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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ensembldb_2.23.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.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 ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.23.1’
* 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 ‘ensembldb’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
EnsDb-AnnotationDbi 3.626  0.495   5.404
Filter-classes      2.440  1.426   6.099
* 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:
  
      not
  
  
  Attaching package: 'ensembldb'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > library(EnsDb.Hsapiens.v86)
  > edb <- EnsDb.Hsapiens.v86
  > 
  > test_check("ensembldb")
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MySQL-backend.Rmd’ using ‘UTF-8’... OK
  ‘coordinate-mapping-use-cases.Rmd’ using ‘UTF-8’... OK
  ‘coordinate-mapping.Rmd’ using ‘UTF-8’... OK
  ‘ensembldb.Rmd’ using ‘UTF-8’... OK
  ‘proteins.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MySQL-backend.Rmd’ using rmarkdown
--- finished re-building ‘MySQL-backend.Rmd’

--- re-building ‘coordinate-mapping-use-cases.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping-use-cases_files/figure-html/olig-plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping-use-cases_files/figure-html/sim2-plot-1.png" but not available.
Killed
--- re-building ‘coordinate-mapping.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping_files/figure-html/genomeToTranscript-ex1-plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping_files/figure-html/proteinToGenome-SYP-plot-1.png" but not available.
--- finished re-building ‘coordinate-mapping.Rmd’

--- re-building ‘ensembldb.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/ensembldb_files/figure-html/granges-zbtb16-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/ensembldb_files/figure-html/gviz-plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/ensembldb_files/figure-html/unnamed-chunk-3-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/ensembldb_files/figure-html/gviz-separate-tracks-1.png" but not available.
Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘ensembldb.Rmd’

--- re-building ‘proteins.Rmd’ using rmarkdown
--- finished re-building ‘proteins.Rmd’

SUMMARY: processing the following file failed:
  ‘coordinate-mapping-use-cases.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ensembldb
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ensembldb’ ...
** 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 (ensembldb)

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(ensembldb)
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: GenomicRanges
Loading required package: stats4
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
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:testthat':

    not


Attaching package: 'ensembldb'

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

    filter

> library(EnsDb.Hsapiens.v86)
> edb <- EnsDb.Hsapiens.v86
> 
> test_check("ensembldb")
Killed