##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings chimeraviz_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/chimeraviz.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 ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.28.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biostrings', 'GenomicRanges', 'IRanges', 'Gviz', 'S4Vectors',
  'ensembldb', 'AnnotationFilter', 'data.table'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘chimeraviz’ 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 ... NOTE
Namespace in Imports field not imported from: 'magick'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_fusion_transcript_with_protein_domain: no visible binding for
  global variable 'protein_domain_location'
Undefined global functions or variables:
  protein_domain_location
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘chimeraviz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_fusion
> ### Title: Plot a fusion event with transcripts, coverage and ideograms.
> ### Aliases: plot_fusion plot_fusion_separate plot_fusion_together
> 
> ### ** Examples
> 
> # Load data and example fusion event
> defuse833ke <- system.file(
+   "extdata",
+   "defuse_833ke_results.filtered.tsv",
+   package="chimeraviz")
> fusions <- import_defuse(defuse833ke, "hg19", 1)
> fusion <- get_fusion_by_id(fusions, 5267)
> # Load edb
> edbSqliteFile <- system.file(
+   "extdata",
+   "Homo_sapiens.GRCh37.74.sqlite",
+   package="chimeraviz")
> edb <- ensembldb::EnsDb(edbSqliteFile)
> # bamfile with reads in the regions of this fusion event
> bamfile5267 <- system.file(
+   "extdata",
+   "fusion5267and11759reads.bam",
+   package="chimeraviz")
> # Temporary file to store the plot
> pngFilename <- tempfile(
+   pattern = "fusionPlot",
+   fileext = ".png",
+   tmpdir = tempdir())
> # Open device
> png(pngFilename, width = 1000, height = 750)
> # Plot!
> plot_fusion(
+   fusion = fusion,
+   bamfile = bamfile5267,
+   edb = edb,
+   non_ucsc = TRUE)
Fetching transcripts for gene partners..
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 514308 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      shift
  
  The following object is masked from 'package:IRanges':
  
      shift
  
  The following objects are masked from 'package:S4Vectors':
  
      first, second
  
  
  
  > 
  > test_check("chimeraviz")
* 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: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.