 1.5.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicPlot_1.5.2.tar.gz |
StartedAt: 2024-12-24 07:03:06 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:16:35 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 809.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomicPlot.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicPlot_1.5.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicPlot.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicPlot/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicPlot’ version ‘1.5.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 25 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 for sufficient/correct file permissions ... OK * checking whether package ‘GenomicPlot’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicPlot.Rcheck/00install.out’ for details. * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 24.063 5.670 28.204 plot_region 19.246 6.520 18.679 plot_locus 18.183 4.362 18.702 plot_5parts_metagene 15.246 6.127 17.756 plot_start_end 15.507 3.449 18.221 plot_locus_with_random 13.822 3.215 13.801 plot_peak_annotation 10.444 0.135 10.600 get_txdb_features 8.916 0.275 9.211 get_targeted_genes 8.730 0.180 8.932 prepare_5parts_genomic_features 6.395 0.023 6.439 * 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: 5 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicPlot.Rcheck/00check.log’ for details.
GenomicPlot.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GenomicPlot ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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’ Warning: program compiled against libxml 212 using older 211 ** 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’ Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (GenomicPlot)
GenomicPlot.Rcheck/tests/test-plotFunctions.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 Loading required package: GenomeInfoDb Warning: program compiled against libxml 212 using older 211 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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds Keeping standard chromosomes only File /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds already exists. Use overwriteObjectAsRds = TRUE to overwrite the file Warning messages: 1: 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. 2: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object > > 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) ── Warning: testing plot_peak_annotation ─────────────────────────────────────── genome version information is not available for this TxDb object Backtrace: ▆ 1. └─GenomicPlot::plot_peak_annotation(...) 2. └─txdbmaker::makeTxDbFromGRanges(gff) 3. └─txdbmaker::makeTxDb(...) 4. └─txdbmaker:::.makeTxDb_normarg_chrominfo(chrominfo) ── 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 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 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(...) ── 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 159.501 38.340 167.157
GenomicPlot.Rcheck/tests/test-shortFunctions.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 Loading required package: GenomeInfoDb Warning: program compiled against libxml 212 using older 211 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 40 0.40 ── 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 31.594 1.572 33.175
GenomicPlot.Rcheck/GenomicPlot-Ex.timings
name | user | system | elapsed | |
aov_TukeyHSD | 0.018 | 0.000 | 0.019 | |
check_constraints | 0.191 | 0.044 | 4.294 | |
custom_TxDb_from_GTF | 1.311 | 0.124 | 1.439 | |
draw_boxplot_by_factor | 0.548 | 0.048 | 0.597 | |
draw_boxplot_wo_outlier | 0.270 | 0.008 | 0.278 | |
draw_combo_plot | 2.274 | 0.247 | 2.528 | |
draw_locus_profile | 0.469 | 0.028 | 0.498 | |
draw_matrix_heatmap | 1.660 | 0.072 | 1.736 | |
draw_mean_se_barplot | 0.502 | 0.019 | 0.522 | |
draw_quantile_plot | 0.604 | 0.012 | 0.617 | |
draw_rank_plot | 0.575 | 0.044 | 0.620 | |
draw_region_landmark | 0.013 | 0.000 | 0.013 | |
draw_region_name | 0.009 | 0.000 | 0.008 | |
draw_region_profile | 0.337 | 0.019 | 0.357 | |
draw_stacked_profile | 2.119 | 0.092 | 2.215 | |
effective_size | 0.690 | 0.251 | 0.891 | |
extract_longest_tx | 1.597 | 0.236 | 1.836 | |
filter_by_nonoverlaps_stranded | 0.403 | 0.003 | 0.407 | |
filter_by_overlaps_nonstranded | 1.377 | 0.348 | 1.727 | |
filter_by_overlaps_stranded | 0.299 | 0.000 | 0.300 | |
find_mate | 0.002 | 0.000 | 0.002 | |
gene2tx | 0.326 | 0.000 | 0.330 | |
get_genomic_feature_coordinates | 2.210 | 0.052 | 2.265 | |
get_targeted_genes | 8.730 | 0.180 | 8.932 | |
get_txdb_features | 8.916 | 0.275 | 9.211 | |
gr2df | 0.035 | 0.004 | 0.040 | |
handle_bam | 0.171 | 0.008 | 0.182 | |
handle_bed | 0.121 | 0.008 | 0.131 | |
handle_bedGraph | 0.077 | 0.000 | 0.078 | |
handle_bw | 0.357 | 0.004 | 0.365 | |
handle_input | 1.525 | 0.016 | 1.548 | |
handle_wig | 0.288 | 0.000 | 0.288 | |
impute_hm | 0.007 | 0.000 | 0.006 | |
inspect_matrix | 0.015 | 0.000 | 0.014 | |
make_subTxDb_from_GTF | 0.817 | 0.012 | 0.831 | |
overlap_pair | 0.372 | 0.016 | 0.389 | |
overlap_quad | 3.669 | 0.028 | 3.705 | |
overlap_triple | 1.190 | 0.008 | 1.201 | |
parallel_countOverlaps | 0.462 | 0.222 | 0.626 | |
parallel_scoreMatrixBin | 0.631 | 0.403 | 0.970 | |
plot_5parts_metagene | 15.246 | 6.127 | 17.756 | |
plot_bam_correlation | 1.303 | 0.429 | 1.682 | |
plot_locus | 18.183 | 4.362 | 18.702 | |
plot_locus_with_random | 13.822 | 3.215 | 13.801 | |
plot_named_list | 1.021 | 0.020 | 1.043 | |
plot_overlap_bed | 1.656 | 0.016 | 1.676 | |
plot_overlap_genes | 1.277 | 0.056 | 1.337 | |
plot_peak_annotation | 10.444 | 0.135 | 10.600 | |
plot_region | 19.246 | 6.520 | 18.679 | |
plot_start_end | 15.507 | 3.449 | 18.221 | |
plot_start_end_with_random | 24.063 | 5.670 | 28.204 | |
prepare_3parts_genomic_features | 1.928 | 0.020 | 1.953 | |
prepare_5parts_genomic_features | 6.395 | 0.023 | 6.439 | |
process_scoreMatrix | 0.024 | 0.000 | 0.025 | |
rank_rows | 0.01 | 0.00 | 0.01 | |
ratio_over_input | 0.000 | 0.000 | 0.001 | |
rm_outlier | 0.004 | 0.000 | 0.005 | |
setImportParams | 0.000 | 0.000 | 0.001 | |
set_seqinfo | 0.003 | 0.000 | 0.004 | |
start_parallel | 0.005 | 0.200 | 0.148 | |
stop_parallel | 0.015 | 0.175 | 0.133 | |