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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recoup_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/recoup.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* 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 ‘recoup/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘recoup’ version ‘1.35.0’
* 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 ‘recoup’ 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
Unexported objects imported by ':::' calls:
  ‘biomaRt:::.generateFilterXML’ ‘biomaRt:::.setResultColNames’
  ‘biomaRt:::martCheck’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘biomaRt:::martVSchema’ ‘txdbmaker:::GFF_FEATURE_TYPES’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘makeHorizontalAnnotation’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readBamIntervals: no visible binding for global variable ‘bam.file’
recoupCorrelation: no visible binding for global variable ‘Index’
recoupCorrelation: no visible binding for global variable ‘Coverage’
recoupCorrelation: no visible binding for global variable ‘Condition’
recoupCorrelation: no visible binding for global variable ‘Design’
recoupHeatmap : <anonymous>: no visible global function definition for
  ‘grid.text’
recoupProfile: no visible binding for global variable ‘Signal’
recoupProfile: no visible binding for global variable ‘Condition’
recoupProfile: no visible binding for global variable ‘Design’
Undefined global functions or variables:
  Condition Coverage Design Index Signal bam.file grid.text
* checking Rd files ... NOTE
checkRd: (-1) recoup.Rd:210-211: Lost braces
   210 |     \code{region}{Minimum flank is 0bp and maximum is
       |                  ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coverageRef.Rd: makeGRangesFromDataFrame
  recoup.Rd: GRanges, findOverlaps, ggplot, Heatmap,
    makeGRangesFromDataFrame
  recoupPlot.Rd: draw
  rpMatrix.Rd: makeGRangesFromDataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... ERROR
Running examples in ‘recoup-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAnnotation
> ### Title: Annotation downloader
> ### Aliases: getAnnotation
> 
> ### ** Examples
> 
>     mm10.genes <- getAnnotation("mm10","gene")
Using Ensembl host https://aug2020.archive.ensembl.org
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─recoup::getAnnotation("mm10", "gene")
  2.   └─recoup:::getEnsemblAnnotation(org, type, ver)
  3.     └─biomaRt::useMart(biomart = dat, host = host, dataset = getDataset(org))
  4.       └─biomaRt:::.useMart(...)
  5.         └─biomaRt:::.listMarts(...)
  6.           └─biomaRt:::bmRequest(...)
  7.             └─httr2::req_perform(request)
  8.               └─httr2:::handle_resp(req, resp, error_call = error_call)
  9.                 └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 10.                   ├─rlang::catch_cnd(...)
 11.                   │ ├─rlang::eval_bare(...)
 12.                   │ ├─base::tryCatch(...)
 13.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 16.                   │ └─base::force(expr)
 17.                   └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
coverageRef 4.716  0.217   5.009
* 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: 1 ERROR, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/recoup.Rcheck/00check.log’
for details.