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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singIST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singIST_0.99.85.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/singIST.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singIST/DESCRIPTION’ ... OK
* this is package ‘singIST’ version ‘0.99.85’
* 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 ‘singIST’ 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 whether startup messages can be suppressed ... 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
singIST_treat 3.87  0.213  13.286
helpers       3.03  0.252  19.948
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singIST
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘singIST’ ...
** this is package ‘singIST’ version ‘0.99.85’
** 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 (singIST)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(singIST)
> 
> test_check("singIST")
[ FAIL 0 | WARN 0 | SKIP 25 | PASS 12 ]

══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test-CIP_GIP.R:2:5', 'test-asmbPLSDAcvloo.R:2:5',
  'test-biological_link_function.R:2:5', 'test-celltype_mapping.R:2:5',
  'test-celltype_recap.R:2:5', 'test-derive_contributions.R:2:5',
  'test-derive_scores.R:2:5', 'test-diff_expressed.R:2:5',
  'test-gene_contrib.R:2:5', 'test-hyperparameters.R:2:5',
  'test-mappingorganism.R:2:5', 'test-matrixToBlock.R:2:5',
  'test-multiple_check.R:2:5', 'test-multiple_fitOptimal.R:2:5',
  'test-multiple_singISTrecapitulations.R:2:5', 'test-orthology_mapping.R:2:5',
  'test-pathway.R:2:5', 'test-permut_asmbplsda.R:2:5',
  'test-setGeneSetsCelltype.R:2:5', 'test-singIST_treat.R:2:5',
  'test-singISTrecapitulations.R:2:5', 'test-superpathway_recap.R:2:5',
  'test-superpathwayfitmodel.R:2:5', 'test-superpathwayinput.R:2:5',
  'test-wilcox_CIP_GIP.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 25 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  7.446   0.514   8.532