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###
### 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      23.247  5.441  27.270
plot_region                     19.675  6.986  19.367
plot_locus                      18.098  3.697  18.013
plot_5parts_metagene            15.079  6.379  17.781
plot_start_end                  15.687  3.360  18.304
plot_locus_with_random          14.409  4.335  15.191
plot_peak_annotation            10.446  0.187  10.655
get_txdb_features                8.962  0.187   9.169
get_targeted_genes               8.709  0.172   8.898
prepare_5parts_genomic_features  6.155  0.036   6.200
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-plotFunctions.R’

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GenomicPlot
###
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* 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)

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
+    )
+ })