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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings nipalsMCIA_1.3.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.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 ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘1.3.1’
* 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 ‘nipalsMCIA’ 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
block_weights_heatmap          7.369  0.162   7.531
nipals_multiblock              7.348  0.024   7.373
projection_plot                6.031  0.004   6.035
vis_load_plot                  5.758  0.009   5.798
vis_load_ord                   5.514  0.019   5.534
global_scores_eigenvalues_plot 5.404  0.081   5.486
ord_loadings                   5.434  0.020   5.453
get_colors                     5.361  0.065   5.427
get_metadata_colors            5.345  0.006   5.353
* 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 ‘Analysis-of-MCIA-Decomposition.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-1-mcia-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-1-visualize-clusters-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-1-visualize-clusters-color-col-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-1-global-heatmap-colored-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-2-block-heatmap-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-2-loadings-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-2-factor-1-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-2-factor-2-1.jpeg" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Analysis-of-MCIA-Decomposition_files/figure-html/part-2-factor-4-1.jpeg" but not available.
--- finished re-building ‘Analysis-of-MCIA-Decomposition.Rmd’

--- re-building ‘Predicting-New-Scores.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/vign_test/nipalsMCIA/vignettes/Predicting-New-Scores_files/figure-html/visualize-training-model-1.jpeg" but not available.
Warning in file("", "w+b") :
  cannot open file '/tmp/Rtmpp4lgzE/Rf190ab83b9ae450': No space left on device

Quitting from lines 130-132 [generate-new-scores] (Predicting-New-Scores.Rmd)
Error: processing vignette 'Predicting-New-Scores.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Predicting-New-Scores.Rmd’

Warning in gzfile(file, mode) :
  cannot open compressed file '/tmp/Rtmp1Pmv0O/file18f6a1255ea3b6.rds', probable reason 'No space left on device'
Error in gzfile(file, mode) : cannot open the connection
Calls: <Anonymous> -> saveRDS -> gzfile
Execution halted

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Fatal error: cannot create 'R_TempDir'
* DONE

Status: 2 ERRORs, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck/00check.log’
for details.