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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_2.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.13.0’
* 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
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 21:18:34] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Contains 8 files.
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 21:18:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-27 21:18:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 21:18:34] [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(s) in Rd file 'run_gsva.Rd':
  ‘GSVA::gsva’ ‘GeneSetCollection’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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     18.437  0.121  18.656
get_dorothea  17.492  0.416  20.793
run_aucell     7.218  0.466   7.760
get_progeny    5.141  0.461  13.021
get_collectri  4.786  0.336  10.290
* 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:
   55. │   ├─rlang::exec(...)
   56. │   └─OmnipathR (local) `<fn>`(...)
   57. ├─OmnipathR:::load_success(.)
   58. │ └─from_cache %<>% if_null(data %>% is_from_cache)
   59. ├─OmnipathR:::if_null(., data %>% is_from_cache)
   60. │ └─value1 %>% is.null %>% if (value2) value1
   61. ├─data %>% is_from_cache
   62. ├─OmnipathR:::is_from_cache(.)
   63. │ └─obj %>% attr("origin") %>% ...
   64. └─OmnipathR::omnipath_cache_save(., url = url, post = post)
   65.   └─base::saveRDS(data, target_path)
  
  [ 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-3.21-bioc/meat/decoupleR.Rcheck/00check.log’
for details.