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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaseqR2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings metaseqR2_1.19.1.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'metaseqR2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaseqR2' version '1.19.1'
* 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 whether package 'metaseqR2' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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
getUcscUtr: no visible binding for global variable 'customDir'
Undefined global functions or variables:
  customDir
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  metaseqr2.Rd: render
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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'metaseqR2-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAnnotation
> ### Title: Annotation downloader
> ### Aliases: getAnnotation
> 
> ### ** Examples
> 
> mm10Genes <- getAnnotation("mm10","gene")
Using Ensembl host https://jan2024.archive.ensembl.org
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─metaseqR2::getAnnotation("mm10", "gene")
  2.   └─metaseqR2:::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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  1 Test Suite : 
  metaseqR2 RUnit Tests - 2 test functions, 1 error, 0 failures
  ERROR in test_estimate_aufc_weights: Error in req_perform(request) : HTTP 500 Internal Server Error.
  
  Test files with failing tests
  
     test_estimate_aufc_weights.R 
       test_estimate_aufc_weights 
  
  
  Error in BiocGenerics:::testPackage("metaseqR2") : 
    unit tests failed for package metaseqR2
  In addition: Warning message:
  The column that contains the gene biotypes ("embedCols$btCol") is missing with embedded annotation! Biotype filters and certain plots will not be available... 
  Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck/00check.log'
for details.