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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:XINA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings XINA_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/XINA.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘XINA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XINA’ version ‘1.28.0’
* 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 ‘XINA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘mclust::count’ by ‘plyr::count’ when loading ‘XINA’
See ‘/home/biocbuild/bbs-3.22-bioc/meat/XINA.Rcheck/00install.out’ for details.
* 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
Non-topic package-anchored link(s) in Rd file 'xina_enrichment.Rd':
  ‘[STRINGdb]{get_enrichment}’

Non-topic package-anchored link(s) in Rd file 'xina_plot_single.Rd':
  ‘[base]{Round}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
xina_clustering                   19.760  0.095  19.855
plot_condition_compositions       16.978  0.004  16.984
plot_clusters                     10.586  0.004  10.592
mutate_colors                     10.402  0.060  10.462
get_condition_biased_comigrations  6.043  0.074   6.117
xina_plot_all                      5.023  0.142   5.159
* 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 ‘xina_user_code.Rmd’ using rmarkdown

Quitting from xina_user_code.Rmd:118-121 [XINA clustering]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `svd()`:
! infinite or missing values in 'x'
---
Backtrace:
     ▆
  1. └─XINA::xina_clustering(...)
  2.   ├─mclust::Mclust(superset[data_column], G = 2:nClusters)
  3.   │ └─base::eval(mc, parent.frame())
  4.   │   └─base::eval(mc, parent.frame())
  5.   └─mclust::mclustBIC(data = `<dbl>`, G = 2:nClusters)
  6.     ├─mclust::me(...)
  7.     │ └─base::eval(mc, parent.frame())
  8.     │   └─base::eval(mc, parent.frame())
  9.     └─mclust::meVEE(...)
 10.       └─base::svd(shape.o, nu = 0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'xina_user_code.Rmd' failed with diagnostics:
infinite or missing values in 'x'
--- failed re-building ‘xina_user_code.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL XINA
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘XINA’ ...
** this is package ‘XINA’ version ‘1.28.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘mclust::count’ by ‘plyr::count’ when loading ‘XINA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘mclust::count’ by ‘plyr::count’ when loading ‘XINA’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘mclust::count’ by ‘plyr::count’ when loading ‘XINA’
** testing if installed package keeps a record of temporary installation path
* DONE (XINA)