##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicPlot_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicPlot.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 R 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 loading without being on the library search path ... 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’
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
* 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 ... ERROR
Running examples in ‘GenomicPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_start_end
> ### Title: Plot signals around the start and the end of genomic features
> ### Aliases: plot_start_end
> 
> ### ** Examples
> 
> 
> txdb <- AnnotationDbi::loadDb(system.file("extdata", "txdb.sql", 
+     package = "GenomicPlot"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 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"
+ )
> 
> plot_start_end(
+     queryFiles = bamQueryFiles,
+     inputFiles = bamInputFiles,
+     txdb = txdb,
+     centerFiles = "intron",
+     binSize = 10,
+     importParams = bamimportParams,
+     ext = c(-500, 200, -200, 500),
+     hl = c(-100, 100, -100, 100),
+     insert = 100,
+     stranded = TRUE,
+     scale = FALSE,
+     smooth = TRUE,
+     transform = "log2",
+     outPrefix = NULL,
+     nc = 2
+ )
565 418 
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicPlot.Rcheck/00check.log’
for details.