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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:drugfindR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings drugfindR_0.99.2516.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/drugfindR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘drugfindR/DESCRIPTION’ ... OK
* this is package ‘drugfindR’ version ‘0.99.2516’
* 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 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 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 3.68  0.201  42.572
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: 'new_response' is not an exported object from 'namespace:httr2'
  Backtrace:
      ▆
   1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:631:5
   2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
  ── Error ('test-getConcordants.R:794:5'): getConcordants with DataFrame handles empty results ──
  Error: 'new_response' is not an exported object from 'namespace:httr2'
  Backtrace:
      ▆
   1. └─drugfindR:::getTestFixture("empty_ilincs_response") at test-getConcordants.R:794:5
   2.   └─drugfindR:::createEmptyIlincsResponse() at tests/testthat/helpers.R:223:5
  
  [ FAIL 20 | WARN 0 | SKIP 56 | PASS 603 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/drugfindR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL drugfindR
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘drugfindR’ ...
** this is package ‘drugfindR’ version ‘0.99.2516’
** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 20 | WARN 0 | SKIP 56 | PASS 603 ]

══ 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-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-getConcordants.R:676:5',
  'test-getConcordants.R:716:5', 'test-getConcordants.R:754:5',
  '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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-consensusConcordants.R:129:5'): .validateConsensusConcordantsInput validates dataframe content ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. ├─drugfindR:::.processIlincsResponse(...) at test-consensusConcordants.R:129:5
 2. │ └─httr2::resp_status(response)
 3. │   └─httr2:::check_response(resp)
 4. │     └─httr2:::is_response(resp)
 5. └─drugfindR:::getTestFixture("empty_ilincs_response")
 6.   └─drugfindR:::createEmptyIlincsResponse() at tests/testthat/helpers.R:223:5
── Error ('test-getSignature.R:124:5'): .createSignatureRequest creates valid httr2 request object ──
Error in `req_get_url(request)`: could not find function "req_get_url"
── Error ('test-getSignature.R:152:13'): .createSignatureRequest works with different signature IDs ──
Error in `req_get_url(request)`: could not find function "req_get_url"
── Error ('test-getConcordants.R:181:5'): .generateIlincsRequest creates valid httr2 request object ──
Error in `req_get_url(request)`: could not find function "req_get_url"
── Error ('test-getConcordants.R:215:5'): .generateIlincsRequest works with different libraries ──
Error in `req_get_url(requestCP)`: could not find function "req_get_url"
Backtrace:
    ▆
 1. └─httr2::url_parse(req_get_url(requestCP)) at test-getConcordants.R:215:5
 2.   └─httr2:::check_string(url)
 3.     └─httr2:::.rlang_check_is_string(...)
 4.       └─rlang::is_string(x)
── Error ('test-getConcordants.R:314:5'): .processIlincsResponse handles successful responses correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:314:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:338:5'): .processIlincsResponse handles CP library responses correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:338:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:354:5'): .processIlincsResponse rounds numerical values correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:354:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:370:5'): .processIlincsResponse handles different signature directions ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:370:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:379:5'): .processIlincsResponse handles empty concordance tables ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture("empty_ilincs_response", seed = .testSeed) at test-getConcordants.R:379:5
 2.   └─drugfindR:::createEmptyIlincsResponse() at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:392:5'): .processIlincsResponse handles 400 errors correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture("error_ilincs_response_400", seed = .testSeed) at test-getConcordants.R:392:5
 2.   └─drugfindR:::createIlincsErrorResponse400() at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:407:5'): .processIlincsResponse handles 500 errors correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture("error_ilincs_response_500", seed = .testSeed) at test-getConcordants.R:407:5
 2.   └─drugfindR:::createIlincsErrorResponse500() at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:472:5'): .processIlincsResponseSuccess handles CP library correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:472:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:507:5'): .processIlincsResponseSuccess handles KD library correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:507:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:530:5'): .processIlincsResponseSuccess handles OE library correctly ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:530:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:553:5'): .processIlincsResponse dispatcher works correctly for success case ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:553:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:565:5'): .processIlincsResponse dispatcher works correctly for empty case ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture("empty_ilincs_response", seed = .testSeed) at test-getConcordants.R:565:5
 2.   └─drugfindR:::createEmptyIlincsResponse() at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:580:5'): .processIlincsResponse dispatcher works correctly for error case ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-getConcordants.R:580:5
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. ├─drugfindR:::.processIlincsResponse(...)
  8. │ └─httr2::resp_status(response)
  9. │   └─httr2:::check_response(resp)
 10. │     └─httr2:::is_response(resp)
 11. └─drugfindR:::getTestFixture("error_ilincs_response_400")
 12.   └─drugfindR:::createIlincsErrorResponse400() at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:631:5'): getConcordants accepts S4Vectors::DataFrame as input and returns DataFrame ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture(...) at test-getConcordants.R:631:5
 2.   └─drugfindR:::createValidIlincsResponse(seed = seed, ...) at tests/testthat/helpers.R:223:5
── Error ('test-getConcordants.R:794:5'): getConcordants with DataFrame handles empty results ──
Error: 'new_response' is not an exported object from 'namespace:httr2'
Backtrace:
    ▆
 1. └─drugfindR:::getTestFixture("empty_ilincs_response") at test-getConcordants.R:794:5
 2.   └─drugfindR:::createEmptyIlincsResponse() at tests/testthat/helpers.R:223:5

[ FAIL 20 | WARN 0 | SKIP 56 | PASS 603 ]
Error: Test failures
Execution halted