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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:drugfindR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings drugfindR_0.99.1349.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/drugfindR.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 ‘drugfindR/DESCRIPTION’ ... OK
* this is package ‘drugfindR’ version ‘0.99.1349’
* 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 ‘drugfindR’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
getConcordants 0.993  0.054  41.507
* 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 drugfindR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘drugfindR’ ...
** this is package ‘drugfindR’ version ‘0.99.1349’
** using staged installation
** R
** 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 (drugfindR)

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.

> # nolint start: unused_import_linter
> library(testthat)
> library(drugfindR)
> # nolint end
> 
> test_check("drugfindR")
Starting 2 test processes.
[ FAIL 0 | WARN 0 | SKIP 56 | PASS 699 ]

══ Skipped tests (56) ══════════════════════════════════════════════════════════
• Duplicate handling not implemented yet (2): 'test-prepareSignature.R:297:5',
  'test-prepareSignature.R:384:5'
• Have to figure out how to trigger 500 errors (1):
  'test-getConcordants.R:299:5'
• On CRAN (52): 'test-getConcordants.R:676:5', 'test-getConcordants.R:716:5',
  'test-getConcordants.R:754:5', 'test-investigateSignature.R:95:5',
  'test-investigateSignature.R:120:5', 'test-investigateSignature.R:141:5',
  'test-investigateSignature.R:165:5', 'test-investigateSignature.R:186:5',
  'test-investigateSignature.R:205:5', 'test-investigateSignature.R:214:5',
  'test-investigateSignature.R:222:5', 'test-investigateSignature.R:238:5',
  'test-investigateSignature.R:274:5', 'test-investigateSignature.R:300:5',
  'test-investigateSignature.R:328:5', 'test-investigateSignature.R:359:5',
  'test-investigateSignature.R:391:5', 'test-investigateSignature.R:414:5',
  'test-investigateSignature.R:437:5', 'test-investigateSignature.R:464:5',
  'test-investigateSignature.R:488:5', 'test-investigateSignature.R:516:5',
  'test-investigateSignature.R:530:5', 'test-investigateSignature.R:550:5',
  'test-investigateSignature.R:570:5', 'test-investigateTarget.R:48:5',
  'test-investigateTarget.R:75:5', 'test-investigateTarget.R:98:5',
  'test-investigateTarget.R:117:5', 'test-investigateTarget.R:136:5',
  'test-investigateTarget.R:169:5', 'test-investigateTarget.R:211:5',
  'test-investigateTarget.R:247:5', 'test-investigateTarget.R:275:5',
  'test-investigateTarget.R:282:5', 'test-investigateTarget.R:293:5',
  'test-investigateTarget.R:320:5', 'test-investigateTarget.R:354:5',
  'test-investigateTarget.R:375:5', 'test-investigateTarget.R:400:5',
  'test-investigateTarget.R:427:5', 'test-utilities.R:495:5',
  'test-utilities.R:519:5', 'test-utilities.R:543:5', 'test-utilities.R:557:5',
  'test-utilities.R:570:5', 'test-utilities.R:598:5', 'test-utilities.R:633:5',
  'test-utilities.R:668:5', 'test-utilities.R:701:5', 'test-utilities.R:724:5',
  'test-utilities.R:743:5'
• Verbose response config option is not testable right now (1):
  'test-getConcordants.R:273:5'

[ FAIL 0 | WARN 0 | SKIP 56 | PASS 699 ]
> 
> proc.time()
   user  system elapsed 
  7.745   0.815   5.927