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February 24, 2026 14:48
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test issues for plyranges importing DFplyr
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| ❯ checking examples ... [14s/14s] ERROR | |
| Running examples in ‘plyranges-Ex.R’ failed | |
| The error most likely occurred in: | |
| > base::assign(".ptime", proc.time(), pos = "CheckExEnv") | |
| > ### Name: read_bed | |
| > ### Title: Read a BED or BEDGraph file | |
| > ### Aliases: read_bed read_bed_graph read_narrowpeaks | |
| > | |
| > ### ** Examples | |
| > | |
| > test_path <- system.file("tests", package = "rtracklayer") | |
| > bed_file <- file.path(test_path, "test.bed") | |
| > gr <- read_bed(bed_file) | |
| Error in (function (cond) : | |
| error in evaluating the argument 'x' in selecting a method for function 'elementType': node stack overflow | |
| Calls: read_bed ... .findMethodInTable -> is -> stopifnot -> <Anonymous> | |
| Execution halted | |
| ❯ checking tests ... | |
| See below... | |
| ❯ checking for future file timestamps ... NOTE | |
| unable to verify current time | |
| ── Test failures ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── testthat ──── | |
| > library(testthat) | |
| > library(plyranges) | |
| Loading required package: BiocGenerics | |
| Loading required package: generics | |
| Attaching package: 'generics' | |
| The following objects are masked from 'package:base': | |
| as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, | |
| setequal, union | |
| 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, is.unsorted, lapply, | |
| mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, | |
| rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, | |
| unsplit, which.max, which.min | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Loading required package: stats4 | |
| Attaching package: 'S4Vectors' | |
| The following object is masked from 'package:utils': | |
| findMatches | |
| The following objects are masked from 'package:base': | |
| I, expand.grid, unname | |
| Loading required package: GenomicRanges | |
| Loading required package: Seqinfo | |
| Loading required package: dplyr | |
| Attaching package: 'dplyr' | |
| The following objects are masked from 'package:GenomicRanges': | |
| intersect, setdiff, union | |
| The following object is masked from 'package:Seqinfo': | |
| intersect | |
| The following objects are masked from 'package:IRanges': | |
| collapse, desc, intersect, setdiff, slice, union | |
| The following objects are masked from 'package:S4Vectors': | |
| first, intersect, rename, setdiff, setequal, union | |
| The following objects are masked from 'package:BiocGenerics': | |
| combine, intersect, setdiff, setequal, union | |
| The following object is masked from 'package:generics': | |
| explain | |
| The following objects are masked from 'package:stats': | |
| filter, lag | |
| The following objects are masked from 'package:base': | |
| intersect, setdiff, setequal, union | |
| Attaching package: 'plyranges' | |
| The following objects are masked from 'package:dplyr': | |
| between, n, n_distinct | |
| > | |
| > test_check("plyranges") | |
| Saving _problems/test-add-nearest-distance-32.R | |
| Saving _problems/test-add-nearest-distance-55.R | |
| Saving _problems/test-io-bam-31.R | |
| Saving _problems/test-io-bed-81.R | |
| Saving _problems/test-io-bed-123.R | |
| Saving _problems/test-io-bed-138.R | |
| Saving _problems/test-io-bedGraph-22.R | |
| Saving _problems/test-io-bedGraph-26.R | |
| Saving _problems/test-io-bedGraph-29.R | |
| Saving _problems/test-io-bedGraph-35.R | |
| Saving _problems/test-io-bedGraph-47.R | |
| Saving _problems/test-io-bedGraph-51.R | |
| Saving _problems/test-io-bedGraph-64.R | |
| Saving _problems/test-io-bedGraph-70.R | |
| Saving _problems/test-io-bedGraph-74.R | |
| Saving _problems/test-io-bedGraph-81.R | |
| Saving _problems/test-io-gff-69.R | |
| Saving _problems/test-io-gff-146.R | |
| Saving _problems/test-join-distance-33.R | |
| Saving _problems/test-join-distance-45.R | |
| Saving _problems/test-nearest-24.R | |
| Saving _problems/test-nearest-36.R | |
| Saving _problems/test-unnest-26.R | |
| [ FAIL 30 | WARN 18 | SKIP 0 | PASS 351 ] | |
| ══ Warnings ════════════════════════════════════════════════════════════════════ | |
| ── Warning ('test-io-bedGraph.R:21:3'): read_bed_graph returns correct GRanges ── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg) at test-io-bedGraph.R:21:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:25:3'): read_bed_graph returns correct GRanges ── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg) at test-io-bedGraph.R:25:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:28:3'): read_bed_graph returns correct GRanges ── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg_con) at test-io-bedGraph.R:28:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:34:3'): read_bed_graph returns correct GRanges ── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg, overlap_ranges = correct_gr[3:4]) at test-io-bedGraph.R:34:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:46:3'): read_bed_graph returns correct GRanges ── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg, genome_info = "hg19") at test-io-bedGraph.R:46:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:50:3'): read_bed_graph returns correct GRanges ── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg, genome_info = hg19_gr) at test-io-bedGraph.R:50:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:63:3'): writing bedGraph files works ─────────── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg_out) at test-io-bedGraph.R:63:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:69:3'): writing bedGraph files works ─────────── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg_out) at test-io-bedGraph.R:69:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:73:3'): writing bedGraph files works ─────────── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg_out_file) at test-io-bedGraph.R:73:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─rtracklayer::import(con, "bedGraph", ...) | |
| 6. └─rtracklayer (local) .local(con, format, text, ...) | |
| 7. └─rtracklayer::GenomicData(...) | |
| 8. └─GenomicRanges::GRanges(...) | |
| 9. └─GenomicRanges:::new_GRanges(...) | |
| 10. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-bedGraph.R:80:3'): writing bedGraph files works ─────────── | |
| You supplied metadata columns of length 6 to set on an object of length 9. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_bed_graph(test_bg_gz) at test-io-bedGraph.R:80:3 | |
| 2. ├─rtracklayer::import.bedGraph(...) | |
| 3. └─rtracklayer::import.bedGraph(...) | |
| 4. ├─BiocIO::import(con, "bedGraph", ...) | |
| 5. └─BiocIO::import(con, "bedGraph", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::GenomicData(...) | |
| 10. └─GenomicRanges::GRanges(...) | |
| 11. └─GenomicRanges:::new_GRanges(...) | |
| 12. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-gff.R:69:3'): reading GFF files returns correct GRanges ─── | |
| You supplied metadata columns of length 27 to set on an object of length 31. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_gff3(test_gff3) at test-io-gff.R:69:3 | |
| 2. ├─rtracklayer::import.gff3(...) | |
| 3. └─rtracklayer::import.gff3(...) | |
| 4. ├─BiocIO::import(con, "gff3", ...) | |
| 5. └─BiocIO::import(con, "gff3", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::readGFFAsGRanges(...) | |
| 10. └─GenomicRanges::makeGRangesFromDataFrame(...) | |
| 11. └─GenomicRanges::GRanges(...) | |
| 12. └─GenomicRanges:::new_GRanges(...) | |
| 13. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-io-gff.R:135:3'): writing/reading other GFF files ──────────── | |
| The phase information is missing for some CDS. The written file will contain | |
| some CDS with no phase information. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::write_gff1(correct_gff3, test_gff_out) at test-io-gff.R:135:3 | |
| 2. ├─rtracklayer::export.gff1(x, file, index = index) | |
| 3. └─rtracklayer::export.gff1(x, file, index = index) | |
| 4. ├─BiocIO::export(object, con, "gff1", ...) | |
| 5. └─BiocIO::export(object, con, "gff1", ...) | |
| 6. ├─BiocIO::export(object, FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::export(object, FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(object, con, format, ...) | |
| ── Warning ('test-io-gff.R:140:3'): writing/reading other GFF files ──────────── | |
| The phase information is missing for some CDS. The written file will contain | |
| some CDS with no phase information. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::write_gff2(correct_gff3, test_gff_out) at test-io-gff.R:140:3 | |
| 2. ├─rtracklayer::export.gff2(x, file, index = index) | |
| 3. └─rtracklayer::export.gff2(x, file, index = index) | |
| 4. ├─BiocIO::export(object, con, "gff2", ...) | |
| 5. └─BiocIO::export(object, con, "gff2", ...) | |
| 6. ├─BiocIO::export(object, FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::export(object, FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(object, con, format, ...) | |
| ── Warning ('test-io-gff.R:145:3'): writing/reading other GFF files ──────────── | |
| The phase information is missing for some CDS. The written file will contain | |
| some CDS with no phase information. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::write_gff3(correct_gff3, test_gff_out) at test-io-gff.R:145:3 | |
| 2. ├─rtracklayer::export.gff3(x, file, index = index) | |
| 3. └─rtracklayer::export.gff3(x, file, index = index) | |
| 4. ├─BiocIO::export(object, con, "gff3", ...) | |
| 5. └─BiocIO::export(object, con, "gff3", ...) | |
| 6. ├─BiocIO::export(object, FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::export(object, FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(object, con, format, ...) | |
| ── Warning ('test-io-gff.R:146:3'): writing/reading other GFF files ──────────── | |
| You supplied metadata columns of length 27 to set on an object of length 31. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_gff3(test_gff_out) at test-io-gff.R:146:3 | |
| 2. ├─rtracklayer::import.gff3(...) | |
| 3. └─rtracklayer::import.gff3(...) | |
| 4. ├─BiocIO::import(con, "gff3", ...) | |
| 5. └─BiocIO::import(con, "gff3", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::readGFFAsGRanges(...) | |
| 10. └─GenomicRanges::makeGRangesFromDataFrame(...) | |
| 11. └─GenomicRanges::GRanges(...) | |
| 12. └─GenomicRanges:::new_GRanges(...) | |
| 13. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Warning ('test-join-mcols.R:7:3'): join_mcols works with different types of y ── | |
| You supplied metadata columns of length 5 to set on an object of length 6. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::join_mcols_left(x, y, by = "id") at test-join-mcols.R:7:3 | |
| 2. ├─S4Vectors::`mcols<-`(`*tmp*`, value = new_mcols) | |
| 3. └─S4Vectors::`mcols<-`(`*tmp*`, value = new_mcols) | |
| 4. ├─S4Vectors::`elementMetadata<-`(x, ..., value = value) | |
| 5. └─S4Vectors::`elementMetadata<-`(x, ..., value = value) | |
| 6. └─S4Vectors:::normarg_mcols(value, class(x), length(x)) | |
| ── Warning ('test-join-mcols.R:10:3'): join_mcols works with different types of y ── | |
| You supplied metadata columns of length 5 to set on an object of length 6. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::join_mcols_left(x, ydf, by = "id") at test-join-mcols.R:10:3 | |
| 2. ├─S4Vectors::`mcols<-`(`*tmp*`, value = new_mcols) | |
| 3. └─S4Vectors::`mcols<-`(`*tmp*`, value = new_mcols) | |
| 4. ├─S4Vectors::`elementMetadata<-`(x, ..., value = value) | |
| 5. └─S4Vectors::`elementMetadata<-`(x, ..., value = value) | |
| 6. └─S4Vectors:::normarg_mcols(value, class(x), length(x)) | |
| ── Warning ('test-join-mcols.R:13:3'): join_mcols works with different types of y ── | |
| You supplied metadata columns of length 5 to set on an object of length 6. | |
| However please note that the latter is not a multiple of the former. | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::join_mcols_left(x, ytib, by = "id") at test-join-mcols.R:13:3 | |
| 2. ├─S4Vectors::`mcols<-`(`*tmp*`, value = new_mcols) | |
| 3. └─S4Vectors::`mcols<-`(`*tmp*`, value = new_mcols) | |
| 4. ├─S4Vectors::`elementMetadata<-`(x, ..., value = value) | |
| 5. └─S4Vectors::`elementMetadata<-`(x, ..., value = value) | |
| 6. └─S4Vectors:::normarg_mcols(value, class(x), length(x)) | |
| ══ Failed tests ════════════════════════════════════════════════════════════════ | |
| ── Error ('test-add-nearest-distance.R:32:3'): add_nearest_distance works on GRanges ── | |
| Error: cannot subset by character when rownames are NULL | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::join_nearest(query, subject, distance = TRUE) at test-add-nearest-distance.R:32:3 | |
| 2. └─plyranges:::expand_by_hits(x, y, suffix, hits, hits_mcols_to_keep = distance_col) | |
| 3. └─plyranges:::add_hits_mcols(left, hits, hits_mcols_to_keep) | |
| 4. ├─mcols(hits)[hits_mcols_to_keep] | |
| 5. └─mcols(hits)[hits_mcols_to_keep] | |
| 6. └─DFplyr:::.s4_subset(x, i, j, ..., drop = drop) | |
| 7. ├─S4Vectors::extractROWS(x, i) | |
| 8. └─S4Vectors::extractROWS(x, i) | |
| 9. └─S4Vectors::normalizeSingleBracketSubscript(...) | |
| 10. ├─S4Vectors::NSBS(...) | |
| 11. └─S4Vectors::NSBS(...) | |
| 12. └─S4Vectors:::.subscript_error(...) | |
| ── Error ('test-add-nearest-distance.R:55:3'): add_nearest_distance works on IRanges ── | |
| Error: cannot subset by character when rownames are NULL | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::join_nearest(query_ir, subject_ir, distance = TRUE) at test-add-nearest-distance.R:55:3 | |
| 2. └─plyranges:::expand_by_hits(x, y, suffix, hits, hits_mcols_to_keep = distance_col) | |
| 3. └─plyranges:::add_hits_mcols(left, hits, hits_mcols_to_keep) | |
| 4. ├─mcols(hits)[hits_mcols_to_keep] | |
| 5. └─mcols(hits)[hits_mcols_to_keep] | |
| 6. └─DFplyr:::.s4_subset(x, i, j, ..., drop = drop) | |
| 7. ├─S4Vectors::extractROWS(x, i) | |
| 8. └─S4Vectors::extractROWS(x, i) | |
| 9. └─S4Vectors::normalizeSingleBracketSubscript(...) | |
| 10. ├─S4Vectors::NSBS(...) | |
| 11. └─S4Vectors::NSBS(...) | |
| 12. └─S4Vectors:::.subscript_error(...) | |
| ── Error ('test-coverage.R:54:1'): Compatible with GenomicRanges ─────────────── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Error ('test-disjoin.R:85:5'): matches HelloRanges multinter ──────────────── | |
| Error in `S4Vectors:::normarg_mcols(mcols, Class, ans_len)`: trying to set zero length metadata columns on a non-zero length object | |
| Backtrace: | |
| ▆ | |
| 1. ├─S4Vectors::List(...) at test-disjoin.R:84:3 | |
| 2. └─base::lapply(...) | |
| 3. └─plyranges (local) FUN(X[[i]], ...) | |
| 4. ├─dplyr::mutate(read_bed(x), grp = sub(".bed$", "", basename(x))) at test-disjoin.R:85:5 | |
| 5. └─plyranges::read_bed(x) | |
| 6. ├─rtracklayer::import.bed(...) | |
| 7. └─rtracklayer::import.bed(...) | |
| 8. ├─BiocIO::import(con, format = "bed", ...) | |
| 9. └─BiocIO::import(con, format = "bed", ...) | |
| 10. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 11. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 12. └─rtracklayer (local) .local(con, format, text, ...) | |
| 13. └─rtracklayer::GenomicData(...) | |
| 14. └─GenomicRanges::GRanges(...) | |
| 15. └─GenomicRanges:::new_GRanges(...) | |
| 16. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Error ('test-flank.R:3:1'): matches HelloRanges ───────────────────────────── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Error ('test-groups.R:50:1'): group by matches HelloRanges ────────────────── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Error ('test-io-bam.R:30:3'): overlaps works as expected ──────────────────── | |
| Error in `new_Rle(values, lengths)`: Rle of type 'S4' is not supported | |
| Backtrace: | |
| ▆ | |
| 1. ├─read_bam(fl, paired = TRUE) %>% ... at test-io-bam.R:30:3 | |
| 2. ├─dplyr::filter(...) | |
| 3. └─plyranges:::filter.DeferredGenomicRanges(...) | |
| 4. ├─plyranges:::load_genomic_file(.data@ops) | |
| 5. └─plyranges:::load_genomic_file.BamFileOperator(.data@ops) | |
| 6. └─plyranges:::paired_alignments(ops) | |
| 7. ├─GenomicAlignments::readGAlignmentPairs(...) | |
| 8. └─GenomicAlignments::readGAlignmentPairs(...) | |
| 9. └─GenomicAlignments:::.make_GAlignmentPairs_from_GAlignments(...) | |
| 10. ├─S4Vectors::Rle(mcols(gal, use.names = FALSE)[, "groupid"]) | |
| 11. └─S4Vectors::Rle(mcols(gal, use.names = FALSE)[, "groupid"]) | |
| 12. └─S4Vectors:::new_Rle(values, lengths) | |
| ── Error ('test-io-bed.R:24:1'): read_bed returns correct GRanges ────────────── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Error ('test-io-bed.R:83:1'): write bed returns correct bed files ─────────── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Error ('test-io-bed.R:125:1'): read_narrowpeaks returns correct GRanges ───── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Failure ('test-io-bedGraph.R:22:3'): read_bed_graph returns correct GRanges ── | |
| Expected `test_gr` to be identical to `correct_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 4, 1 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (4, 1) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: character, numeric > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is character, current is numeric > > | |
| ── Failure ('test-io-bedGraph.R:26:3'): read_bed_graph returns correct GRanges ── | |
| Expected `test_gr` to be identical to `correct_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 4, 1 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (4, 1) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: character, numeric > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is character, current is numeric > > | |
| ── Failure ('test-io-bedGraph.R:29:3'): read_bed_graph returns correct GRanges ── | |
| Expected `test_gr` to be identical to `correct_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 4, 1 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (4, 1) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: character, numeric > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is character, current is numeric > > | |
| ── Failure ('test-io-bedGraph.R:35:3'): read_bed_graph returns correct GRanges ── | |
| Expected `correct_which` to be identical to `test_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 1, 4 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (1, 4) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: numeric, character > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is numeric, current is character > > | |
| ── Failure ('test-io-bedGraph.R:47:3'): read_bed_graph returns correct GRanges ── | |
| Expected `correct_genome` to be identical to `test_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 1, 4 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (1, 4) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: numeric, character > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is numeric, current is character > > | |
| ── Failure ('test-io-bedGraph.R:51:3'): read_bed_graph returns correct GRanges ── | |
| Expected `correct_genome` to be identical to `test_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 1, 4 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (1, 4) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: numeric, character > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is numeric, current is character > > | |
| ── Failure ('test-io-bedGraph.R:64:3'): writing bedGraph files works ─────────── | |
| Expected `correct_gr` to be identical to `test_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 1, 4 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (1, 4) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: numeric, character > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is numeric, current is character > > | |
| ── Failure ('test-io-bedGraph.R:70:3'): writing bedGraph files works ─────────── | |
| Expected `correct_gr` to be identical to `test_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 1, 4 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (1, 4) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: numeric, character > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is numeric, current is character > > | |
| ── Failure ('test-io-bedGraph.R:74:3'): writing bedGraph files works ─────────── | |
| Expected `correct_gr` to be identical to `test_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 1, 4 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (1, 4) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: numeric, character > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is numeric, current is character > > | |
| ── Failure ('test-io-bedGraph.R:81:3'): writing bedGraph files works ─────────── | |
| Expected `correct_gr` to be identical to `test_gr`. | |
| Differences: | |
| Attributes: < Component "elementMetadata": Lengths: 1, 4 > | |
| Attributes: < Component "elementMetadata": Names: Lengths (1, 4) differ (string compare on first 1) > | |
| Attributes: < Component "elementMetadata": Names: 1 string mismatch > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Names: 1 string mismatch > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Length mismatch: comparison on first 1 components > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: Modes: numeric, character > > | |
| Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component 1: target is numeric, current is character > > | |
| ── Error ('test-io-gff.R:69:3'): reading GFF files returns correct GRanges ───── | |
| Error in `validObject(ans)`: invalid class "GRanges" object: | |
| names of metadata columns cannot be one of "seqnames", "ranges", | |
| "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", | |
| "width", "element" | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_gff3(test_gff3) at test-io-gff.R:69:3 | |
| 2. ├─rtracklayer::import.gff3(...) | |
| 3. └─rtracklayer::import.gff3(...) | |
| 4. ├─BiocIO::import(con, "gff3", ...) | |
| 5. └─BiocIO::import(con, "gff3", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::readGFFAsGRanges(...) | |
| 10. └─GenomicRanges::makeGRangesFromDataFrame(...) | |
| 11. └─GenomicRanges::GRanges(...) | |
| 12. └─methods::validObject(ans) | |
| ── Error ('test-io-gff.R:146:3'): writing/reading other GFF files ────────────── | |
| Error in `validObject(ans)`: invalid class "GRanges" object: | |
| names of metadata columns cannot be one of "seqnames", "ranges", | |
| "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", | |
| "width", "element" | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::read_gff3(test_gff_out) at test-io-gff.R:146:3 | |
| 2. ├─rtracklayer::import.gff3(...) | |
| 3. └─rtracklayer::import.gff3(...) | |
| 4. ├─BiocIO::import(con, "gff3", ...) | |
| 5. └─BiocIO::import(con, "gff3", ...) | |
| 6. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 7. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 8. └─rtracklayer (local) .local(con, format, text, ...) | |
| 9. └─rtracklayer::readGFFAsGRanges(...) | |
| 10. └─GenomicRanges::makeGRangesFromDataFrame(...) | |
| 11. └─GenomicRanges::GRanges(...) | |
| 12. └─methods::validObject(ans) | |
| ── Error ('test-join-distance.R:33:3'): join_nearest behaves correctly on GRanges ── | |
| Error: cannot subset by character when rownames are NULL | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges (local) test_nearest_join_distance(query, subject, join_nearest) at test-join-distance.R:33:3 | |
| 2. └─plyranges (local) join_fun(query, subject, distance = TRUE) at test-join-distance.R:4:3 | |
| 3. └─plyranges:::expand_by_hits(x, y, suffix, hits, hits_mcols_to_keep = distance_col) | |
| 4. └─plyranges:::add_hits_mcols(left, hits, hits_mcols_to_keep) | |
| 5. ├─mcols(hits)[hits_mcols_to_keep] | |
| 6. └─mcols(hits)[hits_mcols_to_keep] | |
| 7. └─DFplyr:::.s4_subset(x, i, j, ..., drop = drop) | |
| 8. ├─S4Vectors::extractROWS(x, i) | |
| 9. └─S4Vectors::extractROWS(x, i) | |
| 10. └─S4Vectors::normalizeSingleBracketSubscript(...) | |
| 11. ├─S4Vectors::NSBS(...) | |
| 12. └─S4Vectors::NSBS(...) | |
| 13. └─S4Vectors:::.subscript_error(...) | |
| ── Error ('test-join-distance.R:45:3'): join_nearest works on IRanges ────────── | |
| Error: cannot subset by character when rownames are NULL | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges (local) test_nearest_join_distance(...) at test-join-distance.R:45:3 | |
| 2. └─plyranges (local) join_fun(query, subject, distance = TRUE) at test-join-distance.R:4:3 | |
| 3. └─plyranges:::expand_by_hits(x, y, suffix, hits, hits_mcols_to_keep = distance_col) | |
| 4. └─plyranges:::add_hits_mcols(left, hits, hits_mcols_to_keep) | |
| 5. ├─mcols(hits)[hits_mcols_to_keep] | |
| 6. └─mcols(hits)[hits_mcols_to_keep] | |
| 7. └─DFplyr:::.s4_subset(x, i, j, ..., drop = drop) | |
| 8. ├─S4Vectors::extractROWS(x, i) | |
| 9. └─S4Vectors::extractROWS(x, i) | |
| 10. └─S4Vectors::normalizeSingleBracketSubscript(...) | |
| 11. ├─S4Vectors::NSBS(...) | |
| 12. └─S4Vectors::NSBS(...) | |
| 13. └─S4Vectors:::.subscript_error(...) | |
| ── Failure ('test-nearest.R:23:3'): nearest/follows/precedes matches IRanges methods ── | |
| Expected `mcols(result)$subject` to be identical to `...[]`. | |
| Differences: | |
| Types not compatible: character is not S4 | |
| ── Failure ('test-nearest.R:35:3'): nearest/follows/precedes matches IRanges methods ── | |
| Expected `result_pairs$subject` to be identical to `...[]`. | |
| Differences: | |
| Types not compatible: character is not S4 | |
| ── Error ('test-reduce.R:64:1'): non-standard evaluation works as expected ───── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Error ('test-reduce.R:115:5'): grouping then reducing works as expected ───── | |
| Error in `S4Vectors:::normarg_mcols(mcols, Class, ans_len)`: trying to set zero length metadata columns on a non-zero length object | |
| Backtrace: | |
| ▆ | |
| 1. ├─methods::as(...) at test-reduce.R:114:3 | |
| 2. │ └─methods:::.class1(object) | |
| 3. └─base::lapply(...) | |
| 4. └─plyranges (local) FUN(X[[i]], ...) | |
| 5. ├─dplyr::mutate(read_bed(x), grp = sub(".bed$", "", basename(x))) at test-reduce.R:115:5 | |
| 6. └─plyranges::read_bed(x) | |
| 7. ├─rtracklayer::import.bed(...) | |
| 8. └─rtracklayer::import.bed(...) | |
| 9. ├─BiocIO::import(con, format = "bed", ...) | |
| 10. └─BiocIO::import(con, format = "bed", ...) | |
| 11. ├─BiocIO::import(FileForFormat(con, format), ...) | |
| 12. └─rtracklayer::import(FileForFormat(con, format), ...) | |
| 13. └─rtracklayer (local) .local(con, format, text, ...) | |
| 14. └─rtracklayer::GenomicData(...) | |
| 15. └─GenomicRanges::GRanges(...) | |
| 16. └─GenomicRanges:::new_GRanges(...) | |
| 17. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len) | |
| ── Error: (code run outside of `test_that()`) ────────────────────────────────── | |
| <nodeStackOverflowError/stackOverflowError/error/condition> | |
| Error: node stack overflow | |
| ── Error ('test-unnest.R:26:3'): expanding makes sense ───────────────────────── | |
| Error: cannot subset by character when rownames are NULL | |
| Backtrace: | |
| ▆ | |
| 1. └─plyranges::expand_ranges(gr, .recursive = TRUE) at test-unnest.R:26:3 | |
| 2. ├─S4Vectors::expand(...) | |
| 3. └─S4Vectors::expand(...) | |
| 4. └─S4Vectors (local) .local(x, ...) | |
| 5. └─S4Vectors:::.expand(df, colnames, keepEmptyRows, recursive) | |
| 6. └─S4Vectors:::.expandCols(x, colname, keepEmptyRows) | |
| 7. ├─x[colnames] | |
| 8. └─x[colnames] | |
| 9. └─DFplyr:::.s4_subset(x, i, j, ..., drop = drop) | |
| 10. ├─S4Vectors::extractROWS(x, i) | |
| 11. └─S4Vectors::extractROWS(x, i) | |
| 12. └─S4Vectors::normalizeSingleBracketSubscript(...) | |
| 13. ├─S4Vectors::NSBS(...) | |
| 14. └─S4Vectors::NSBS(...) | |
| 15. └─S4Vectors:::.subscript_error(...) | |
| [ FAIL 30 | WARN 18 | SKIP 0 | PASS 351 ] | |
| Error: | |
| ! Test failures. | |
| Execution halted |
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