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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GSgalgoR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GSgalgoR_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GSgalgoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSgalgoR’ version ‘1.19.0’
* 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 ‘GSgalgoR’ 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  galgo.Rd: survival
  non_dominated_summary.Rd: survival
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
plot_pareto              2.649  0.077   6.082
callback_base_report     2.473  0.137   8.531
callback_default         2.112  0.401   7.988
classify_multiple        2.244  0.155   7.678
galgo                    1.960  0.218   5.388
callback_base_return_pop 1.792  0.369   7.768
create_centroids         2.079  0.044   5.244
to_dataframe             1.930  0.177   5.574
non_dominated_summary    1.755  0.182   5.192
to_list                  1.783  0.134   5.372
callback_no_report       1.687  0.153   7.447
* 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 ‘GSgalgoR.rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/plot_pareto-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/plot_pareto-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/pam50_surv_UPP-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/pam50_surv_TRANSBIG-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/pareto_2-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/pareto_2-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/galgo_train_surv-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/galgo_test_surv-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/vign_test/GSgalgoR/vignettes/GSgalgoR_files/figure-html/test_pam50-1.png" but not available.
--- finished re-building ‘GSgalgoR.rmd’

--- re-building ‘GSgalgoR_callbacks.rmd’ using rmarkdown

Quitting from GSgalgoR_callbacks.rmd:135-148 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sample.int()`:
! NA in probability vector
---
Backtrace:
    ▆
 1. └─GSgalgoR::galgo(...)
 2.   └─GSgalgoR:::offsprings(X1, chrom_length, population, TournamentSize)
 3.     └─GSgalgoR:::asymetric_mutation(off2)
 4.       └─base::sample(...)
 5.         └─base::sample.int(length(x), size, replace, prob)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GSgalgoR_callbacks.rmd' failed with diagnostics:
NA in probability vector
--- failed re-building ‘GSgalgoR_callbacks.rmd’

SUMMARY: processing the following file failed:
  ‘GSgalgoR_callbacks.rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck/00check.log’
for details.