| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-01-28 11:09:58 -0500 (Sat, 28 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4465 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4246 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4269 |
| 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 | ||||
|
To the developers/maintainers of the StructuralVariantAnnotation package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/StructuralVariantAnnotation.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1972/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| StructuralVariantAnnotation 1.15.0 (landing page) Daniel Cameron
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | NA | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: StructuralVariantAnnotation |
| Version: 1.15.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:StructuralVariantAnnotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings StructuralVariantAnnotation_1.15.0.tar.gz |
| StartedAt: 2023-01-28 07:19:52 -0500 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 07:33:24 -0500 (Sat, 28 Jan 2023) |
| EllapsedTime: 812.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: StructuralVariantAnnotation.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:StructuralVariantAnnotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings StructuralVariantAnnotation_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/StructuralVariantAnnotation.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* 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 for sufficient/correct file permissions ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findBreakpointOverlaps 7.273 0.048 9.776
breakpointRanges 5.895 0.212 8.156
breakendRanges 5.836 0.116 7.794
countBreakpointOverlaps 5.012 0.031 6.540
numtDetect 4.008 0.018 5.177
* 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
‘/Users/biocbuild/bbs-3.17-bioc/meat/StructuralVariantAnnotation.Rcheck/00check.log’
for details.
StructuralVariantAnnotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL StructuralVariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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)
StructuralVariantAnnotation.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
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
StructuralVariantAnnotation.Rcheck/StructuralVariantAnnotation-Ex.timings
| name | user | system | elapsed | |
| breakendRanges | 5.836 | 0.116 | 7.794 | |
| breakpointRanges | 5.895 | 0.212 | 8.156 | |
| breakpointgr2bedpe | 3.487 | 0.025 | 4.647 | |
| countBreakpointOverlaps | 5.012 | 0.031 | 6.540 | |
| findBreakpointOverlaps | 7.273 | 0.048 | 9.776 | |
| hasPartner | 3.505 | 0.040 | 4.652 | |
| isStructural | 1.094 | 0.016 | 1.498 | |
| isSymbolic | 1.124 | 0.020 | 1.501 | |
| numtDetect | 4.008 | 0.018 | 5.177 | |
| pairs2breakpointgr | 3.802 | 0.023 | 4.901 | |
| partner | 3.289 | 0.022 | 4.316 | |