[R-pkg-team] Bug#1025045: Test failure in StructuralVariantAnnotation

[Andreas Tille]

Control: tags -1 upstream
Control: forwarded -1 Daniel Cameron <daniel.l.cameron at gmail.com>

Hi Daniel,

when upgrading StructuralVariantAnnotation to its latest version (1.13.0)
I noticed that some of its tests are failing.  I have reported this to
the Debian bug tracking system[1].  The errors are starting with

[ FAIL 30 | WARN 4 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-extensions-VCF.R:28'): INFO column import ──────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'breakpointRanges': no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─StructuralVariantAnnotation::breakpointRanges(.testrecord(c("chr10\t2991435\tINV\tN\t<INV>\t.\tLowQual\tSVTYPE=INV;CHR2=chr1;END=19357517;CT=3to5"))) at test-extensions-VCF.R:28:8
  2. ├─StructuralVariantAnnotation:::.testrecord(c("chr10\t2991435\tINV\tN\t<INV>\t.\tLowQual\tSVTYPE=INV;CHR2=chr1;END=19357517;CT=3to5"))
  3. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  4. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  5. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  6. │     └─VariantAnnotation:::.readVcf(...)
  7. │       └─VariantAnnotation:::.scanVcfToVCF(...)
  8. │         ├─VariantAnnotation::scanVcfHeader(file)
  9. │         └─VariantAnnotation::scanVcfHeader(file)
 10. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 11. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 12. │             └─BiocGenerics::Map(...)
 13. │               ├─BiocGenerics (local) standardGeneric("Map")
 14. │               │ ├─BiocGenerics::eval(mc, env)
 15. │               │ └─base::eval(mc, env)
 16. │               │   └─base::eval(mc, env)
 17. │               └─base::Map(f = f, ...)
 18. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 19. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 20. │                     ├─Rsamtools::scanBcfHeader(bf)
 21. │                     └─Rsamtools::scanBcfHeader(bf)
 22. └─base::.handleSimpleError(...)
 23.   └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:49'): Delly TRA ───────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'breakpointRanges': no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─StructuralVariantAnnotation::breakpointRanges(.testrecord(c("chr10\t2991435\tTRA00000001\tN\t<TRA>\t.\tLowQual\tCIEND=0,100;CIPOS=0,50;SVTYPE=TRA;CHR2=chr1;END=19357517;CT=3to5"))) at test-extensions-VCF.R:49:4
  2. ├─StructuralVariantAnnotation:::.testrecord(c("chr10\t2991435\tTRA00000001\tN\t<TRA>\t.\tLowQual\tCIEND=0,100;CIPOS=0,50;SVTYPE=TRA;CHR2=chr1;END=19357517;CT=3to5"))
  3. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  4. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  5. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  6. │     └─VariantAnnotation:::.readVcf(...)
  7. │       └─VariantAnnotation:::.scanVcfToVCF(...)
  8. │         ├─VariantAnnotation::scanVcfHeader(file)
  9. │         └─VariantAnnotation::scanVcfHeader(file)
 10. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 11. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 12. │             └─BiocGenerics::Map(...)
 13. │               ├─BiocGenerics (local) standardGeneric("Map")
 14. │               │ ├─BiocGenerics::eval(mc, env)
 15. │               │ └─base::eval(mc, env)
 16. │               │   └─base::eval(mc, env)
 17. │               └─base::Map(f = f, ...)
 18. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 19. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 20. │                     ├─Rsamtools::scanBcfHeader(bf)
 21. │                     └─Rsamtools::scanBcfHeader(bf)
 22. └─base::.handleSimpleError(...)
 23.   └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:71'): empty VCF ───────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'breakpointRanges': no 'header' line "#CHROM POS ID..."?


You can find a full build log here

   https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-structuralvariantannotation/28747149/log.gz

Kind regards

     Andreas.


[1] https://bugs.debian.org/1025045

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