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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dar_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘dar’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
step_aldex         18.426  3.080  22.771
step_deseq          6.620  0.096   6.742
step_metagenomeseq  3.659  0.079  11.050
prep                2.279  0.065  40.323
export_steps        1.684  0.208  14.377
import_steps        1.508  0.081  44.960
recipe              0.853  0.026  19.138
* 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 dar
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘dar’ ...
** this is package ‘dar’ version ‘1.4.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (dar)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.

> library(testthat)
> library(dar)
> 
> test_check("dar")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 81 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (9): 'test-roxytest-tests-bake.R:18:3',
  'test-roxytest-tests-lefse.R:15:3', 'test-roxytest-tests-misc.R:73:3',
  'test-roxytest-tests-misc.R:101:3', 'test-roxytest-tests-misc.R:108:3',
  'test-roxytest-tests-pkg_check.R:6:3', 'test-roxytest-tests-maaslin2.R:16:3',
  'test-roxytest-tests-read_data.R:24:3',
  'test-roxytest-tests-steps_and_checks.R:7:3'
• Temporary disabling due to problems with the ANCOM package (1):
  'test-roxytest-tests-ancom.R:6:3'

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 81 ]
> 
> proc.time()
   user  system elapsed 
218.396  14.006 313.904