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ge11232002 / CNEr

Conserved Noncoding Elements (CNEs) Identification and Visualisation
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Rtest error:invalid class “CNE” object: The file `assembly1Fn` must exist! #24

Closed fubingting closed 3 years ago

fubingting commented 3 years ago

When I test with cner@1.26.0, the following error occurs： test commond： Rscript testthat.R Error log The number of axt files 1 The number of axt alignments is 50 The number of axt files 1 The number of axt alignments is 352 The number of axt files 1 The number of axt alignments is 50 The number of axt files 1 The number of axt alignments is 50 The number of axt files 1 The number of axt alignments is 50 ══ Skipped tests ══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════ ● empty test (1)

══ Warnings ═══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════ ── Warning (test_Axt.R:80:3): test_subAxt ────────────────────────────────────── mustOpen: Can't open /single_sequences.2bit to read: No such file or directory Backtrace:

  1. CNEr::readAxt(axtFilesHg38DanRer10, tAssemblyFn, qAssemblyFn) test_Axt.R:80:2
  2. CNEr:::seqinfoFn(qAssemblyFn)
  3. rtracklayer::seqinfo(TwoBitFile(fn))
  4. rtracklayer:::.seqlengths_TwoBitFile(x) ── Warning (test_Axt.R:115:3): test_fixCoordinates ───────────────────────────── mustOpen: Can't open /single_sequences.2bit to read: No such file or directory Backtrace:
  5. CNEr::readAxt(axtFnDanRer10Hg38, tAssemblyFn = tAssemblyFn, qAssemblyFn = qAssemblyFn) test_Axt.R:115:2
  6. CNEr:::seqinfoFn(tAssemblyFn)
  7. rtracklayer::seqinfo(TwoBitFile(fn))
  8. rtracklayer:::.seqlengths_TwoBitFile(x) ── Warning (test_Axt.R:141:3): test_subAxt ───────────────────────────────────── mustOpen: Can't open /single_sequences.2bit to read: No such file or directory Backtrace:
  9. CNEr::readAxt(axtFn, tAssemblyFn, qAssemblyFn) test_Axt.R:141:2
  10. CNEr:::seqinfoFn(tAssemblyFn)
  11. rtracklayer::seqinfo(TwoBitFile(fn))
  12. rtracklayer:::.seqlengths_TwoBitFile(x) ── Warning (test_Axt.R:167:3): test_makeAxtTracks ────────────────────────────── mustOpen: Can't open /single_sequences.2bit to read: No such file or directory Backtrace:
  13. CNEr::readAxt(axtFn, tAssemblyFn, qAssemblyFn) test_Axt.R:167:2
  14. CNEr:::seqinfoFn(tAssemblyFn)
  15. rtracklayer::seqinfo(TwoBitFile(fn))
  16. rtracklayer:::.seqlengths_TwoBitFile(x)

══ Failed tests ═══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════ ── Error (test_Axt.R:80:3): test_subAxt ──────────────────────────────────────── Error: UCSC library operation failed Backtrace: █

  1. └─CNEr::readAxt(axtFilesHg38DanRer10, tAssemblyFn, qAssemblyFn) test_Axt.R:80:2
  2. └─CNEr:::seqinfoFn(qAssemblyFn)
  3. ├─GenomeInfoDb::seqinfo(TwoBitFile(fn))
  4. └─rtracklayer::seqinfo(TwoBitFile(fn))
  5. └─rtracklayer:::.seqlengths_TwoBitFile(x) ── Error (test_Axt.R:115:3): test_fixCoordinates ─────────────────────────────── Error: UCSC library operation failed Backtrace: █
  6. └─CNEr::readAxt(axtFnDanRer10Hg38, tAssemblyFn = tAssemblyFn, qAssemblyFn = qAssemblyFn) test_Axt.R:115:2
  7. └─CNEr:::seqinfoFn(tAssemblyFn)
  8. ├─GenomeInfoDb::seqinfo(TwoBitFile(fn))
  9. └─rtracklayer::seqinfo(TwoBitFile(fn))
  10. └─rtracklayer:::.seqlengths_TwoBitFile(x) ── Error (test_Axt.R:141:3): test_subAxt ─────────────────────────────────────── Error: UCSC library operation failed Backtrace: █
  11. └─CNEr::readAxt(axtFn, tAssemblyFn, qAssemblyFn) test_Axt.R:141:2
  12. └─CNEr:::seqinfoFn(tAssemblyFn)
  13. ├─GenomeInfoDb::seqinfo(TwoBitFile(fn))
  14. └─rtracklayer::seqinfo(TwoBitFile(fn))
  15. └─rtracklayer:::.seqlengths_TwoBitFile(x) ── Error (test_Axt.R:167:3): test_makeAxtTracks ──────────────────────────────── Error: UCSC library operation failed Backtrace: █
  16. └─CNEr::readAxt(axtFn, tAssemblyFn, qAssemblyFn) test_Axt.R:167:2
  17. └─CNEr:::seqinfoFn(tAssemblyFn)
  18. ├─GenomeInfoDb::seqinfo(TwoBitFile(fn))
  19. └─rtracklayer::seqinfo(TwoBitFile(fn))
  20. └─rtracklayer:::.seqlengths_TwoBitFile(x) ── Error (test_ceScan.R:14:3): test_ceScan ───────────────────────────────────── Error: there is no package called ‘BSgenome.Drerio.UCSC.danRer10’ Backtrace: █
  21. └─base::library(BSgenome.Drerio.UCSC.danRer10) test_ceScan.R:14:2 ── Error (test_CNE.R:56:3): test_CNE ─────────────────────────────────────────── Error: invalid class “CNE” object: The file assembly1Fn must exist! Backtrace: █
  22. └─CNEr::CNE(...) test_CNE.R:56:2
  23. └─methods::new(...)
  24. ├─methods::initialize(value, ...)
  25. └─methods::initialize(value, ...)
  26. └─methods::validObject(.Object)

[ FAIL 6 | WARN 4 | SKIP 1 | PASS 69 ]

ge11232002 commented 3 years ago

You need to have the packages under "SUGGEST" installed to run those tests.