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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BioPlex_1.16.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/BioPlex.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BioPlex/DESCRIPTION’ ... OK
* this is package ‘BioPlex’ version ‘1.16.1’
* 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 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 34.908  0.882  56.345
annotatePFAM                      14.959  1.313  36.619
hasSubunit                         6.543  0.120   6.899
corum2graphlist                    6.199  0.406  26.911
bioplex2graph                      6.312  0.214   7.320
mapSummarizedExperimentOntoGraph   6.095  0.151   6.617
getCorum                           2.041  0.095  12.423
corum2list                         1.833  0.096  22.140
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/BioPlex.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BioPlex
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BioPlex’ ...
** this is package ‘BioPlex’ version ‘1.16.1’
** 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)