Source: r-bioc-structuralvariantannotation
Version: 1.13.0+ds-1
Severity: normal
X-Debbugs-Cc: 1023...@bugs.debian.org
Hi,
the package fails its autopkgtest. The errors starts 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.
-- System Information:
Debian Release: bookworm/sid
APT prefers testing
APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'), (5,
'experimental'), (1, 'buildd-experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 6.0.0-2-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8),
LANGUAGE=de_DE:de
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
