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This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for StructuralVariantAnnotation on palomino5


To the developers/maintainers of the StructuralVariantAnnotation package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1968/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
StructuralVariantAnnotation 1.15.0  (landing page)
Daniel Cameron
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/StructuralVariantAnnotation
git_branch: master
git_last_commit: da12360
git_last_commit_date: 2022-11-01 11:19:59 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  

Summary

Package: StructuralVariantAnnotation
Version: 1.15.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:StructuralVariantAnnotation.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings StructuralVariantAnnotation_1.15.0.tar.gz
StartedAt: 2022-12-29 04:01:17 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:05:58 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 281.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: StructuralVariantAnnotation.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:StructuralVariantAnnotation.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings StructuralVariantAnnotation_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/StructuralVariantAnnotation.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'StructuralVariantAnnotation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'StructuralVariantAnnotation' version '1.15.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'StructuralVariantAnnotation' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   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))
  
  [ FAIL 45 | WARN 27 | SKIP 0 | PASS 105 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/StructuralVariantAnnotation.Rcheck/00check.log'
for details.

Installation output

StructuralVariantAnnotation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL StructuralVariantAnnotation
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'StructuralVariantAnnotation' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (StructuralVariantAnnotation)

Tests output

StructuralVariantAnnotation.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(StructuralVariantAnnotation)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: rtracklayer
Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> 
> test_check("StructuralVariantAnnotation")
[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[W::bcf_hdr_check_sanity] PL should be declared as Number=G
[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

[ FAIL 45 | WARN 27 | SKIP 0 | PASS 105 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-BreakpointGRanges.R:27'): .constrict ───────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'start': error in evaluating the argument 'x' in selecting a method for function 'start': error in evaluating the argument 'x' in selecting a method for function 'breakpointRanges': no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:27:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─stats::start(...)
  5. ├─StructuralVariantAnnotation:::.constrict(...)
  6. │ └─stats::start(gr)
  7. ├─StructuralVariantAnnotation::breakpointRanges(...)
  8. ├─StructuralVariantAnnotation:::.testrecord(...)
  9. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
 10. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
 11. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 12. │     └─VariantAnnotation:::.readVcf(...)
 13. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 14. │         ├─VariantAnnotation::scanVcfHeader(file)
 15. │         └─VariantAnnotation::scanVcfHeader(file)
 16. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 17. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 18. │             └─BiocGenerics::Map(...)
 19. │               ├─BiocGenerics (local) standardGeneric("Map")
 20. │               │ ├─BiocGenerics::eval(mc, env)
 21. │               │ └─base::eval(mc, env)
 22. │               │   └─base::eval(mc, env)
 23. │               └─base::Map(f = f, ...)
 24. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 25. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 26. │                     ├─Rsamtools::scanBcfHeader(bf)
 27. │                     └─Rsamtools::scanBcfHeader(bf)
 28. ├─base::.handleSimpleError(...)
 29. │ └─base (local) h(simpleError(msg, call))
 30. ├─base::.handleSimpleError(...)
 31. │ └─base (local) h(simpleError(msg, call))
 32. └─base::.handleSimpleError(...)
 33.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:41'): findBreakpointOverlaps ───────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': error in evaluating the argument 'x' in selecting a method for function 'breakpointRanges': no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:41:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─BiocGenerics::as.data.frame(...)
  5. ├─StructuralVariantAnnotation::findBreakpointOverlaps(...)
  6. │ └─StructuralVariantAnnotation:::.assertValidBreakpointGRanges(query)
  7. ├─StructuralVariantAnnotation::breakpointRanges(...)
  8. ├─StructuralVariantAnnotation:::.testrecord(...)
  9. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
 10. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
 11. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 12. │     └─VariantAnnotation:::.readVcf(...)
 13. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 14. │         ├─VariantAnnotation::scanVcfHeader(file)
 15. │         └─VariantAnnotation::scanVcfHeader(file)
 16. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 17. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 18. │             └─BiocGenerics::Map(...)
 19. │               ├─BiocGenerics (local) standardGeneric("Map")
 20. │               │ ├─BiocGenerics::eval(mc, env)
 21. │               │ └─base::eval(mc, env)
 22. │               │   └─base::eval(mc, env)
 23. │               └─base::Map(f = f, ...)
 24. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 25. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 26. │                     ├─Rsamtools::scanBcfHeader(bf)
 27. │                     └─Rsamtools::scanBcfHeader(bf)
 28. ├─base::.handleSimpleError(...)
 29. │ └─base (local) h(simpleError(msg, call))
 30. └─base::.handleSimpleError(...)
 31.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:93'): findBreakpointOverlaps: delly vs truth ──
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("chr12\t6905246\tDEL00000292\tN\t<DEL>\t.\tPASS\tPRECISE;CIEND=-52,52;CIPOS=-52,52;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.6.8;CHR2=chr12;END=100419669;CT=3to5;INSLEN=0;PE=28;MAPQ=34;SR=30;SRQ=1;CONSENSUS=GTGCATACATTTCAGTGACCCGTTTTAGAAACAGAATTAATATGGTGAATAGAGAAAGAAGAAATCAGTGACTTTGGCCAGGCACAGTAGCTCACATCTGTAATCCCAGCACTTTGGGAGGCTGAGACAGTTGGTTGCTTGAGCCCAGGAGT"))) at test-BreakpointGRanges.R:93:8
  2. ├─StructuralVariantAnnotation:::.testrecord(c("chr12\t6905246\tDEL00000292\tN\t<DEL>\t.\tPASS\tPRECISE;CIEND=-52,52;CIPOS=-52,52;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.6.8;CHR2=chr12;END=100419669;CT=3to5;INSLEN=0;PE=28;MAPQ=34;SR=30;SRQ=1;CONSENSUS=GTGCATACATTTCAGTGACCCGTTTTAGAAACAGAATTAATATGGTGAATAGAGAAAGAAGAAATCAGTGACTTTGGCCAGGCACAGTAGCTCACATCTGTAATCCCAGCACTTTGGGAGGCTGAGACAGTTGGTTGCTTGAGCCCAGGAGT"))
  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-BreakpointGRanges.R:105'): countBreakpointOverlaps ─────────────
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. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:105:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::countBreakpointOverlaps(...)
  5. ├─StructuralVariantAnnotation::breakpointRanges(...)
  6. ├─StructuralVariantAnnotation:::.testrecord(...)
  7. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  9. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 10. │     └─VariantAnnotation:::.readVcf(...)
 11. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 12. │         ├─VariantAnnotation::scanVcfHeader(file)
 13. │         └─VariantAnnotation::scanVcfHeader(file)
 14. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 16. │             └─BiocGenerics::Map(...)
 17. │               ├─BiocGenerics (local) standardGeneric("Map")
 18. │               │ ├─BiocGenerics::eval(mc, env)
 19. │               │ └─base::eval(mc, env)
 20. │               │   └─base::eval(mc, env)
 21. │               └─base::Map(f = f, ...)
 22. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 23. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 24. │                     ├─Rsamtools::scanBcfHeader(bf)
 25. │                     └─Rsamtools::scanBcfHeader(bf)
 26. └─base::.handleSimpleError(...)
 27.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:118'): countBreakpointOverlaps uniqueAllocation ──
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. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:118:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::countBreakpointOverlaps(...)
  5. ├─StructuralVariantAnnotation::breakpointRanges(...)
  6. ├─StructuralVariantAnnotation:::.testrecord(...)
  7. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  9. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 10. │     └─VariantAnnotation:::.readVcf(...)
 11. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 12. │         ├─VariantAnnotation::scanVcfHeader(file)
 13. │         └─VariantAnnotation::scanVcfHeader(file)
 14. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 16. │             └─BiocGenerics::Map(...)
 17. │               ├─BiocGenerics (local) standardGeneric("Map")
 18. │               │ ├─BiocGenerics::eval(mc, env)
 19. │               │ └─base::eval(mc, env)
 20. │               │   └─base::eval(mc, env)
 21. │               └─base::Map(f = f, ...)
 22. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 23. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 24. │                     ├─Rsamtools::scanBcfHeader(bf)
 25. │                     └─Rsamtools::scanBcfHeader(bf)
 26. └─base::.handleSimpleError(...)
 27.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:132'): extractBreakpointSequence ───────────
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. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:132:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::extractBreakpointSequence(...)
  5. │ └─StructuralVariantAnnotation::extractReferenceSequence(...)
  6. │   ├─assertthat::assert_that(is(gr, "GRanges"))
  7. │   │ └─assertthat::see_if(..., env = env, msg = msg)
  8. │   │   ├─base::tryCatch(...)
  9. │   │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10. │   │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11. │   │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 12. │   │   └─base::eval(assertion, env)
 13. │   │     └─base::eval(assertion, env)
 14. │   └─methods::is(gr, "GRanges")
 15. ├─StructuralVariantAnnotation::breakpointRanges(...)
 16. ├─StructuralVariantAnnotation:::.testrecord(...)
 17. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
 18. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
 19. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 20. │     └─VariantAnnotation:::.readVcf(...)
 21. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 22. │         ├─VariantAnnotation::scanVcfHeader(file)
 23. │         └─VariantAnnotation::scanVcfHeader(file)
 24. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 25. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 26. │             └─BiocGenerics::Map(...)
 27. │               ├─BiocGenerics (local) standardGeneric("Map")
 28. │               │ ├─BiocGenerics::eval(mc, env)
 29. │               │ └─base::eval(mc, env)
 30. │               │   └─base::eval(mc, env)
 31. │               └─base::Map(f = f, ...)
 32. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 33. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 34. │                     ├─Rsamtools::scanBcfHeader(bf)
 35. │                     └─Rsamtools::scanBcfHeader(bf)
 36. └─base::.handleSimpleError(...)
 37.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:168'): extractReferenceSequence ────────────
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. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:168:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::extractReferenceSequence(...)
  5. │ ├─assertthat::assert_that(is(gr, "GRanges"))
  6. │ │ └─assertthat::see_if(..., env = env, msg = msg)
  7. │ │   ├─base::tryCatch(...)
  8. │ │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │ │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. │ │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │ │   └─base::eval(assertion, env)
 12. │ │     └─base::eval(assertion, env)
 13. │ └─methods::is(gr, "GRanges")
 14. ├─StructuralVariantAnnotation::breakpointRanges(...)
 15. ├─StructuralVariantAnnotation:::.testrecord(...)
 16. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
 17. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
 18. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 19. │     └─VariantAnnotation:::.readVcf(...)
 20. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 21. │         ├─VariantAnnotation::scanVcfHeader(file)
 22. │         └─VariantAnnotation::scanVcfHeader(file)
 23. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 24. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 25. │             └─BiocGenerics::Map(...)
 26. │               ├─BiocGenerics (local) standardGeneric("Map")
 27. │               │ ├─BiocGenerics::eval(mc, env)
 28. │               │ └─base::eval(mc, env)
 29. │               │   └─base::eval(mc, env)
 30. │               └─base::Map(f = f, ...)
 31. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 32. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 33. │                     ├─Rsamtools::scanBcfHeader(bf)
 34. │                     └─Rsamtools::scanBcfHeader(bf)
 35. └─base::.handleSimpleError(...)
 36.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:192'): calculateReferenceHomology ──────────
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. ├─testthat::expect_gte(...) at test-BreakpointGRanges.R:192:2
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::calculateReferenceHomology(...)
  5. │ ├─StructuralVariantAnnotation:::.replaceNa(...)
  6. │ └─BiocGenerics::pmin(anchorLength, abs(gr$svLen) + 1)
  7. │   └─BiocGenerics (local) standardGeneric("pmin")
  8. │     ├─BiocGenerics::eval(quote(list(...)), env)
  9. │     └─base::eval(quote(list(...)), env)
 10. │       └─base::eval(quote(list(...)), env)
 11. ├─StructuralVariantAnnotation::breakpointRanges(...)
 12. ├─StructuralVariantAnnotation:::.testrecord(...)
 13. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
 14. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
 15. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 16. │     └─VariantAnnotation:::.readVcf(...)
 17. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 18. │         ├─VariantAnnotation::scanVcfHeader(file)
 19. │         └─VariantAnnotation::scanVcfHeader(file)
 20. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 21. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 22. │             └─BiocGenerics::Map(...)
 23. │               ├─BiocGenerics (local) standardGeneric("Map")
 24. │               │ ├─BiocGenerics::eval(mc, env)
 25. │               │ └─base::eval(mc, env)
 26. │               │   └─base::eval(mc, env)
 27. │               └─base::Map(f = f, ...)
 28. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 29. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 30. │                     ├─Rsamtools::scanBcfHeader(bf)
 31. │                     └─Rsamtools::scanBcfHeader(bf)
 32. └─base::.handleSimpleError(...)
 33.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:253'): simpleEventLength ───────────────────
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. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:253:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::simpleEventLength(...)
  5. ├─StructuralVariantAnnotation::breakpointRanges(...)
  6. ├─StructuralVariantAnnotation:::.testrecord(...)
  7. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  9. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 10. │     └─VariantAnnotation:::.readVcf(...)
 11. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 12. │         ├─VariantAnnotation::scanVcfHeader(file)
 13. │         └─VariantAnnotation::scanVcfHeader(file)
 14. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 16. │             └─BiocGenerics::Map(...)
 17. │               ├─BiocGenerics (local) standardGeneric("Map")
 18. │               │ ├─BiocGenerics::eval(mc, env)
 19. │               │ └─base::eval(mc, env)
 20. │               │   └─base::eval(mc, env)
 21. │               └─base::Map(f = f, ...)
 22. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 23. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 24. │                     ├─Rsamtools::scanBcfHeader(bf)
 25. │                     └─Rsamtools::scanBcfHeader(bf)
 26. └─base::.handleSimpleError(...)
 27.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:265'): simpleEventType ─────────────────────
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. ├─testthat::expect_equal(...) at test-BreakpointGRanges.R:265:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::simpleEventType(...)
  5. ├─StructuralVariantAnnotation::breakpointRanges(...)
  6. ├─StructuralVariantAnnotation:::.testrecord(...)
  7. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  9. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 10. │     └─VariantAnnotation:::.readVcf(...)
 11. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 12. │         ├─VariantAnnotation::scanVcfHeader(file)
 13. │         └─VariantAnnotation::scanVcfHeader(file)
 14. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 16. │             └─BiocGenerics::Map(...)
 17. │               ├─BiocGenerics (local) standardGeneric("Map")
 18. │               │ ├─BiocGenerics::eval(mc, env)
 19. │               │ └─base::eval(mc, env)
 20. │               │   └─base::eval(mc, env)
 21. │               └─base::Map(f = f, ...)
 22. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 23. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 24. │                     ├─Rsamtools::scanBcfHeader(bf)
 25. │                     └─Rsamtools::scanBcfHeader(bf)
 26. └─base::.handleSimpleError(...)
 27.   └─base (local) h(simpleError(msg, call))
── Error ('test-BreakpointGRanges.R:286'): findInsDupOverlaps ──────────────────
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(...) at test-BreakpointGRanges.R:286:8
  2. ├─StructuralVariantAnnotation:::.testrecord(...)
  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-BreakpointGRanges.R:315'): findTransitiveCalls imprecise ───────
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(...) at test-BreakpointGRanges.R:315:8
  2. ├─StructuralVariantAnnotation:::.testrecord(...)
  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-BreakpointGRanges.R:332'): findTransitiveCalls loop ────────────
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(...) at test-BreakpointGRanges.R:332:8
  2. ├─StructuralVariantAnnotation:::.testrecord(...)
  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-BreakpointGRanges.R:373'): .traversable_segments ───────────────
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(...) at test-BreakpointGRanges.R:373:8
  2. ├─StructuralVariantAnnotation:::.testrecord(...)
  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-BreakpointGRanges.R:426'): findTransitiveCalls precise ─────────
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(...) at test-BreakpointGRanges.R:426:8
  2. ├─StructuralVariantAnnotation:::.testrecord(...)
  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: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..."?
Backtrace:
     ▆
  1. ├─testthat::expect_equal(0, length(breakpointRanges(.testrecord(c())))) at test-extensions-VCF.R:71:8
  2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::breakpointRanges(.testrecord(c()))
  5. ├─StructuralVariantAnnotation:::.testrecord(c())
  6. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  7. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  9. │     └─VariantAnnotation:::.readVcf(...)
 10. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 11. │         ├─VariantAnnotation::scanVcfHeader(file)
 12. │         └─VariantAnnotation::scanVcfHeader(file)
 13. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 14. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │             └─BiocGenerics::Map(...)
 16. │               ├─BiocGenerics (local) standardGeneric("Map")
 17. │               │ ├─BiocGenerics::eval(mc, env)
 18. │               │ └─base::eval(mc, env)
 19. │               │   └─base::eval(mc, env)
 20. │               └─base::Map(f = f, ...)
 21. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 22. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 23. │                     ├─Rsamtools::scanBcfHeader(bf)
 24. │                     └─Rsamtools::scanBcfHeader(bf)
 25. └─base::.handleSimpleError(...)
 26.   └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:86'): isStructural ────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'isStructural': no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─testthat::expect_true(isStructural(.testrecord("chr1\t1\t.\tATT\tAGGA\t.\t.\t"))) at test-extensions-VCF.R:86:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::isStructural(.testrecord("chr1\t1\t.\tATT\tAGGA\t.\t.\t"))
  5. ├─StructuralVariantAnnotation:::.testrecord("chr1\t1\t.\tATT\tAGGA\t.\t.\t")
  6. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  7. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  9. │     └─VariantAnnotation:::.readVcf(...)
 10. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 11. │         ├─VariantAnnotation::scanVcfHeader(file)
 12. │         └─VariantAnnotation::scanVcfHeader(file)
 13. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 14. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │             └─BiocGenerics::Map(...)
 16. │               ├─BiocGenerics (local) standardGeneric("Map")
 17. │               │ ├─BiocGenerics::eval(mc, env)
 18. │               │ └─base::eval(mc, env)
 19. │               │   └─base::eval(mc, env)
 20. │               └─base::Map(f = f, ...)
 21. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 22. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 23. │                     ├─Rsamtools::scanBcfHeader(bf)
 24. │                     └─Rsamtools::scanBcfHeader(bf)
 25. └─base::.handleSimpleError(...)
 26.   └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:91'): .svLen ──────────────────────────────────
Error in `scanBcfHeader(bf)`: no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-extensions-VCF.R:91:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation:::.svLen(.testrecord("chr1\t100\t.\tA\t<DEL>\t.\t.\tSVLEN=-1"))
  5. │ ├─assertthat::assert_that(.hasSingleAllelePerRecord(vcf))
  6. │ │ └─assertthat::see_if(..., env = env, msg = msg)
  7. │ │   ├─base::tryCatch(...)
  8. │ │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │ │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. │ │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │ │   └─base::eval(assertion, env)
 12. │ │     └─base::eval(assertion, env)
 13. │ └─StructuralVariantAnnotation:::.hasSingleAllelePerRecord(vcf)
 14. │   ├─assertthat::assert_that(is(vcf, "VCF"))
 15. │   │ └─assertthat::see_if(..., env = env, msg = msg)
 16. │   │   ├─base::tryCatch(...)
 17. │   │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 18. │   │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19. │   │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 20. │   │   └─base::eval(assertion, env)
 21. │   │     └─base::eval(assertion, env)
 22. │   └─methods::is(vcf, "VCF")
 23. └─StructuralVariantAnnotation:::.testrecord("chr1\t100\t.\tA\t<DEL>\t.\t.\tSVLEN=-1")
 24.   ├─VariantAnnotation::readVcf(.testfile(filename), "")
 25.   └─VariantAnnotation::readVcf(.testfile(filename), "")
 26.     └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 27.       └─VariantAnnotation:::.readVcf(...)
 28.         └─VariantAnnotation:::.scanVcfToVCF(...)
 29.           ├─VariantAnnotation::scanVcfHeader(file)
 30.           └─VariantAnnotation::scanVcfHeader(file)
 31.             ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 32.             └─Rsamtools::scanBcfHeader(file[[1]], ...)
 33.               └─BiocGenerics::Map(...)
 34.                 ├─BiocGenerics (local) standardGeneric("Map")
 35.                 │ ├─BiocGenerics::eval(mc, env)
 36.                 │ └─base::eval(mc, env)
 37.                 │   └─base::eval(mc, env)
 38.                 └─base::Map(f = f, ...)
 39.                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 40.                     └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 41.                       ├─Rsamtools::scanBcfHeader(bf)
 42.                       └─Rsamtools::scanBcfHeader(bf)
── Error ('test-extensions-VCF.R:107'): breakpointRanges creates placeholder names ──
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. ├─testthat::expect_warning(...) at test-extensions-VCF.R:107:8
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─testthat::expect_named(...)
  7. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  8. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  9. ├─StructuralVariantAnnotation::breakpointRanges(...)
 10. ├─StructuralVariantAnnotation:::.testrecord(...)
 11. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
 12. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
 13. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
 14. │     └─VariantAnnotation:::.readVcf(...)
 15. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 16. │         ├─VariantAnnotation::scanVcfHeader(file)
 17. │         └─VariantAnnotation::scanVcfHeader(file)
 18. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 19. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 20. │             └─BiocGenerics::Map(...)
 21. │               ├─BiocGenerics (local) standardGeneric("Map")
 22. │               │ ├─BiocGenerics::eval(mc, env)
 23. │               │ └─base::eval(mc, env)
 24. │               │   └─base::eval(mc, env)
 25. │               └─base::Map(f = f, ...)
 26. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 27. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 28. │                     ├─Rsamtools::scanBcfHeader(bf)
 29. │                     └─Rsamtools::scanBcfHeader(bf)
 30. └─base::.handleSimpleError(...)
 31.   └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:116'): breakpointRanges non-symbolic alleles ──
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("chr1\t1\t.\tATT\tAGGA\t.\t.\t")) at test-extensions-VCF.R:116:8
  2. ├─StructuralVariantAnnotation:::.testrecord("chr1\t1\t.\tATT\tAGGA\t.\t.\t")
  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:140'): breakpointRanges intervals ─────────────
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("chr1\t100\t.\tA\tAT\t.\t.\tHOMLEN=0")) at test-extensions-VCF.R:140:8
  2. ├─StructuralVariantAnnotation:::.testrecord("chr1\t100\t.\tA\tAT\t.\t.\tHOMLEN=0")
  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:171'): breakpointRanges DEL ───────────────────
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("chr1\t100\t.\tA\t<DEL>\t.\t.\tSVLEN=-1")) at test-extensions-VCF.R:171:8
  2. ├─StructuralVariantAnnotation:::.testrecord("chr1\t100\t.\tA\t<DEL>\t.\t.\tSVLEN=-1")
  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:185'): breakpointRanges should fix positive DEL event size ──
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("chr1\t100\t.\tA\t<DEL>\t.\t.\tSVLEN=10")) at test-extensions-VCF.R:185:8
  2. ├─StructuralVariantAnnotation:::.testrecord("chr1\t100\t.\tA\t<DEL>\t.\t.\tSVLEN=10")
  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:196'): breakpointRanges breakend ──────────────
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. ├─testthat::expect_equal(...) at test-extensions-VCF.R:196:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::breakpointRanges(...)
  5. ├─StructuralVariantAnnotation:::.testrecord(...)
  6. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  7. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  9. │     └─VariantAnnotation:::.readVcf(...)
 10. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 11. │         ├─VariantAnnotation::scanVcfHeader(file)
 12. │         └─VariantAnnotation::scanVcfHeader(file)
 13. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 14. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │             └─BiocGenerics::Map(...)
 16. │               ├─BiocGenerics (local) standardGeneric("Map")
 17. │               │ ├─BiocGenerics::eval(mc, env)
 18. │               │ └─base::eval(mc, env)
 19. │               │   └─base::eval(mc, env)
 20. │               └─base::Map(f = f, ...)
 21. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 22. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 23. │                     ├─Rsamtools::scanBcfHeader(bf)
 24. │                     └─Rsamtools::scanBcfHeader(bf)
 25. └─base::.handleSimpleError(...)
 26.   └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:207'): breakpointRanges INV ───────────────────
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("chr1\t321682\tINV0\tT\t<INV>\t6\tPASS\tSVTYPE=INV;END=421681")) at test-extensions-VCF.R:207:8
  2. ├─StructuralVariantAnnotation:::.testrecord("chr1\t321682\tINV0\tT\t<INV>\t6\tPASS\tSVTYPE=INV;END=421681")
  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:222'): breakpointRanges DUP ───────────────────
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(...) at test-extensions-VCF.R:222:8
  2. ├─StructuralVariantAnnotation:::.testrecord(...)
  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:260'): nominalPosition should ignore confidence intervals ──
Error in `scanBcfHeader(bf)`: no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. └─StructuralVariantAnnotation:::.testrecord(c("chr1\t100\t.\tA\t<DEL>\t14\tPASS\tSVTYPE=DEL;END=200")) at test-extensions-VCF.R:260:8
  2.   ├─VariantAnnotation::readVcf(.testfile(filename), "")
  3.   └─VariantAnnotation::readVcf(.testfile(filename), "")
  4.     └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  5.       └─VariantAnnotation:::.readVcf(...)
  6.         └─VariantAnnotation:::.scanVcfToVCF(...)
  7.           ├─VariantAnnotation::scanVcfHeader(file)
  8.           └─VariantAnnotation::scanVcfHeader(file)
  9.             ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 10.             └─Rsamtools::scanBcfHeader(file[[1]], ...)
 11.               └─BiocGenerics::Map(...)
 12.                 ├─BiocGenerics (local) standardGeneric("Map")
 13.                 │ ├─BiocGenerics::eval(mc, env)
 14.                 │ └─base::eval(mc, env)
 15.                 │   └─base::eval(mc, env)
 16.                 └─base::Map(f = f, ...)
 17.                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 18.                     └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 19.                       ├─Rsamtools::scanBcfHeader(bf)
 20.                       └─Rsamtools::scanBcfHeader(bf)
── Error ('test-extensions-VCF.R:267'): nominalPosition should ignore micro-homology ──
Error in `scanBcfHeader(bf)`: no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. └─StructuralVariantAnnotation:::.testrecord(c("chr1\t100\t.\tA\t<DEL>\t14\tPASS\tSVTYPE=DEL;END=200")) at test-extensions-VCF.R:267:8
  2.   ├─VariantAnnotation::readVcf(.testfile(filename), "")
  3.   └─VariantAnnotation::readVcf(.testfile(filename), "")
  4.     └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  5.       └─VariantAnnotation:::.readVcf(...)
  6.         └─VariantAnnotation:::.scanVcfToVCF(...)
  7.           ├─VariantAnnotation::scanVcfHeader(file)
  8.           └─VariantAnnotation::scanVcfHeader(file)
  9.             ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 10.             └─Rsamtools::scanBcfHeader(file[[1]], ...)
 11.               └─BiocGenerics::Map(...)
 12.                 ├─BiocGenerics (local) standardGeneric("Map")
 13.                 │ ├─BiocGenerics::eval(mc, env)
 14.                 │ └─base::eval(mc, env)
 15.                 │   └─base::eval(mc, env)
 16.                 └─base::Map(f = f, ...)
 17.                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 18.                     └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 19.                       ├─Rsamtools::scanBcfHeader(bf)
 20.                       └─Rsamtools::scanBcfHeader(bf)
── Error ('test-extensions-VCF.R:272'): breakpointRanges should not include breakends ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'isSymbolic': no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─testthat::expect_true(isSymbolic(.testrecord(c("chr1\t100\t.\tA\tAAA.\t14\tPASS\tSVTYPE=BND")))) at test-extensions-VCF.R:272:8
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─StructuralVariantAnnotation::isSymbolic(.testrecord(c("chr1\t100\t.\tA\tAAA.\t14\tPASS\tSVTYPE=BND")))
  5. ├─StructuralVariantAnnotation:::.testrecord(c("chr1\t100\t.\tA\tAAA.\t14\tPASS\tSVTYPE=BND"))
  6. │ ├─VariantAnnotation::readVcf(.testfile(filename), "")
  7. │ └─VariantAnnotation::readVcf(.testfile(filename), "")
  8. │   └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  9. │     └─VariantAnnotation:::.readVcf(...)
 10. │       └─VariantAnnotation:::.scanVcfToVCF(...)
 11. │         ├─VariantAnnotation::scanVcfHeader(file)
 12. │         └─VariantAnnotation::scanVcfHeader(file)
 13. │           ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 14. │           └─Rsamtools::scanBcfHeader(file[[1]], ...)
 15. │             └─BiocGenerics::Map(...)
 16. │               ├─BiocGenerics (local) standardGeneric("Map")
 17. │               │ ├─BiocGenerics::eval(mc, env)
 18. │               │ └─base::eval(mc, env)
 19. │               │   └─base::eval(mc, env)
 20. │               └─base::Map(f = f, ...)
 21. │                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 22. │                   └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 23. │                     ├─Rsamtools::scanBcfHeader(bf)
 24. │                     └─Rsamtools::scanBcfHeader(bf)
 25. └─base::.handleSimpleError(...)
 26.   └─base (local) h(simpleError(msg, call))
── Error ('test-extensions-VCF.R:277'): breakendRanges should include breakends ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'breakendRanges': no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. ├─StructuralVariantAnnotation::breakendRanges(.testrecord(c("chr1\t100\t.\tA\tTGC.\t14\tPASS\tSVTYPE=BND"))) at test-extensions-VCF.R:277:8
  2. ├─StructuralVariantAnnotation:::.testrecord(c("chr1\t100\t.\tA\tTGC.\t14\tPASS\tSVTYPE=BND"))
  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:283'): align_breakpoint should handle all orientations ──
Error in `scanBcfHeader(bf)`: no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. └─StructuralVariantAnnotation:::.testrecord(...) at test-extensions-VCF.R:283:8
  2.   ├─VariantAnnotation::readVcf(.testfile(filename), "")
  3.   └─VariantAnnotation::readVcf(.testfile(filename), "")
  4.     └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  5.       └─VariantAnnotation:::.readVcf(...)
  6.         └─VariantAnnotation:::.scanVcfToVCF(...)
  7.           ├─VariantAnnotation::scanVcfHeader(file)
  8.           └─VariantAnnotation::scanVcfHeader(file)
  9.             ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 10.             └─Rsamtools::scanBcfHeader(file[[1]], ...)
 11.               └─BiocGenerics::Map(...)
 12.                 ├─BiocGenerics (local) standardGeneric("Map")
 13.                 │ ├─BiocGenerics::eval(mc, env)
 14.                 │ └─base::eval(mc, env)
 15.                 │   └─base::eval(mc, env)
 16.                 └─base::Map(f = f, ...)
 17.                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 18.                     └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 19.                       ├─Rsamtools::scanBcfHeader(bf)
 20.                       └─Rsamtools::scanBcfHeader(bf)
── Error ('test-extensions-VCF.R:321'): align_breakpoint centre should ensure odd length homology is consistent on both sides ──
Error in `scanBcfHeader(bf)`: no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. └─StructuralVariantAnnotation:::.testrecord(...) at test-extensions-VCF.R:321:8
  2.   ├─VariantAnnotation::readVcf(.testfile(filename), "")
  3.   └─VariantAnnotation::readVcf(.testfile(filename), "")
  4.     └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  5.       └─VariantAnnotation:::.readVcf(...)
  6.         └─VariantAnnotation:::.scanVcfToVCF(...)
  7.           ├─VariantAnnotation::scanVcfHeader(file)
  8.           └─VariantAnnotation::scanVcfHeader(file)
  9.             ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 10.             └─Rsamtools::scanBcfHeader(file[[1]], ...)
 11.               └─BiocGenerics::Map(...)
 12.                 ├─BiocGenerics (local) standardGeneric("Map")
 13.                 │ ├─BiocGenerics::eval(mc, env)
 14.                 │ └─base::eval(mc, env)
 15.                 │   └─base::eval(mc, env)
 16.                 └─base::Map(f = f, ...)
 17.                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 18.                     └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 19.                       ├─Rsamtools::scanBcfHeader(bf)
 20.                       └─Rsamtools::scanBcfHeader(bf)
── Error ('test-extensions-VCF.R:354'): align_breakpoint should not touch other variants ──
Error in `scanBcfHeader(bf)`: no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. └─StructuralVariantAnnotation:::.testrecord(...) at test-extensions-VCF.R:354:8
  2.   ├─VariantAnnotation::readVcf(.testfile(filename), "")
  3.   └─VariantAnnotation::readVcf(.testfile(filename), "")
  4.     └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  5.       └─VariantAnnotation:::.readVcf(...)
  6.         └─VariantAnnotation:::.scanVcfToVCF(...)
  7.           ├─VariantAnnotation::scanVcfHeader(file)
  8.           └─VariantAnnotation::scanVcfHeader(file)
  9.             ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 10.             └─Rsamtools::scanBcfHeader(file[[1]], ...)
 11.               └─BiocGenerics::Map(...)
 12.                 ├─BiocGenerics (local) standardGeneric("Map")
 13.                 │ ├─BiocGenerics::eval(mc, env)
 14.                 │ └─base::eval(mc, env)
 15.                 │   └─base::eval(mc, env)
 16.                 └─base::Map(f = f, ...)
 17.                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 18.                     └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 19.                       ├─Rsamtools::scanBcfHeader(bf)
 20.                       └─Rsamtools::scanBcfHeader(bf)
── Error ('test-extensions-VCF.R:412'): VCFv4.4 use ALT instead of SVTYPE ──────
Error in `scanBcfHeader(bf)`: no 'header' line "#CHROM POS ID..."?
Backtrace:
     ▆
  1. └─StructuralVariantAnnotation:::.testrecordv44(...) at test-extensions-VCF.R:412:8
  2.   ├─VariantAnnotation::readVcf(.testfile(filename), "")
  3.   └─VariantAnnotation::readVcf(.testfile(filename), "")
  4.     └─VariantAnnotation (local) .local(file, genome = genome, param = param, ...)
  5.       └─VariantAnnotation:::.readVcf(...)
  6.         └─VariantAnnotation:::.scanVcfToVCF(...)
  7.           ├─VariantAnnotation::scanVcfHeader(file)
  8.           └─VariantAnnotation::scanVcfHeader(file)
  9.             ├─Rsamtools::scanBcfHeader(file[[1]], ...)
 10.             └─Rsamtools::scanBcfHeader(file[[1]], ...)
 11.               └─BiocGenerics::Map(...)
 12.                 ├─BiocGenerics (local) standardGeneric("Map")
 13.                 │ ├─BiocGenerics::eval(mc, env)
 14.                 │ └─base::eval(mc, env)
 15.                 │   └─base::eval(mc, env)
 16.                 └─base::Map(f = f, ...)
 17.                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 18.                     └─Rsamtools (local) `<fn>`(dots[[1L]][[1L]])
 19.                       ├─Rsamtools::scanBcfHeader(bf)
 20.                       └─Rsamtools::scanBcfHeader(bf)
── Error ('test-extensions-VCF.R:434'): VCFv4.4 CNV & SVCLAIM ──────────────────
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(...) at test-extensions-VCF.R:434:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:447'): VCFv4.4 SVLEN>END ──────────────────────
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(...) at test-extensions-VCF.R:447:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:456'): VCFv4.4 CIEND>CILEN DEL ────────────────
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(...) at test-extensions-VCF.R:456:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:481'): VCFv4.4 CIEND CILEN INV ────────────────
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(...) at test-extensions-VCF.R:481:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:490'): VCFv4.4 CIEND CILEN INS ────────────────
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(...) at test-extensions-VCF.R:490:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:498'): VCFv4.4 ALT symbolic subtypes ──────────
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(...) at test-extensions-VCF.R:498:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:512'): VCFv4.4 EVENT ──────────────────────────
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(...) at test-extensions-VCF.R:512:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:519'): VCFv4.4 non-SV symbolic alleles ────────
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(...) at test-extensions-VCF.R:519:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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:525'): SVLEN ──────────────────────────────────
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(...) at test-extensions-VCF.R:525:8
  2. ├─StructuralVariantAnnotation:::.testrecordv44(...)
  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))

[ FAIL 45 | WARN 27 | SKIP 0 | PASS 105 ]
Error: Test failures
Execution halted

Example timings

StructuralVariantAnnotation.Rcheck/StructuralVariantAnnotation-Ex.timings

nameusersystemelapsed
breakendRanges2.450.082.55
breakpointRanges2.290.112.39
breakpointgr2bedpe1.500.041.54
countBreakpointOverlaps1.810.001.82
findBreakpointOverlaps3.190.023.20
hasPartner1.240.051.28
isStructural0.400.000.41
isSymbolic0.390.000.39
numtDetect1.420.001.42
pairs2breakpointgr1.560.011.58
partner1.170.021.19