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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:glmSparseNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings glmSparseNet_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/glmSparseNet.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-15 22:31:41 UTC
* using option ‘--no-vignettes’
* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘glmSparseNet’ version ‘1.29.0’
* 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 ‘glmSparseNet’ 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 whether startup messages can be suppressed ... 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 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 ‘glmSparseNet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .biomartLoad
> ### Title: Common call to biomaRt to avoid repetitive code
> ### Aliases: .biomartLoad
> 
> ### ** Examples
> 
> glmSparseNet:::.biomartLoad(
+     attributes = c("external_gene_name", "ensembl_gene_id"),
+     filters = "external_gene_name",
+     values = c("MOB1A", "RFLNB", "SPIC", "TP53"),
+     useCache = TRUE,
+     verbose = FALSE
+ )
Warning in .curlWorkaround(.runCache(biomaRt::useEnsembl, biomart = "genes",  :
  There was an problem, calling the function with ssl_verifypeer to FALSE

	: HTTP 500 Internal Server Error.
Warning in force(expr) : restarting interrupted promise evaluation
Error in `httr2::req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─glmSparseNet:::.biomartLoad(...)
  2.   ├─glmSparseNet:::.curlWorkaround(...)
  3.   │ └─httr::with_config(...)
  4.   │   └─base::force(expr)
  5.   ├─glmSparseNet:::.runCache(...)
  6.   └─glmSparseNet:::.runCache(...)
  7.     └─glmSparseNet:::.calculateResult(...)
  8.       └─biomaRt (local) fun(...)
  9.         └─biomaRt:::.listEnsembl(version = version, GRCh = GRCh, mirror = mirror)
 10.           └─biomaRt:::getCurrentEnsemblRelease()
 11.             ├─base::unlist(httr2::resp_body_json(httr2::req_perform(req)))
 12.             ├─httr2::resp_body_json(httr2::req_perform(req))
 13.             │ └─httr2:::check_response(resp)
 14.             │   └─httr2:::is_response(resp)
 15.             └─httr2::req_perform(req)
 16.               └─httr2:::handle_resp(req, resp, error_call = error_call)
 17.                 └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 18.                   ├─rlang::catch_cnd(...)
 19.                   │ ├─rlang::eval_bare(...)
 20.                   │ ├─base::tryCatch(...)
 21.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 22.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 23.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 24.                   │ └─base::force(expr)
 25.                   └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
cv.glmSparseNet 5.337  0.144   5.487
* 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:
  > test_check("glmSparseNet")
  Saving _problems/test-download-13.R
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 214 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (2): 'test-cache.R:38:1', 'test-cache.R:62:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-download.R:10:5'): downloadFileLocal: Detects when download is size 0 ──
  Expected `downloadFileLocal("https://string-db.org/api/tsv-no-header/version")` to produce output.
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 214 ]
  Error:
  ! Test failures.
  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
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/glmSparseNet.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL glmSparseNet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘glmSparseNet’ ...
** this is package ‘glmSparseNet’ version ‘1.29.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (glmSparseNet)

R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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(glmSparseNet)
> 
> test_check("glmSparseNet")
Saving _problems/test-download-13.R
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 214 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-cache.R:38:1', 'test-cache.R:62:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-download.R:10:5'): downloadFileLocal: Detects when download is size 0 ──
Expected `downloadFileLocal("https://string-db.org/api/tsv-no-header/version")` to produce output.

[ FAIL 1 | WARN 0 | SKIP 2 | PASS 214 ]
Error:
! Test failures.
Execution halted