##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gmoviz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings gmoviz_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.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 ‘gmoviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gmoviz’ version ‘1.11.0’
* 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 ‘gmoviz’ can be installed ... 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 ... WARNING
Error in library(gmoviz, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘gmoviz’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘gmoviz_advanced.Rmd’ using ‘UTF-8’... OK
  ‘gmoviz_overview.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘gmoviz_advanced.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/gmovizInitialise-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/gmovizInitialise-pretty-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/gmovizInitialise-covRect-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/smoothing-windowing-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/gmovizInitialise-labels-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/labels_from_gff-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/zooming_ideo-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/gmovizInitialise-custom_sector_width-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/gmovizInitialise-zooming-after-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/drawFeatureTrack-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/feature_label_cutoff-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/change_label_cutoff-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/numeric_data_plots-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/numeric_data_with_features-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_advanced_files/figure-html/circlize_annotation-1.jpeg" but not available.
--- finished re-building ‘gmoviz_advanced.Rmd’

--- re-building ‘gmoviz_overview.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/sectors-tracks-figure-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/cnd-style1-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/cnd-style2-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/cnd-singleins-style34-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/cnd-multiple-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/cnd-labels-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/cnd-coverage-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/either_side-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/either_side-2.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/aobf_example-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/aobf_basic-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/aobf_coverage_labels-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/aobf_single_val-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/aobf_es_GRanges-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/fdd-plasmid-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/plasmid-map-coverage-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/fdd-complex-construct-plot-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/vign_test/gmoviz/vignettes/gmoviz_overview_files/figure-html/fdd-link-1.jpeg" but not available.
Killed
SUMMARY: processing the following file failed:
  ‘gmoviz_overview.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/gmoviz.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL gmoviz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘gmoviz’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (gmoviz)

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(gmoviz)
Loading required package: circlize
========================================
circlize version 0.4.15
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("gmoviz")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
 17.210   0.483  17.695