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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_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GSgalgoR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GSgalgoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSgalgoR’ version ‘1.20.0’
* 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              4.007  0.168   7.638
callback_base_report     2.503  0.390   8.373
to_dataframe             2.796  0.078   6.734
to_list                  2.748  0.109   7.121
classify_multiple        2.340  0.164   8.175
create_centroids         2.450  0.037   6.360
non_dominated_summary    1.909  0.305   5.602
callback_default         1.946  0.204   7.867
galgo                    1.954  0.055   5.803
callback_base_return_pop 1.874  0.104   7.832
callback_no_report       1.801  0.157   7.779
* 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:237-252 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GSgalgoR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GSgalgoR’ ...
** this is package ‘GSgalgoR’ version ‘1.20.0’
** 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 (GSgalgoR)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GSgalgoR)
> 
> test_check("GSgalgoR")
..........         k                      rnkIndex   CrowD
result.1 8 0.02212350 201.10126        1     Inf
result.3 9 0.02402496 160.41638        1 1.37352
result.4 8 0.03651880  48.37265        1     Inf
         k                      rnkIndex    CrowD
result.1 8 0.02212350 201.10126        1      Inf
result.3 2 0.11803624  30.01863        1      Inf
result.4 4 0.04509859 173.43985        1 1.798893
......[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 19.081   2.658  86.648