##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:xenLite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings xenLite_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/xenLite.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* 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 ‘xenLite/DESCRIPTION’ ... OK
* this is package ‘xenLite’ version ‘1.1.0’
* 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 ‘xenLite’ 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 ... NOTE
e2sym: no visible binding for global variable ‘e79sym’
plotXenGgprep: no visible binding for global variable ‘vertex_x’
plotXenGgprep: no visible binding for global variable ‘vertex_y’
plotXenGgprep: no visible binding for global variable ‘cell_id’
plotXenGgprep: no visible binding for global variable ‘sizq’
Undefined global functions or variables:
  cell_id e79sym sizq vertex_x vertex_y
* 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 ... ERROR
Running examples in ‘xenLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cacheMtif
> ### Title: cache and/or retrieve path to an ome.tif file for demonstration
> ### Aliases: cacheMtif
> 
> ### ** Examples
> 
> pa <- cacheMtif()
Warning: download failed
  web resource path: ‘https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/morphology_focus_0001.ome.tif’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a5e15e966ce3_morphology_focus_0001.ome.tif’
  reason: Timeout was reached [mghp.osn.xsede.org]: Connection timed out after 10001 milliseconds
Warning: bfcadd() failed; resource removed
  rid: BFC2581
  fpath: ‘https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/morphology_focus_0001.ome.tif’
  reason: download failed
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
Calls: cacheMtif -> bfcadd -> bfcadd -> .util_download
Execution halted
* 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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/xenLite.Rcheck/00check.log’
for details.