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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:chimeraviz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings chimeraviz_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/chimeraviz.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.25.0’
* 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 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..
..transcripts fetched.
Fusion is intrachromosomal..
..but on different strands. Plot separate!
Selecting transcripts for RCC1..
..found transcripts of type exonBoundary
Selecting transcripts for HENMT1..
..found transcripts of type exonBoundary
As HENMT1 is on the minus strand, the plot for this gene will be reversed
> # Close device
> dev.off()
pdf 
  2 
> 
> # Example using a .bedGraph file instead of a .bam file:
> # 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)
> # bedgraphfile with coverage data from the regions of this fusion event
> bedgraphfile <- system.file(
+   "extdata",
+   "fusion5267and11759reads.bedGraph",
+   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,
+   bedgraphfile = bedgraphfile,
+   edb = edb,
+   non_ucsc = TRUE)
Fetching transcripts for gene partners..
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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")
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘chimeraviz-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘chimeraviz-vignette.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL chimeraviz
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘chimeraviz’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chimeraviz)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(testthat)
> library(chimeraviz)
Loading required package: Biostrings
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: GenomicRanges
Loading required package: Gviz
Loading required package: grid

Attaching package: 'grid'

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

    pattern

Loading required package: ensembldb
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")'.

Loading required package: AnnotationFilter

Attaching package: 'AnnotationFilter'

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

    feature

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

    not


Attaching package: 'ensembldb'

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

    filter

Loading required package: data.table

Attaching package: 'data.table'

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

    shift

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

    shift

The following objects are masked from 'package:S4Vectors':

    first, second



> 
> test_check("chimeraviz")
Killed