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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘decoupleR’ 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 ... NOTE
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 00:34:43] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Contains 8 files.
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 00:34:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 00:34:43] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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 ... WARNING
Missing link or links in Rd file 'run_gsva.Rd':
  ‘GSVA::gsva’ ‘GeneSetCollection’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
run_fgsea     8.335  0.024   8.360
get_dorothea  6.600  0.118   9.697
get_progeny   2.673  0.129  10.725
get_collectri 1.929  0.105   7.634
* 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:
  [120] 0.112          | 0.112            [120]
  [121] 0.991          - 1.000            [121]
  [122] 0.991          - 1.000            [122]
  [123] 0.123          - 0.126            [123]
  [124] 0.123          - 0.126            [124]
  [125] 0.156          | 0.156            [125]
  [126] 0.156          | 0.156            [126]
  [127] 0.592          | 0.592            [127]
  
    `actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
  `expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
  
  [ FAIL 1 | WARN 9 | SKIP 0 | PASS 34 ]
  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, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck/00check.log’
for details.