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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings maser_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/maser.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 ‘maser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maser’ version ‘1.17.0’
* 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 ‘maser’ 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 ... NOTE
availableFeaturesUniprotKB: no visible global function definition for
  'read.csv'
availableFeaturesUniprotKB: no visible binding for global variable
  'Category'
availableFeaturesUniprotKB: no visible binding for global variable
  'Name'
filterByIds: no visible binding for global variable 'ID'
mapTranscriptsA3SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsA5SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsMXEevent: no visible global function definition for
  'subjectHits'
mapTranscriptsRIevent: no visible global function definition for
  'subjectHits'
mapTranscriptsSEevent: no visible global function definition for
  'subjectHits'
overlappingFeatures: no visible global function definition for
  'subjectHits'
urlTracksUniprotKB: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  Category ID Name read.csv subjectHits
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘maser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filterByEventId
> ### Title: Filter splicing events based on event identifier and type.
> ### Aliases: filterByEventId
> 
> ### ** Examples
> 
> path <- system.file("extdata", file.path("MATS_output"), package = "maser")
> hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Introduction.Rmd’ using ‘UTF-8’... OK
  ‘Protein_mapping.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-16-1.png" but not available.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Protein_mapping.Rmd’ using rmarkdown
Killed
SUMMARY: processing the following file failed:
  ‘Protein_mapping.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/maser.Rcheck/00check.log’
for details.

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