Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Work-around for bug (https://github.com/hadley/testthat/issues/144)
  > Sys.setenv("R_TESTS" = "")
  > 
  > # library 
  > library(testthat)
  > library(HTSSIP)
  > 
  > # test check
  > test_check('HTSSIP')
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  Failed with error:  'namespace 'S4Vectors' 0.30.2 is already loaded, but >= 0.33.7 is required'
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  Failed with error:  'namespace 'S4Vectors' 0.30.2 is already loaded, but >= 0.33.7 is required'
  Sparsity threshold: 0 
  Density window: 1.7-1.75 
  Failed with error:  'namespace 'S4Vectors' 0.30.2 is already loaded, but >= 0.33.7 is required'
  [ FAIL 3 | WARN 10 | SKIP 18 | PASS 102 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (17)
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-DESeq2_l2fc.R:2:3): DESeq2_l2fc runs with default params ────────
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: namespace 'S4Vectors' 0.30.2 is already loaded, but >= 0.33.7 is required
  Backtrace:
      ▆
   1. ├─HTSSIP::DESeq2_l2fc(...) at test-DESeq2_l2fc.R:2:2
   2. │ └─base::apply(DESeq2::counts(dds), 1, gm_mean)
   3. └─base::loadNamespace(x)
   4.   ├─base::namespaceImport(...)
   5.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   6.     ├─base::namespaceImport(...)
   7.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
  ── Error (test-DESeq2_l2fc.R:15:3): DESeq2_l2fc runs with sparsity_apply=heavy ──
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: namespace 'S4Vectors' 0.30.2 is already loaded, but >= 0.33.7 is required
  Backtrace:
      ▆
   1. ├─HTSSIP::DESeq2_l2fc(...) at test-DESeq2_l2fc.R:15:2
   2. │ └─base::apply(DESeq2::counts(dds), 1, gm_mean)
   3. └─base::loadNamespace(x)
   4.   ├─base::namespaceImport(...)
   5.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   6.     ├─base::namespaceImport(...)
   7.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
  ── Error (test-HRSIP.R:3:3): HRSIP runs with default ───────────────────────────
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: namespace 'S4Vectors' 0.30.2 is already loaded, but >= 0.33.7 is required
  Backtrace:
       ▆
    1. ├─HTSSIP::HRSIP(...) at test-HRSIP.R:3:2
    2. │ └─plyr::mdply(...)
    3. │   └─plyr::adply(...)
    4. │     └─plyr::ldply(...)
    5. │       └─plyr::llply(...)
    6. │         ├─plyr:::loop_apply(n, do.ply)
    7. │         └─plyr `<fn>`(1L)
    8. │           └─plyr .fun(piece, ...)
    9. │             ├─base::do.call(flat, c(args, list(...)))
   10. │             └─HTSSIP `<fn>`(...)
   11. │               └─base::apply(DESeq2::counts(dds), 1, gm_mean)
   12. └─base::loadNamespace(x)
   13.   ├─base::namespaceImport(...)
   14.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15.     ├─base::namespaceImport(...)
   16.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
  
  [ FAIL 3 | WARN 10 | SKIP 18 | PASS 102 ]
  Error: Test failures
  Execution halted