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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OGRE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OGRE_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OGRE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OGRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OGRE’ version ‘1.4.0’
* 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 ‘OGRE’ 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 ... ERROR
Running examples in ‘OGRE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gvizPlot
> ### Title: Generate Gviz plot
> ### Aliases: gvizPlot
> 
> ### ** Examples
> 
> myOGRE <- makeExampleOGREDataSet()
Initializing OGREDataSet... 
> myOGRE <- loadAnnotations(myOGRE)
Reading query dataset... 
Reading subject datasets... 
> myOGRE <- fOverlaps(myOGRE)
> myOGRE <- gvizPlot(myOGRE,query="ENSG00000142168")
Plotting query: ENSG00000142168
Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
Calls: gvizPlot ... browserSession -> new -> initialize -> initialize -> .local
Execution halted
* 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:
   13.             │ ├─BiocGenerics::eval(expression, envir = callEnv)
   14.             │ └─base::eval(expression, envir = callEnv)
   15.             │   └─base::eval(expression, envir = callEnv)
   16.             ├─rtracklayer::browserSession()
   17.             └─rtracklayer::browserSession()
   18.               ├─rtracklayer::browserSession("UCSC", ...)
   19.               └─rtracklayer::browserSession("UCSC", ...)
   20.                 └─methods::new(class, ...)
   21.                   ├─methods::initialize(value, ...)
   22.                   └─rtracklayer::initialize(value, ...)
   23.                     └─rtracklayer (local) .local(.Object, ...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OGRE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OGRE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘OGRE’ ...
** 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 (OGRE)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(OGRE)
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

> 
> test_check("OGRE")
Initializing OGREDataSet... 
Initializing OGREDataSet... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
loading from cache
require("GenomicRanges")
Added protCodingGenes
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Plotting query: ENSG00000142168
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
2023-10-18 12:14:19.411 R[31994:43960077] XType: com.apple.fonts is not accessible.
2023-10-18 12:14:19.411 R[31994:43960077] XType: XTFontStaticRegistry is enabled.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_gvizPlot.R:5:2'): Check class of gvizPlot ──────────────────────
Error in `.local(.Object, ...)`: Failed to obtain 'hguid' cookie
Backtrace:
     ▆
  1. └─OGRE::gvizPlot(myOGRE, query = "ENSG00000142168") at test_gvizPlot.R:5:1
  2.   └─Gviz::IdeogramTrack(genome = "hg38", chromosome = chr)
  3.     └─methods::new(...)
  4.       ├─methods::initialize(value, ...)
  5.       └─Gviz::initialize(value, ...)
  6.         └─Gviz (local) .local(.Object, ...)
  7.           └─Gviz:::.cacheGenomes(genome = genome)
  8.             ├─Gviz::.doCache(...)
  9.             │ ├─BiocGenerics::eval(expression, envir = callEnv)
 10.             │ └─base::eval(expression, envir = callEnv)
 11.             │   └─base::eval(expression, envir = callEnv)
 12.             ├─Gviz::.doCache(...)
 13.             │ ├─BiocGenerics::eval(expression, envir = callEnv)
 14.             │ └─base::eval(expression, envir = callEnv)
 15.             │   └─base::eval(expression, envir = callEnv)
 16.             ├─rtracklayer::browserSession()
 17.             └─rtracklayer::browserSession()
 18.               ├─rtracklayer::browserSession("UCSC", ...)
 19.               └─rtracklayer::browserSession("UCSC", ...)
 20.                 └─methods::new(class, ...)
 21.                   ├─methods::initialize(value, ...)
 22.                   └─rtracklayer::initialize(value, ...)
 23.                     └─rtracklayer (local) .local(.Object, ...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
Error: Test failures
Execution halted