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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CoSIA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CoSIA_1.10.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CoSIA.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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CoSIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoSIA’ version ‘1.10.1’
* 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 ‘CoSIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
plotCVGEx-CoSIAn-method      169.731  6.324 176.658
plotCVGEx                    166.992  6.179 173.973
plotSpeciesGEx                60.770  1.651  62.705
plotSpeciesGEx-CoSIAn-method  61.071  0.678  62.192
getTissues                    59.485  1.620  61.387
plotDSGEx                     58.359  0.964  59.610
plotDSGEx-CoSIAn-method       57.149  2.066  59.498
plotTissueGEx                 57.807  1.251  59.377
plotTissueGEx-CoSIAn-method   57.133  1.296  58.727
getGExMetrics                 12.408  0.525  13.216
getGExMetrics-CoSIAn-method   12.398  0.498  13.214
getGEx                        12.153  0.606  13.038
getGEx-CoSIAn-method          12.216  0.515  13.076
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CoSIA
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘CoSIA’ ...
** this is package ‘CoSIA’ version ‘1.10.1’
** 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 (CoSIA)