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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:crumblr.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings crumblr_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-22 03:31:21 UTC
* checking for file ‘crumblr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crumblr’ version ‘1.5.0’
* 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 ‘crumblr’ 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
diffTree           30.657  0.521  31.179
plotForest-methods 15.685  0.237  15.923
treeTest           15.163  0.033  15.196
plotTreeTestBeta   14.690  0.126  14.817
plotTreeTest       14.165  0.043  14.209
* 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 ‘crumblr.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_files/figure-html/vp-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_files/figure-html/pca-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_files/figure-html/hclust-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_files/figure-html/treeTest-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_files/figure-html/treeTest-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_files/figure-html/combined-1.png" but not available.
--- finished re-building ‘crumblr.Rmd’

--- re-building ‘crumblr_theory.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_theory_files/figure-html/plot1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/vign_test/crumblr/vignettes/crumblr_theory_files/figure-html/plot2-1.png" but not available.
--- finished re-building ‘crumblr_theory.Rmd’

--- re-building ‘integration.Rmd’ using rmarkdown

Quitting from integration.Rmd:45-70 [preprocess.data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─ExperimentHub::ExperimentHub()
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'integration.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘integration.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/crumblr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL crumblr
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘crumblr’ ...
** this is package ‘crumblr’ version ‘1.5.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (crumblr)