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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings INSPEcT_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.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 ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘1.29.0’
* 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 ‘INSPEcT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.8Mb
* 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
output_pars: no visible global function definition for ‘plot.new’
plotSingleRNADynamic: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new
Consider adding
  importFrom("graphics", "lines", "plot.new")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
makeSimDataset                  119.230  0.020 124.722
quantifyExpressionsFromBAMs      51.072  0.112  51.782
INSPEcT_diffsteady-class         43.702  0.141  49.021
rocThresholds                    40.497  0.004  40.505
makeSimModel                     40.302  0.000  41.477
rocCurve                         39.889  0.016  39.925
compareSteady                    37.720  0.012  42.227
plotMA                           37.281  0.004  37.305
modelRates                       24.432  0.004  32.209
quantifyExpressionsFromTrCounts  22.972  0.647  29.544
newINSPEcT                       21.949  0.001  24.187
processingDelay                  20.291  0.008  20.301
makeOscillatorySimModel           9.487  0.012  10.293
compareSteadyNoNascent            8.362  0.000   9.028
inspectFromPCR                    5.035  0.000   6.078
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘INSPEcT.Rmd’ using ‘UTF-8’... OK
  ‘INSPEcT_GUI.rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘INSPEcT.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/vign_test/INSPEcT/vignettes/INSPEcT_files/figure-html/inHeatmapNascentTimeCourse-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/vign_test/INSPEcT/vignettes/INSPEcT_files/figure-html/firstGuessCompareDDP-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/vign_test/INSPEcT/vignettes/INSPEcT_files/figure-html/viewModelRatesAndInHeatmapNascentTimeCourse-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/vign_test/INSPEcT/vignettes/INSPEcT_files/figure-html/plotGeneNascentTimeCourse-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/vign_test/INSPEcT/vignettes/INSPEcT_files/figure-html/chi2NascentTimeCourse-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/vign_test/INSPEcT/vignettes/INSPEcT_files/figure-html/plotGeneNascentTimeCourseNF-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/vign_test/INSPEcT/vignettes/INSPEcT_files/figure-html/firstGuessCompare-1.png" but not available.
Killed
--- re-building ‘INSPEcT_GUI.rmd’ using rmarkdown
--- finished re-building ‘INSPEcT_GUI.rmd’

SUMMARY: processing the following file failed:
  ‘INSPEcT.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.

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