##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicPlot_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GenomicPlot.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... 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 16.535  8.276  19.189
plot_region                12.377  5.847  12.023
plot_locus                 11.682  3.988  11.650
plot_5parts_metagene        9.348  4.560  10.112
plot_locus_with_random      8.923  3.248   8.860
plot_start_end              9.078  2.208   9.912
plot_peak_annotation        5.764  0.068   5.847
get_targeted_genes          5.294  0.083   5.405
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GenomicPlot.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicPlot
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 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 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds
Keeping standard chromosomes only
File /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 
 97.486  34.315 100.022 

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

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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 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        41             0.41
── 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 
 18.514   1.107  19.675