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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmicsMLRepoR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmicsMLRepoR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmicsMLRepoR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmicsMLRepoR’ version ‘1.0.0’
* 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 ‘OmicsMLRepoR’ 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 loading without being on the library search path ... 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
.getAllTargetForms: no visible binding for global variable ‘.’
.getOntos: no visible binding for global variable ‘.’
ontoTreePlot: no visible binding for global variable ‘iri’
ontoTreePlot: no visible binding for global variable ‘text’
ontoTreePlot: no visible binding for global variable ‘parent’
ontoTreePlot: no visible binding for global variable ‘from’
ontoTreePlot: no visible binding for global variable ‘to’
Undefined global functions or variables:
  . from iri parent text to
Consider adding
  importFrom("graphics", "text")
to your NAMESPACE file.
* 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 ‘OmicsMLRepoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMetadata
> ### Title: Download a harmonized metadata table
> ### Aliases: getMetadata
> 
> ### ** Examples
> 
> cmd <- getMetadata("cMD")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [zenodo.org]: Failed to connect to zenodo.org port 443 after 10001 ms: Timeout was reached
Calls: getMetadata ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
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:
    4. │   └─BiocFileCache::bfcneedsupdate(bfc, rid)
    5. │     └─base::vapply(rids, helper, logical(1), x = x)
    6. │       └─BiocFileCache (local) FUN(X[[i]], ...)
    7. │         └─BiocFileCache:::.httr_get_cache_info(fpath)
    8. │           ├─base::withCallingHandlers(...)
    9. │           └─httr::HEAD(link)
   10. │             └─httr:::request_perform(req, hu$handle$handle)
   11. │               ├─httr:::request_fetch(req$output, req$url, handle)
   12. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   13. │                 └─curl::curl_fetch_memory(url, handle = handle)
   14. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 19 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmicsMLRepoR.Rcheck/00check.log’
for details.