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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicPlot.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomicPlot_1.3.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GenomicPlot.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicPlot/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicPlot' version '1.3.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenomicPlot' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_targeted_genes: no visible binding for global variable '5'UTR'
get_targeted_genes: no visible binding for global variable '3'UTR'
handle_bam: no visible global function definition for 'seqlevelsStyle'
handle_bam: no visible global function definition for
  'seqlevelsStyle<-'
handle_bed: no visible global function definition for 'seqlevelsStyle'
handle_bed: no visible global function definition for
  'seqlevelsStyle<-'
handle_bedGraph: no visible global function definition for
  'seqlevelsStyle'
handle_bedGraph: no visible global function definition for
  'seqlevelsStyle<-'
handle_bw: no visible global function definition for 'seqlevelsStyle'
handle_bw: no visible global function definition for 'seqlevelsStyle<-'
plot_bam_correlation: no visible binding for global variable '.'
plot_peak_annotation: no visible binding for global variable '.'
Undefined global functions or variables:
  . 3'UTR 5'UTR seqlevelsStyle seqlevelsStyle<-
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
plot_start_end_with_random      14.61   0.86  267.72
plot_start_end                   9.79   0.53  133.25
plot_peak_annotation             9.57   0.33   10.10
get_targeted_genes               8.68   0.59    9.63
plot_5parts_metagene             8.38   0.79  214.55
plot_locus                       8.70   0.32   94.47
get_txdb_features                7.50   0.24    8.01
plot_locus_with_random           6.26   0.43   95.64
plot_region                      6.39   0.28  132.11
prepare_5parts_genomic_features  5.17   0.22    5.62
plot_bam_correlation             1.14   0.15   25.20
effective_size                   0.64   0.10   27.25
parallel_countOverlaps           0.36   0.12   25.47
parallel_scoreMatrixBin          0.31   0.05   21.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-plotFunctions.R'

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GenomicPlot
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'GenomicPlot' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicPlot)

R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GenomicPlot)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> library(testthat)
> 
> Sys.setenv("R_TESTS" = "")
> 
> data(gf5_meta)
> data(gf5_genomic)
> 
> gtffile <- system.file("extdata", "gencode.v19.annotation_chr19.gtf",
+                        package = "GenomicPlot")
> txdb <- custom_TxDb_from_GTF(gtffile, genome = "hg19")
Reading existing granges.rds object from F:/biocbuild/bbs-3.20-bioc/R/library/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds
Keeping standard chromosomes only
File F:/biocbuild/bbs-3.20-bioc/R/library/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds already exists.
                  Use overwriteObjectAsRds = TRUE to overwrite the file
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
> 
> bedQueryFiles <- c(
+    system.file("extdata", "test_chip_peak_chr19.narrowPeak",
+                package = "GenomicPlot"),
+    system.file("extdata", "test_chip_peak_chr19.bed", package = "GenomicPlot"),
+    system.file("extdata", "test_clip_peak_chr19.bed", package = "GenomicPlot")
+ )
> names(bedQueryFiles) <- c("NarrowPeak", "SummitPeak", "iCLIPPeak")
> 
> bedImportParams <- setImportParams(
+    offset = 0, fix_width = 100, fix_point = "center", norm = FALSE,
+    useScore = FALSE, outRle = TRUE, useSizeFactor = FALSE, genome = "hg19"
+ )
> 
> bamQueryFiles <- system.file("extdata", "treat_chr19.bam",
+                              package = "GenomicPlot")
> names(bamQueryFiles) <- "clip_bam"
> bamInputFiles <- system.file("extdata", "input_chr19.bam",
+                              package = "GenomicPlot")
> names(bamInputFiles) <- "clip_input"
> 
> bamImportParams <- setImportParams(
+    offset = -1, fix_width = 0, fix_point = "start", norm = TRUE,
+    useScore = FALSE, outRle = TRUE, useSizeFactor = FALSE, genome = "hg19"
+ )
> 
> chipQueryFiles <- system.file("extdata", "chip_treat_chr19.bam",
+                               package = "GenomicPlot")
> names(chipQueryFiles) <- "chip_bam"
> chipInputFiles <- system.file("extdata", "chip_input_chr19.bam",
+                               package = "GenomicPlot")
> names(chipInputFiles) <- "chip_input"
> 
> chipImportParams <- setImportParams(
+    offset = 0, fix_width = 150, fix_point = "start", norm = TRUE,
+    useScore = FALSE, outRle = TRUE, useSizeFactor = FALSE, genome = "hg19"
+ )
> 
> 
> test_that("testing parallel_countOverlaps", {
+    importParams <- setImportParams(fix_width = 100, outRle = FALSE)
+    out_list <- handle_input(
+       inputFiles = bedQueryFiles,
+       importParams = importParams, verbose = FALSE, nc = 2
+    )
+ 
+    chromInfo <- circlize::read.chromInfo(species = "hg19")$df
+    seqi <- Seqinfo(seqnames = chromInfo$chr, seqlengths = chromInfo$end,
+                    isCircular = rep(FALSE, nrow(chromInfo)),
+                    genome = "hg19")
+    grange_list <- lapply(out_list, function(x) x$query)
+    tilewidth <- 100000
+    tileBins <- tileGenome(seqi, tilewidth = tilewidth,
+                           cut.last.tile.in.chrom = TRUE)
+ 
+    score_list1 <- parallel_countOverlaps(grange_list, tileBins, nc = 2)
+ })
── Skip: testing parallel_countOverlaps ────────────────────────────────────────
Reason: empty test

> 
> test_that("testing parallel_scoreMatrixBin", {
+ 
+    queryRegion <- handle_input(chipQueryFiles, chipImportParams,
+                                verbose = TRUE)[[1]]$query
+ 
+    importParams <- setImportParams(outRle = FALSE)
+ 
+    windowRegion <- handle_bed(bedQueryFiles[1], importParams, verbose = TRUE)$query
+ 
+    out <- parallel_scoreMatrixBin(
+       queryRegions = queryRegion,
+       windowRs = windowRegion,
+       bin_num = 50,
+       bin_op = "mean",
+       weight_col = "score",
+       stranded = TRUE,
+       nc = 2
+    )
+ })
── Skip: testing parallel_scoreMatrixBin ───────────────────────────────────────
Reason: empty test

> 
> test_that("testing handle_bed", {
+    out <- handle_bed(bedQueryFiles[1], bedImportParams, verbose = TRUE)
+ })
── Skip: testing handle_bed ────────────────────────────────────────────────────
Reason: empty test

> 
> test_that("testing effective_size", {
+    importParams <- setImportParams(outRle = FALSE)
+    out_list <- handle_input(
+       inputFiles = c(chipQueryFiles, chipInputFiles),
+       importParams = importParams, verbose = TRUE, nc = 2
+    )
+ 
+    out <- effective_size(out_list, outRle = TRUE)
+ })
── Skip: testing effective_size ────────────────────────────────────────────────
Reason: empty test

> 
> test_that("testing handle_input", {
+ 
+    queryFiles2 <- system.file("extdata", "test_wig_chr19_+.wig",
+                               package = "GenomicPlot")
+    names(queryFiles2) <- "test_wig"
+ 
+    queryFiles3 <- system.file("extdata", "test_wig_chr19_+.bw",
+                               package = "GenomicPlot")
+    names(queryFiles3) <- "test_bw"
+ 
+    importParams <- setImportParams()
+ 
+    out <- handle_input(c(bamQueryFiles, queryFiles2, queryFiles3),
+                        importParams, verbose = TRUE)
+ })
── Skip: testing handle_input ──────────────────────────────────────────────────
Reason: empty test

> 
> test_that("testing plot_bam_correlation", {
+ 
+    importParams <- setImportParams(fix_width = 150, outRle = FALSE)
+ 
+    plot_bam_correlation(
+       bamFiles = c(chipQueryFiles, chipInputFiles), binSize = 100000,
+       outPrefix = NULL, importParams = importParams, nc = 2, verbose = FALSE
+    )
+ })
── Skip: testing plot_bam_correlation ──────────────────────────────────────────
Reason: empty test

> 
> test_that("testing plot_overlap_bed", {
+    importParams <- setImportParams(fix_width = 100, outRle = FALSE)
+    plot_overlap_bed(
+       bedList = bedQueryFiles, importParams = importParams, pairOnly = FALSE,
+       stranded = FALSE, outPrefix = NULL
+    )
+ })
── Skip: testing plot_overlap_bed ──────────────────────────────────────────────
Reason: empty test

> 
> test_that("testing plot_argument_list", {
+ 
+    alist <- list(
+       "txdb" = txdb, "treat" = bamQueryFiles, "control" = bamInputFiles,
+       "feature" = gf5_meta, "param" = bamImportParams
+    )
+ 
+    p <- GenomicPlot:::plot_named_list(alist)
+ })
── Skip: testing plot_argument_list ────────────────────────────────────────────
Reason: empty test

> 
> 
> test_that("testing plot_peak_annotation", {
+    plot_peak_annotation(
+       peakFile = bedQueryFiles[2], gtfFile = gtffile, importParams = bedImportParams,
+       fiveP = -2000, dsTSS = 200, threeP = 2000, simple = FALSE
+    )
+ })
── Warning: testing plot_peak_annotation ───────────────────────────────────────
The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
Backtrace:
    ▆
 1. └─GenomicPlot::plot_peak_annotation(...)
 2.   └─txdbmaker::makeTxDbFromGRanges(gff)
 3.     └─txdbmaker:::.get_cds_IDX(mcols0$type, mcols0$phase)

── Skip: testing plot_peak_annotation ──────────────────────────────────────────
Reason: empty test

> 
> 
> test_that("testing plot_overlap_genes", {
+    testfile1 <- system.file("extdata", "test_file1.txt",
+                             package = "GenomicPlot")
+    testfile2 <- system.file("extdata", "test_file2.txt",
+                             package = "GenomicPlot")
+    testfile3 <- system.file("extdata", "test_file3.txt",
+                             package = "GenomicPlot")
+    testfile4 <- system.file("extdata", "test_file4.txt",
+                             package = "GenomicPlot")
+    testfiles <- c(testfile1, testfile2, testfile3, testfile4)
+    names(testfiles) <- c("test1", "test2", "test3", "test4")
+ 
+    plot_overlap_genes(testfiles, c(3,2,1,1), pairOnly = FALSE)
+ })
── Skip: testing plot_overlap_genes ────────────────────────────────────────────
Reason: empty test

> 
> test_that("testing plot_5parts_metagene", {
+    plot_5parts_metagene(
+       queryFiles = bedQueryFiles,
+       gFeatures_list = list("metagene" = gf5_meta),
+       inputFiles = NULL,
+       importParams = bedImportParams,
+       verbose = FALSE,
+       smooth = TRUE,
+       scale = FALSE,
+       stranded = TRUE,
+       outPrefix = NULL,
+       transform = NA,
+       heatmap = TRUE,
+       rmOutlier = 0,
+       heatRange = NULL,
+       nc = 2
+    )
+ })
── Skip: testing plot_5parts_metagene ──────────────────────────────────────────
Reason: empty test

> 
> test_that("testing plot_locus", {
+    plot_locus(
+       queryFiles = bedQueryFiles[c(1,3)],
+       centerFiles = bedQueryFiles[2],
+       ext = c(-500, 500),
+       hl = c(-100, 100),
+       inputFiles = NULL,
+       importParams = bedImportParams,
+       shade = TRUE,
+       binSize = 10,
+       refPoint = "center",
+       Xlab = "Summit",
+       verbose = FALSE,
+       smooth = TRUE,
+       scale = FALSE,
+       stranded = TRUE,
+       outPrefix = NULL,
+       transform = NA,
+       heatmap = TRUE,
+       heatRange = NULL,
+       rmOutlier = 0,
+       Ylab = "Coverage/base/peak",
+       nc = 2
+    )
+ 
+    plot_locus(
+       queryFiles = chipQueryFiles,
+       centerFiles = bedQueryFiles[2],
+       ext = c(-500, 500),
+       hl = c(-100, 100),
+       inputFiles = chipInputFiles,
+       importParams = chipImportParams,
+       shade = TRUE,
+       binSize = 10,
+       refPoint = "center",
+       Xlab = "Summit",
+       verbose = FALSE,
+       smooth = TRUE,
+       scale = FALSE,
+       stranded = TRUE,
+       outPrefix = NULL,
+       transform = NA,
+       heatmap = TRUE,
+       heatRange = NULL,
+       rmOutlier = 0,
+       Ylab = "Coverage/base/peak",
+       nc = 2
+    )
+ })
── Skip: testing plot_locus ────────────────────────────────────────────────────
Reason: empty test

> 
> test_that("testing plot_region", {
+    plot_region(
+       queryFiles = chipQueryFiles,
+       centerFiles = bedQueryFiles[1],
+       inputFiles = chipInputFiles,
+       nbins = 100,
+       heatmap = TRUE,
+       scale = FALSE,
+       regionName = "narrowPeak",
+       importParams = chipImportParams,
+       verbose = FALSE,
+       fiveP = -200,
+       threeP = 200,
+       smooth = TRUE,
+       transform = "log2",
+       stranded = TRUE,
+       Ylab = "Coverage/base/peak",
+       outPrefix = NULL,
+       rmOutlier = 0,
+       nc = 2
+    )
+ })
── Skip: testing plot_region ───────────────────────────────────────────────────
Reason: empty test

> 
> test_that("testing plot_start_end", {
+    plot_start_end(
+       queryFiles = bamQueryFiles,
+       inputFiles = bamInputFiles,
+       txdb = txdb,
+       centerFiles = "intron",
+       binSize = 10,
+       importParams = bamImportParams,
+       ext = c(-100, 100, -100, 100),
+       hl = c(-50, 50, -50, 50),
+       insert = 100,
+       stranded = TRUE,
+       scale = FALSE,
+       smooth = TRUE,
+       transform = "log2",
+       outPrefix = NULL,
+       nc = 2
+    )
+ })