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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BioPlex_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/BioPlex.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BioPlex/DESCRIPTION’ ... OK
* this is package ‘BioPlex’ version ‘1.14.0’
* 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 ‘BioPlex’ 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
getCorum: no visible binding for global variable ‘Organism’
Undefined global functions or variables:
  Organism
* 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:
  annotatePFAM.Rd: graph-class, nodeData
  bioplex2graph.Rd: ftM2graphNEL
  ccleProteome2SummarizedExperiment.Rd: SummarizedExperiment-class
  getBioplexProteome.Rd: SummarizedExperiment-class
  getGSE122425.Rd: SummarizedExperiment-class
  mapSummarizedExperimentOntoGraph.Rd: SummarizedExperiment-class,
    graph-class
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
ccleProteome2SummarizedExperiment 35.108  0.939  36.288
annotatePFAM                      14.954  1.042  17.642
hasSubunit                         6.566  0.116   6.902
bioplex2graph                      6.192  0.356   6.585
mapSummarizedExperimentOntoGraph   6.279  0.079   6.433
corum2graphlist                    5.792  0.213   6.116
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘BasicChecks.Rmd’ using rmarkdown

Quitting from BasicChecks.Rmd:370-374 [bp.prot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Stream error in the HTTP/2 framing layer [bioplex.hms.harvard.edu]:
HTTP/2 stream 3 was not closed cleanly: CANCEL (err 8)
---
Backtrace:
     ▆
  1. ├─BioPlex::getBioplexProteome()
  2. │ └─BioPlex:::.getResourceFromCache2(rname, FUN = .bp2se)
  3. │   ├─BiocFileCache::bfcneedsupdate(bfc, rid)
  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(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BasicChecks.Rmd' failed with diagnostics:
Stream error in the HTTP/2 framing layer [bioplex.hms.harvard.edu]:
HTTP/2 stream 3 was not closed cleanly: CANCEL (err 8)
--- failed re-building ‘BasicChecks.Rmd’

--- re-building ‘BioPlex.Rmd’ using rmarkdown
--- finished re-building ‘BioPlex.Rmd’

SUMMARY: processing the following file failed:
  ‘BasicChecks.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/BioPlex.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BioPlex
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘BioPlex’ ...
** this is package ‘BioPlex’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (BioPlex)