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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FELLA_1.25.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.25.0’
* 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 ‘FELLA’ 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
buildGraphFromKEGGREST: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-params.Rd':
  ‘databaseDir’ ‘internalDir’ ‘object’ ‘data’ ‘type’ ‘level’ ‘method’
  ‘methods’ ‘approx’ ‘loadMatrix’ ‘threshold’
  ‘thresholdConnectedComponent’ ‘plimit’ ‘nlimit’ ‘niter’ ‘layout’
  ‘graph’ ‘GOterm’ ‘GONamesAsLabels’ ‘LabelLengthAtPlot’
  ‘godata.options’ ‘mart.options’ ‘p.adjust’ ‘dampingFactor’ ‘t.df’
  ‘compounds’ ‘compoundsBackground’ ‘NamesAsLabels’ ‘capPscores’

Documented arguments not in \usage in Rd file 'infere.con2ec.Rd':
  ‘gene2enyzme’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
data-funs 6.037  0.194   6.231
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘musmusculus.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.20-bioc/R/site
Warning: -library/BiocStyle/resources/tex/Bioconductor',
Warning:                but the package provides `Bioconductor'.
--- finished re-building ‘musmusculus.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-14-1.png" but not available.
--- finished re-building ‘quickstart.Rmd’

--- re-building ‘zebrafish.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.20-bioc/R/site
Warning: -library/BiocStyle/resources/tex/Bioconductor',
Warning:                but the package provides `Bioconductor'.
--- finished re-building ‘zebrafish.Rmd’

--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Available gene annotations: ncbi-geneid, ncbi-proteinid. Using ncbi-geneid
Done.
Building graph...
Filtering 5 pathways.
Done.
Pruning graph...
Current weight: 1 out of 4...
Current weight: 2 out of 4...
Current weight: 3 out of 4...
Current weight: 4 out of 4...
Done.
Computing probabilities for random subgraphs... (this may take a while)
Directory /tmp/Rtmps1yyBY/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)
Warning in asMethod(object) :
  sparse->dense coercion: allocating vector of size 1.1 GiB

Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
 chunk 3 (label = 01_database) 
Error in save(diffusion.matrix, file = paste0(outputDir, "/diffusion.matrix.RData")) : 
  error writing to connection

--- failed re-building ‘FELLA.Rnw’

SUMMARY: processing the following file failed:
  ‘FELLA.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/00check.log’
for details.