Running ‘testthat.R’ [68s/68s]
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 
  ── 1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2)  ─────
  please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
    withDimnames=FALSE)) <- value' when the dimnames on the supplied
    assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
  Backtrace:
   1. HTSSIP::DESeq2_l2fc(...)
   2. DESeq2::DESeq(dds, quiet = TRUE, fitType = "local")
   4. DESeq2::estimateDispersions(...)
   5. DESeq2:::.local(object, ...)
   6. DESeq2::estimateDispersionsGeneEst(...)
   8. SummarizedExperiment::`assays<-`(`*tmp*`, value = `*vtmp*`)
  
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  ── 2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
  please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
    withDimnames=FALSE)) <- value' when the dimnames on the supplied
    assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
  Backtrace:
   1. HTSSIP::DESeq2_l2fc(...)
   2. DESeq2::DESeq(dds, quiet = TRUE, fitType = "local")
   4. DESeq2::estimateDispersions(...)
   5. DESeq2:::.local(object, ...)
   6. DESeq2::estimateDispersionsGeneEst(...)
   8. SummarizedExperiment::`assays<-`(`*tmp*`, value = `*vtmp*`)
  
  Sparsity threshold: 0 
  Density window: 1.7-1.75 
  ── 3. Error: HRSIP runs with default (@test-HRSIP.R#3)  ────────────────────────
  please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
    withDimnames=FALSE)) <- value' when the dimnames on the supplied
    assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
  Backtrace:
    1. HTSSIP::HRSIP(...)
    2. plyr::mdply(...)
    3. plyr::adply(...)
    4. plyr::ldply(...)
    5. plyr::llply(...)
    8. plyr:::.fun(piece, ...)
   11. DESeq2::DESeq(dds, quiet = TRUE, fitType = "local")
   13. DESeq2::estimateDispersions(...)
   14. DESeq2:::.local(object, ...)
   15. DESeq2::estimateDispersionsGeneEst(...)
   17. SummarizedExperiment::`assays<-`(`*tmp*`, value = `*vtmp*`)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 102 | SKIPPED: 18 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  3. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  
  Error: testthat unit tests failed
  Execution halted