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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenVisR_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenVisR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.38.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Found the following non-portable file paths:
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenVisR’ 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 code 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: ‘reshape2’
  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
buildWaterfallPlot,WaterfallData: no visible global function definition
  for ‘tail’
setTierTwo,data.table: no visible global function definition for ‘tail’
setTierTwo,data.table : a: no visible binding for global variable ‘tmp’
toLolliplot,GMS: no visible binding for global variable ‘missingINdex’
Undefined global functions or variables:
  missingINdex tail tmp
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) lohSpec.Rd:46: Lost braces; missing escapes or markup?
    46 | consisting of elements from the set {"M", "F"}. Used to suppress the plotting
       |                                     ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Lolliplot-class 18.745  0.975  46.716
geneViz          5.703  0.098   5.807
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenVisR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘GenVisR’ ...
** 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 (GenVisR)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(GenVisR)
> 
> test_check("GenVisR")
[ FAIL 0 | WARN 9 | SKIP 54 | PASS 510 ]

══ Skipped tests (54) ══════════════════════════════════════════════════════════
• On Bioconductor (54): 'test-Lolliplot-class.R:564:5',
  'test-Lolliplot-class.R:574:6', 'test-Lolliplot-class.R:602:5',
  'test-Lolliplot-class.R:615:5', 'test-Lolliplot-class.R:626:5',
  'test-Lolliplot-class.R:641:5', 'test-Lolliplot-class.R:654:5',
  'test-Lolliplot-class.R:730:5', 'test-Lolliplot-class.R:740:5',
  'test-Lolliplot-class.R:778:5', 'test-MutSpectra-class.R:285:5',
  'test-MutSpectra-class.R:294:5', 'test-MutSpectra-class.R:303:5',
  'test-MutSpectra-class.R:336:5', 'test-MutSpectra-class.R:345:5',
  'test-MutSpectra-class.R:354:5', 'test-MutSpectra-class.R:405:5',
  'test-MutSpectra-class.R:413:5', 'test-MutSpectra-class.R:440:5',
  'test-MutSpectra-class.R:450:5', 'test-Rainfall-class.R:247:5',
  'test-Rainfall-class.R:255:5', 'test-Rainfall-class.R:263:5',
  'test-Rainfall-class.R:297:5', 'test-Rainfall-class.R:305:5',
  'test-Rainfall-class.R:348:5', 'test-Rainfall-class.R:355:5',
  'test-Rainfall-class.R:389:5', 'test-Waterfall-class.R:662:5',
  'test-Waterfall-class.R:670:5', 'test-Waterfall-class.R:678:5',
  'test-Waterfall-class.R:686:5', 'test-Waterfall-class.R:722:5',
  'test-Waterfall-class.R:733:5', 'test-Waterfall-class.R:741:5',
  'test-Waterfall-class.R:750:5', 'test-Waterfall-class.R:758:5',
  'test-Waterfall-class.R:794:5', 'test-Waterfall-class.R:808:5',
  'test-Waterfall-class.R:819:5', 'test-Waterfall-class.R:830:5',
  'test-Waterfall-class.R:841:5', 'test-Waterfall-class.R:852:5',
  'test-Waterfall-class.R:868:5', 'test-Waterfall-class.R:906:5',
  'test-Waterfall-class.R:991:5', 'test-Waterfall-class.R:1005:5',
  'test-Waterfall-class.R:1019:5', 'test-Waterfall-class.R:1033:5',
  'test-Waterfall-class.R:1048:5', 'test-Waterfall-class.R:1062:5',
  'test-Waterfall-class.R:1076:5', 'test-Waterfall-class.R:1105:5',
  'test-Waterfall-class.R:1122:5'

[ FAIL 0 | WARN 9 | SKIP 54 | PASS 510 ]
Deleting unused snapshots:
• Lolliplot-class/drawplot-lolliplot.svg
• Lolliplot-class/final-lolliplot-alter-section-height.svg
• Lolliplot-class/final-lolliplot-base.svg
• Lolliplot-class/lolliplot-density-plot-layer.svg
• Lolliplot-class/lolliplot-density-plot.svg
• Lolliplot-class/lolliplot-plot-base-add-domain-palette.svg
• Lolliplot-class/lolliplot-plot-base-add-labels.svg
• Lolliplot-class/lolliplot-plot-base-add-layer.svg
• Lolliplot-class/lolliplot-plot-base-add-mutation-palette.svg
• Lolliplot-class/lolliplot-plot-base.svg
• MutSpectra-class/drawplot-mutspectra.svg
• MutSpectra-class/final-mutspectra-alter-section-heights.svg
• MutSpectra-class/final-mutspectra-base.svg
• MutSpectra-class/mutspectra-clinical.svg
• MutSpectra-class/mutspectra-frequency-plot-add-layer.svg
• MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-frequency-plot.svg
• MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
• MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-proportion-plot.svg
• Rainfall-class/density-main-plot.svg
• Rainfall-class/density-plot-add-layer.svg
• Rainfall-class/drawplot-rainfall.svg
• Rainfall-class/final-rainfall-alter-section-hieghts.svg
• Rainfall-class/final-rainfall-base.svg
• Rainfall-class/rainfall-main-plot.svg
• Rainfall-class/rainfall-plot-add-layer.svg
• Rainfall-class/rainfall-plot-aesthetic-options.svg
• Waterfall-class/addgene-waterfall.svg
• Waterfall-class/drawplot-waterfall.svg
• Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
• Waterfall-class/final-waterfall-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg
• Waterfall-class/final-waterfall-and-top-sub-plot.svg
• Waterfall-class/final-waterfall-base.svg
• Waterfall-class/gene-plot-add-layers.svg
• Waterfall-class/gene-plot-frequency-complex.svg
• Waterfall-class/gene-plot-frequency-simple.svg
• Waterfall-class/gene-plot-proportion-complex.svg
• Waterfall-class/gene-plot-proportion-simple.svg
• Waterfall-class/main-waterfall-add-layers.svg
• Waterfall-class/main-waterfall-plot-base.svg
• Waterfall-class/main-waterfall-plot-drop-true.svg
• Waterfall-class/main-waterfall-plot-grid-true.svg
• Waterfall-class/main-waterfall-plot-label.svg
• Waterfall-class/main-waterfall-plot-samplenames-false.svg
• Waterfall-class/main-waterfall-plot-xtitle-false.svg
• Waterfall-class/mutation-plot-add-layers.svg
• Waterfall-class/mutation-plot-burden-complex.svg
• Waterfall-class/mutation-plot-burden-simple.svg
• Waterfall-class/mutation-plot-frequency-complex.svg
• Waterfall-class/mutation-plot-frequency-simple.svg
> 
> proc.time()
   user  system elapsed 
 86.650   4.231 109.814