Running 'testthat.R'
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:  'there is no package called 'annotate''
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  Failed with error:  'there is no package called 'annotate''
  Sparsity threshold: 0 
  Density window: 1.7-1.75 
  Failed with error:  'there is no package called 'annotate''
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (17)
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-DESeq2_l2fc.R:2:3): DESeq2_l2fc runs with default params ────────
  Error: there is no package called 'annotate'
  Backtrace:
       █
    1. ├─HTSSIP::DESeq2_l2fc(...) test-DESeq2_l2fc.R:2:2
    2. │ └─base::apply(DESeq2::counts(dds), 1, gm_mean)
    3. └─base::loadNamespace(x)
    4.   ├─base::namespaceImportFrom(...)
    5.   │ └─base::asNamespace(ns)
    6.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    7.     ├─base::namespaceImportFrom(...)
    8.     │ └─base::asNamespace(ns)
    9.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   10.       └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11.         └─base:::withOneRestart(expr, restarts[[1L]])
   12.           └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-DESeq2_l2fc.R:15:3): DESeq2_l2fc runs with sparsity_apply=heavy ──
  Error: there is no package called 'annotate'
  Backtrace:
       █
    1. ├─HTSSIP::DESeq2_l2fc(...) test-DESeq2_l2fc.R:15:2
    2. │ └─base::apply(DESeq2::counts(dds), 1, gm_mean)
    3. └─base::loadNamespace(x)
    4.   ├─base::namespaceImportFrom(...)
    5.   │ └─base::asNamespace(ns)
    6.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    7.     ├─base::namespaceImportFrom(...)
    8.     │ └─base::asNamespace(ns)
    9.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   10.       └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11.         └─base:::withOneRestart(expr, restarts[[1L]])
   12.           └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-HRSIP.R:3:3): HRSIP runs with default ───────────────────────────
  Error: there is no package called 'annotate'
  Backtrace:
       █
    1. ├─HTSSIP::HRSIP(...) 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. │         └─(function (i) ...
    8. │           └─plyr:::.fun(piece, ...)
    9. │             ├─base::do.call(flat, c(args, list(...)))
   10. │             └─(function (physeq, density_min, density_max, design, l2fc_threshold = 0.25, ...
   11. │               └─base::apply(DESeq2::counts(dds), 1, gm_mean)
   12. └─base::loadNamespace(x)
   13.   ├─base::namespaceImportFrom(...)
   14.   │ └─base::asNamespace(ns)
   15.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   16.     ├─base::namespaceImportFrom(...)
   17.     │ └─base::asNamespace(ns)
   18.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   19.       └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   20.         └─base:::withOneRestart(expr, restarts[[1L]])
   21.           └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 10 | SKIP 18 | PASS 102 ]
  Error: Test failures
  Execution halted