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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geomeTriD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geomeTriD_1.2.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/geomeTriD.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geomeTriD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geomeTriD’ version ‘1.2.2’
* 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 ‘geomeTriD’ 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 ... 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
mdsPlot         8.900  0.115  10.110
loopBouquetPlot 6.322  0.169   6.915
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL geomeTriD
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘geomeTriD’ ...
** this is package ‘geomeTriD’ version ‘1.2.2’
** 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 (geomeTriD)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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.

> options(rgl.useNULL=TRUE)
> require("geomeTriD") || stop("unable to load Package:geomeTriD")
Loading required package: geomeTriD
[1] TRUE
> require(rgl) || stop("unable to load rgl")
Loading required package: rgl
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> 
> x <- readRDS(system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds",
+   package = "geomeTriD"
+ ))
> gi <- readRDS(system.file("extdata", "gi.rds", package = "trackViewer"))
> test_check("geomeTriD")
[ FAIL 0 | WARN 20 | SKIP 3 | PASS 92 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_create3dGenomicSignals.R:1:1',
  'test_signalCalculation.R:1:1', 'test_signalCalculation.R:23:1'

[ FAIL 0 | WARN 20 | SKIP 3 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
 98.271   2.832 109.264