Running 'testthat.R' [30s]
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:  'objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix''
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  Failed with error:  'objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix''
  Sparsity threshold: 0 
  Density window: 1.7-1.75 
  Failed with error:  'objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix''
  [ FAIL 3 | WARN 168 | SKIP 18 | PASS 102 ]
  
  ══ Skipped tests (18) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-BD_ordinations.R:8:3', 'test-BD_ordinations.R:18:3',
    'test-BD_ordinations.R:31:3', 'test-BD_ordinations.R:61:3',
    'test-BD_shift.R:13:3', 'test-BD_shift.R:42:3', 'test-BD_shift.R:62:3',
    'test-BD_shift.R:74:3', 'test-HRSIP.R:17:3', 'test-HRSIP.R:35:3',
    'test-HRSIP.R:56:3', 'test-delta_BD.R:36:3', 'test-qPCR.R:34:3',
    'test-qPCR.R:55:3', 'test-qPCR.R:77:3', 'test-qSIP_atom_excess.R:4:3',
    'test-qSIP_atom_excess.R:49:3'
  • empty test (1): 'test-phyloseq_subset.R:75:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-DESeq2_l2fc.R:2:3'): DESeq2_l2fc runs with default params ──────
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  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]])
   8.       └─base::namespaceImportFrom(...)
   9.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-DESeq2_l2fc.R:15:3'): DESeq2_l2fc runs with sparsity_apply=heavy ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  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]])
   8.       └─base::namespaceImportFrom(...)
   9.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test-HRSIP.R:3:3'): HRSIP runs with default ─────────────────────────
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  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 (local) `<fn>`(1L)
    8. │           └─plyr (local) .fun(piece, ...)
    9. │             ├─base::do.call(flat, c(args, list(...)))
   10. │             └─HTSSIP (local) `<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]])
   17.       └─base::namespaceImportFrom(...)
   18.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 3 | WARN 168 | SKIP 18 | PASS 102 ]
  Error: Test failures
  Execution halted