Last updated on 2026-10-27 17:54:53 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1.0.1.0 | 148.95 | 998.10 | 1147.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1.0.1.0 | 161.26 | 455.28 | 616.54 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1.0.1.0 | 106.00 | 719.76 | 825.76 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.0.1.0.1.0 | 177.00 | 424.44 | 601.44 | OK | |
| r-devel-windows-x86_64 | 2.0.1.0.1.0 | 282.00 | 813.00 | 1095.00 | OK | |
| r-patched-linux-x86_64 | 2.0.0.0.1.9 | 215.16 | 443.88 | 659.04 | OK | |
| r-release-linux-x86_64 | 2.0.0.0.1.9 | 217.88 | 150.27 | 368.15 | ERROR | |
| r-release-macos-arm64 | 2.0.1.0.1.0 | 36.00 | 142.00 | 178.00 | OK | |
| r-release-macos-x86_64 | 2.0.1.0.1.0 | 123.00 | 692.00 | 815.00 | OK | |
| r-release-windows-x86_64 | 2.0.1.0.1.0 | 270.00 | 759.00 | 1029.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1.0.1.0 | 53.00 | 161.00 | 214.00 | OK | |
| r-oldrel-macos-x86_64 | 2.0.1.0.1.0 | 120.00 | 706.00 | 826.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1.0.1.0 | 257.00 | 731.00 | 988.00 | ERROR |
Version: 2.0.1.0.1.0
Check: tests
Result: ERROR
Running ‘tinytest.R’ [382s/452s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
> if (requireNamespace("tinytest", quietly = TRUE)) {
+ tinytest::test_package("Rduckhts")
+ } else {
+ message("tinytest not available; skipping tests")
+ }
test_ancestry.R............... 0 tests
test_ancestry.R............... 0 tests
test_ancestry.R............... 0 tests
test_ancestry.R............... 156 tests OK
test_ancestry.R............... 156 tests OK
test_ancestry.R............... 170 tests OK 28.9s
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 54 tests OK 9.5s
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 37 tests OK 0.9s
test_bam_file_offset.R........ 0 tests
test_bam_file_offset.R........ 0 tests
test_bam_file_offset.R........ 0 tests [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
test_bam_file_offset.R........ 280 tests OK 3.0s
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 18 tests OK 0.8s
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 39 tests OK 1.0s
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 18 tests OK 1.1s
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests [W::sam_read1_sam] Parse error at line 4
test_bam_scan.R............... 186 tests OK
test_bam_scan.R............... 194 tests OK
test_bam_scan.R............... 208 tests OK
test_bam_scan.R............... 241 tests OK 4.9s
test_basic.R.................. 0 tests
test_basic.R.................. 1 tests OK
test_basic.R.................. 2 tests OK
test_basic.R.................. 3 tests OK
test_basic.R.................. 4 tests OK
test_basic.R.................. 5 tests OK
test_basic.R.................. 6 tests OK
test_basic.R.................. 7 tests OK
test_basic.R.................. 8 tests OK
test_basic.R.................. 9 tests OK
test_basic.R.................. 10 tests OK
test_basic.R.................. 11 tests OK
test_basic.R.................. 12 tests OK
test_basic.R.................. 13 tests OK
test_basic.R.................. 14 tests OK
test_basic.R.................. 15 tests OK
test_basic.R.................. 16 tests OK
test_basic.R.................. 17 tests OK
test_basic.R.................. 18 tests OK
test_basic.R.................. 19 tests OK
test_basic.R.................. 20 tests OK
test_basic.R.................. 21 tests OK
test_basic.R.................. 22 tests OK
test_basic.R.................. 23 tests OK
test_basic.R.................. 24 tests OK
test_basic.R.................. 25 tests OK
test_basic.R.................. 26 tests OK
test_basic.R.................. 27 tests OK
test_basic.R.................. 28 tests OK
test_basic.R.................. 29 tests OK
test_basic.R.................. 30 tests OK
test_basic.R.................. 31 tests OK
test_basic.R.................. 32 tests OK
test_basic.R.................. 33 tests OK
test_basic.R.................. 34 tests OK
test_basic.R.................. 35 tests OK
test_basic.R.................. 36 tests OK
test_basic.R.................. 37 tests OK
test_basic.R.................. 38 tests OK
test_basic.R.................. 39 tests OK
test_basic.R.................. 40 tests OK
test_basic.R.................. 41 tests OK
test_basic.R.................. 42 tests OK
test_basic.R.................. 43 tests OK
test_basic.R.................. 44 tests OK
test_basic.R.................. 45 tests OK
test_basic.R.................. 46 tests OK
test_basic.R.................. 47 tests OK
test_basic.R.................. 48 tests OK
test_basic.R.................. 49 tests OK
test_basic.R.................. 50 tests OK
test_basic.R.................. 51 tests OK
test_basic.R.................. 52 tests OK
test_basic.R.................. 53 tests OK
test_basic.R.................. 54 tests OK
test_basic.R.................. 55 tests OK
test_basic.R.................. 56 tests OK
test_basic.R.................. 57 tests OK
test_basic.R.................. 58 tests OK
test_basic.R.................. 59 tests OK
test_basic.R.................. 60 tests OK
test_basic.R.................. 61 tests OK
test_basic.R.................. 62 tests OK
test_basic.R.................. 63 tests OK
test_basic.R.................. 64 tests OK
test_basic.R.................. 65 tests OK
test_basic.R.................. 66 tests OK
test_basic.R.................. 67 tests OK
test_basic.R.................. 68 tests OK
test_basic.R.................. 69 tests OK
test_basic.R.................. 70 tests OK
test_basic.R.................. 71 tests OK
test_basic.R.................. 72 tests OK
test_basic.R.................. 73 tests OK
test_basic.R.................. 74 tests OK
test_basic.R.................. 75 tests OK
test_basic.R.................. 76 tests OK
test_basic.R.................. 77 tests OK
test_basic.R.................. 78 tests OK
test_basic.R.................. 78 tests OK
test_basic.R.................. 79 tests OK
test_basic.R.................. 80 tests OK
test_basic.R.................. 81 tests OK
test_basic.R.................. 82 tests OK
test_basic.R.................. 83 tests OK
test_basic.R.................. 84 tests OK
test_basic.R.................. 85 tests OK
test_basic.R.................. 86 tests OK
test_basic.R.................. 87 tests OK
test_basic.R.................. 88 tests OK
test_basic.R.................. 89 tests OK
test_basic.R.................. 89 tests OK
test_basic.R.................. 90 tests OK
test_basic.R.................. 91 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 93 tests OK
test_basic.R.................. 94 tests OK
test_basic.R.................. 95 tests OK
test_basic.R.................. 96 tests OK
test_basic.R.................. 96 tests OK
test_basic.R.................. 97 tests OK
test_basic.R.................. 98 tests OK
test_basic.R.................. 99 tests OK
test_basic.R.................. 100 tests OK
test_basic.R.................. 101 tests OK
test_basic.R.................. 102 tests OK
test_basic.R.................. 103 tests OK
test_basic.R.................. 104 tests OK
test_basic.R.................. 104 tests OK
test_basic.R.................. 105 tests OK
test_basic.R.................. 106 tests OK
test_basic.R.................. 106 tests OK
test_basic.R.................. 107 tests OK
test_basic.R.................. 108 tests OK
test_basic.R.................. 109 tests OK
test_basic.R.................. 110 tests OK
test_basic.R.................. 111 tests OK
test_basic.R.................. 112 tests OK
test_basic.R.................. 113 tests OK
test_basic.R.................. 114 tests OK
test_basic.R.................. 115 tests OK
test_basic.R.................. 116 tests OK
test_basic.R.................. 117 tests OK
test_basic.R.................. 118 tests OK
test_basic.R.................. 119 tests OK
test_basic.R.................. 120 tests OK
test_basic.R.................. 121 tests OK
test_basic.R.................. 122 tests OK
test_basic.R.................. 123 tests OK
test_basic.R.................. 124 tests OK
test_basic.R.................. 125 tests OK
test_basic.R.................. 126 tests OK
test_basic.R.................. 127 tests OK
test_basic.R.................. 128 tests OK
test_basic.R.................. 129 tests OK
test_basic.R.................. 130 tests OK
test_basic.R.................. 131 tests OK
test_basic.R.................. 483 tests OK
test_basic.R.................. 484 tests OK
test_basic.R.................. 485 tests OK
test_basic.R.................. 486 tests OK
test_basic.R.................. 487 tests OK
test_basic.R.................. 488 tests OK
test_basic.R.................. 489 tests OK
test_basic.R.................. 490 tests OK
test_basic.R.................. 491 tests OK
test_basic.R.................. 492 tests OK
test_basic.R.................. 493 tests OK
test_basic.R.................. 494 tests OK
test_basic.R.................. 495 tests OK
test_basic.R.................. 496 tests OK
test_basic.R.................. 497 tests OK
test_basic.R.................. 498 tests OK
test_basic.R.................. 499 tests OK
test_basic.R.................. 500 tests OK
test_basic.R.................. 501 tests OK
test_basic.R.................. 502 tests OK
test_basic.R.................. 503 tests OK
test_basic.R.................. 504 tests OK
test_basic.R.................. 505 tests OK
test_basic.R.................. 506 tests OK
test_basic.R.................. 507 tests OK
test_basic.R.................. 508 tests OK
test_basic.R.................. 509 tests OK
test_basic.R.................. 510 tests OK
test_basic.R.................. 511 tests OK
test_basic.R.................. 512 tests OK
test_basic.R.................. 513 tests OK
test_basic.R.................. 514 tests OK
test_basic.R.................. 515 tests OK
test_basic.R.................. 516 tests OK
test_basic.R.................. 517 tests OK
test_basic.R.................. 518 tests OK
test_basic.R.................. 519 tests OK
test_basic.R.................. 520 tests OK
test_basic.R.................. 521 tests OK
test_basic.R.................. 522 tests OK
test_basic.R.................. 523 tests OK
test_basic.R.................. 524 tests OK
test_basic.R.................. 525 tests OK All basic tests passed!
test_basic.R.................. 525 tests OK 1.8s
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
test_bcf.R.................... 64 tests OK [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
test_bcf.R.................... 258 tests OK [E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
test_bcf.R.................... 2520 tests OK
test_bcf.R.................... 2530 tests OK
test_bcf.R.................... 2553 tests OK [W::vcf_parse] Contig '22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
test_bcf.R.................... 2578 tests OK
test_bcf.R.................... 2582 tests OK 1.1s
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 1 tests OK
test_bcf_file_offset.R........ 2 tests OK
test_bcf_file_offset.R........ 3 tests OK
test_bcf_file_offset.R........ 4 tests OK
test_bcf_file_offset.R........ 4 tests OK
test_bcf_file_offset.R........ 5 tests OK
test_bcf_file_offset.R........ 17 tests OK
test_bcf_file_offset.R........ 18 tests OK
test_bcf_file_offset.R........ 18 tests OK
test_bcf_file_offset.R........ 19 tests OK
test_bcf_file_offset.R........ 20 tests OK
test_bcf_file_offset.R........ 21 tests OK
test_bcf_file_offset.R........ 21 tests OK
test_bcf_file_offset.R........ 22 tests OK
test_bcf_file_offset.R........ 23 tests OK
test_bcf_file_offset.R........ 27 tests OK
test_bcf_file_offset.R........ 28 tests OK
test_bcf_file_offset.R........ 28 tests OK 1.2s
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 6 tests OK [E::vcf_parse] Could not parse the position 'bad'
[E::vcf_parse] Could not parse the position 'bad'
[E::vcf_parse] Could not parse the position 'bad'
test_bcf_regression.R......... 11 tests OK [W::accept_mismatch] read_bcf: FORMAT/XX encoded BCF type CHAR does not match header Type=Integer at chr1:10
test_bcf_regression.R......... 23 tests OK [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
test_bcf_regression.R......... 60 tests OK 4.4s
test_bcftools_norm.R.......... 0 tests
test_bcftools_norm.R.......... 0 tests
test_bcftools_norm.R.......... 0 tests
test_bcftools_norm.R.......... 146 tests OK 2.2s
test_bigwig.R................. 0 tests
test_bigwig.R................. 0 tests
test_bigwig.R................. 0 tests [bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
test_bigwig.R................. 17 tests OK 1.3s
test_bin_counts.R............. 0 tests
test_bin_counts.R............. 0 tests
test_bin_counts.R............. 0 tests
test_bin_counts.R............. 39 tests OK 1.1s
test_cgranges_api.R........... 0 tests
test_cgranges_api.R........... 0 tests
test_cgranges_api.R........... 0 tests
test_cgranges_api.R........... 96 tests OK 1.2s
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 582 tests OK
test_cigar_utils.R............ 617 tests OK 3.9s
test_connection.R............. 0 tests
test_connection.R............. 0 tests
test_connection.R............. 1 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 10 tests OK
test_connection.R............. 15 tests OK
test_connection.R............. 17 tests OK
test_connection.R............. 18 tests OK 2.0s
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 1 tests OK
test_convert_parquet.R........ 2 tests OK
test_convert_parquet.R........ 3 tests OK
test_convert_parquet.R........ 4 tests OK
test_convert_parquet.R........ 23 tests OK
test_convert_parquet.R........ 29 tests OK
test_convert_parquet.R........ 36 tests OK
test_convert_parquet.R........ 42 tests OK 3.4s
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 28 tests OK 2.2s
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 137 tests OK 8.9s
test_database_lifetime.R...... 0 tests
test_database_lifetime.R...... 0 tests
test_database_lifetime.R...... 6 tests OK 2.6s
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 1 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 3 tests OK
test_depth_fraction.R......... 4 tests OK
test_depth_fraction.R......... 5 tests OK
test_depth_fraction.R......... 6 tests OK
test_depth_fraction.R......... 7 tests OK
test_depth_fraction.R......... 7 tests OK
test_depth_fraction.R......... 8 tests OK
test_depth_fraction.R......... 29 tests OK
test_depth_fraction.R......... 29 tests OK
test_depth_fraction.R......... 30 tests OK
test_depth_fraction.R......... 30 tests OK
test_depth_fraction.R......... 30 tests OK
test_depth_fraction.R......... 31 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 33 tests OK
test_depth_fraction.R......... 45 tests OK
test_depth_fraction.R......... 45 tests OK
test_depth_fraction.R......... 46 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 48 tests OK
test_depth_fraction.R......... 49 tests OK
test_depth_fraction.R......... 50 tests OK
test_depth_fraction.R......... 50 tests OK
test_depth_fraction.R......... 51 tests OK
test_depth_fraction.R......... 52 tests OK
test_depth_fraction.R......... 52 tests OK
test_depth_fraction.R......... 52 tests OK
test_depth_fraction.R......... 53 tests OK
test_depth_fraction.R......... 65 tests OK
test_depth_fraction.R......... 65 tests OK
test_depth_fraction.R......... 68 tests OK
test_depth_fraction.R......... 69 tests OK
test_depth_fraction.R......... 69 tests OK
test_depth_fraction.R......... 70 tests OK
test_depth_fraction.R......... 71 tests OK
test_depth_fraction.R......... 71 tests OK
test_depth_fraction.R......... 71 tests OK
test_depth_fraction.R......... 72 tests OK
test_depth_fraction.R......... 72 tests OK
test_depth_fraction.R......... 73 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 75 tests OK
test_depth_fraction.R......... 76 tests OK
test_depth_fraction.R......... 77 tests OK
test_depth_fraction.R......... 78 tests OK
test_depth_fraction.R......... 79 tests OK
test_depth_fraction.R......... 79 tests OK
test_depth_fraction.R......... 80 tests OK
test_depth_fraction.R......... 81 tests OK
test_depth_fraction.R......... 82 tests OK
test_depth_fraction.R......... 83 tests OK
test_depth_fraction.R......... 84 tests OK
test_depth_fraction.R......... 85 tests OK
test_depth_fraction.R......... 86 tests OK
test_depth_fraction.R......... 87 tests OK
test_depth_fraction.R......... 87 tests OK
test_depth_fraction.R......... 88 tests OK
test_depth_fraction.R......... 88 tests OK
test_depth_fraction.R......... 89 tests OK
test_depth_fraction.R......... 89 tests OK
test_depth_fraction.R......... 90 tests OK
test_depth_fraction.R......... 90 tests OK
test_depth_fraction.R......... 91 tests OK
test_depth_fraction.R......... 91 tests OK 3.0s
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 1 tests OK
test_depth_state_model.R...... 2 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 4 tests OK
test_depth_state_model.R...... 5 tests OK
test_depth_state_model.R...... 6 tests OK
test_depth_state_model.R...... 7 tests OK
test_depth_state_model.R...... 8 tests OK
test_depth_state_model.R...... 9 tests OK
test_depth_state_model.R...... 10 tests OK
test_depth_state_model.R...... 11 tests OK
test_depth_state_model.R...... 11 tests OK
test_depth_state_model.R...... 12 tests OK
test_depth_state_model.R...... 12 tests OK
test_depth_state_model.R...... 13 tests OK
test_depth_state_model.R...... 13 tests OK
test_depth_state_model.R...... 13 tests OK
test_depth_state_model.R...... 14 tests OK
test_depth_state_model.R...... 14 tests OK
test_depth_state_model.R...... 15 tests OK
test_depth_state_model.R...... 16 tests OK
test_depth_state_model.R...... 17 tests OK
test_depth_state_model.R...... 18 tests OK
test_depth_state_model.R...... 18 tests OK
test_depth_state_model.R...... 18 tests OK
test_depth_state_model.R...... 19 tests OK
test_depth_state_model.R...... 20 tests OK
test_depth_state_model.R...... 21 tests OK
test_depth_state_model.R...... 21 tests OK
test_depth_state_model.R...... 22 tests OK
test_depth_state_model.R...... 23 tests OK
test_depth_state_model.R...... 24 tests OK
test_depth_state_model.R...... 25 tests OK
test_depth_state_model.R...... 26 tests OK
test_depth_state_model.R...... 27 tests OK
test_depth_state_model.R...... 28 tests OK
test_depth_state_model.R...... 29 tests OK
test_depth_state_model.R...... 30 tests OK
test_depth_state_model.R...... 30 tests OK 26.0s
test_fastq_qc.R............... 0 tests
test_fastq_qc.R............... 0 tests
test_fastq_qc.R............... 0 tests
test_fastq_qc.R............... 22 tests OK 0.9s
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 28 tests OK
test_genbank.R................ 36 tests OK
test_genbank.R................ 59 tests OK 2.7s
test_geno.R................... 0 tests
test_geno.R................... 0 tests
test_geno.R................... 0 tests
test_geno.R................... 0 tests [W::bcf_hdr_check_sanity] PS should be declared as Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1
[W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1
[W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1
[W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1
[W::accept_mismatch] read_geno: FORMAT/PS encoded BCF type CHAR does not match header Type=Integer at chrG:10
[E::vcf_parse] Could not parse the position 'bad'
test_geno.R................... 145 tests OK
test_geno.R................... 145 tests OK
test_geno.R................... 145 tests OK [W::accept_mismatch] read_geno: FORMAT/XX encoded BCF type CHAR does not match header Type=Integer at chr1:10
test_geno.R................... 211 tests OK [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
test_geno.R................... 232 tests OK
test_geno.R................... 331 tests OK 8.6s
test_geno_sites.R............. 0 tests
test_geno_sites.R............. 0 tests
test_geno_sites.R............. 0 tests
test_geno_sites.R............. 182 tests OK 2.9s
test_gxf_named_attributes.R... 0 tests
test_gxf_named_attributes.R... 0 tests
test_gxf_named_attributes.R... 60 tests OK 1.8s
test_htslib_contract.R........ 0 tests
test_htslib_contract.R........ 0 tests
test_htslib_contract.R........ 28 tests OK 2.4s
test_indexes_bgzip.R.......... 0 tests
test_indexes_bgzip.R.......... 0 tests
test_indexes_bgzip.R.......... 0 tests
test_indexes_bgzip.R.......... 0 tests [E::bgzf_uncompress] CRC32 checksum mismatch
[E::bgzf_read_block] BGZF decode jobs returned error 1 for block offset 0
[E::bgzf_read] Read block operation failed with error 1 after 0 of 65536 bytes
[E::bgzf_uncompress] CRC32 checksum mismatch
[E::bgzf_read] Read block operation failed with error 33 after 0 of 65536 bytes
test_indexes_bgzip.R.......... 67 tests OK
test_indexes_bgzip.R.......... 93 tests OK 2.4s
test_insert_size.R............ 0 tests
test_insert_size.R............ 0 tests
test_insert_size.R............ 0 tests [E::hts_open_format] Failed to open file "missing.bam" : No such file or directory
[E::hts_open_format] Failed to open file "missing.bam" : No such file or directory
test_insert_size.R............ 484 tests OK 10.2s
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests [E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_valid.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_valid.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_valid.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid_attr.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid_attr.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid_attr.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_extra_field.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_extra_field.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_extra_field.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid_end.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid_end.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_strict_invalid_end.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_attrs.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_attrs.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gff_attrs.gff3'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gtf_attrs.gtf'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gtf_attrs.gtf'
[E::idx_find_and_load] Could not retrieve index file for '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rduckhts/extdata/gtf_attrs.gtf'
GFF schema with attributes_map=TRUE:
column_name column_type null key default extra
1 seqname VARCHAR YES <NA> <NA> <NA>
2 source VARCHAR YES <NA> <NA> <NA>
3 feature VARCHAR YES <NA> <NA> <NA>
4 start BIGINT YES <NA> <NA> <NA>
5 end BIGINT YES <NA> <NA> <NA>
6 score DOUBLE YES <NA> <NA> <NA>
7 strand VARCHAR YES <NA> <NA> <NA>
8 frame VARCHAR YES <NA> <NA> <NA>
9 attributes VARCHAR YES <NA> <NA> <NA>
10 attributes_map MAP(VARCHAR, VARCHAR) YES <NA> <NA> <NA>
Attributes column type: VARCHAR
Sample MAP content:
attributes
1 Name=OTTHUME00001604789;Parent=OTTHUMT00000055643
Table creation pattern tests passed!
test_integration.R............ 120 tests OK Integration tests completed!
test_integration.R............ 120 tests OK 1.9s
test_intervals.R.............. 0 tests
test_intervals.R.............. 0 tests
test_intervals.R.............. 0 tests [E::fai_retrieve_buffer] FASTA/Q index seek position exceeds the signed offset limit
[E::fai_retrieve_buffer] Failed to retrieve block: unexpected end of file
[E::fai_retrieve_buffer] FASTA/Q index seek position exceeds the signed offset limit
test_intervals.R.............. 45 tests OK
test_intervals.R.............. 45 tests OK
test_intervals.R.............. 59 tests OK 2.1s
test_liftover.R............... 0 tests
test_liftover.R............... 0 tests
test_liftover.R............... 0 tests [E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/duckhts_liftover_4b27e197ac154/missing.chain" : No such file or directory
[E::fai_build3_core] Failed to open the file /home/hornik/tmp/scratch/RtmpfRPjjO/duckhts_liftover_4b27e197ac154/missing.fa : No such file or directory
test_liftover.R............... 264 tests OK 2.6s
test_liftover_stress.R........ 0 tests
test_liftover_stress.R........ 0 tests
test_liftover_stress.R........ 0 tests
test_liftover_stress.R........ 14 tests OK 4.7s
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 1 tests OK
test_macro_installation.R..... 2 tests OK
test_macro_installation.R..... 3 tests OK
test_macro_installation.R..... 4 tests OK
test_macro_installation.R..... 5 tests OK
test_macro_installation.R..... 6 tests OK
test_macro_installation.R..... 7 tests OK
test_macro_installation.R..... 8 tests OK
test_macro_installation.R..... 9 tests OK
test_macro_installation.R..... 10 tests OK
test_macro_installation.R..... 10 tests OK
test_macro_installation.R..... 10 tests OK
test_macro_installation.R..... 11 tests OK
test_macro_installation.R..... 12 tests OK
test_macro_installation.R..... 13 tests OK
test_macro_installation.R..... 14 tests OK
test_macro_installation.R..... 14 tests OK
test_macro_installation.R..... 15 tests OK
test_macro_installation.R..... 16 tests OK
test_macro_installation.R..... 17 tests OK
test_macro_installation.R..... 18 tests OK
test_macro_installation.R..... 18 tests OK 11.7s
test_mosdepth.R............... 0 tests
test_mosdepth.R............... 0 tests
test_mosdepth.R............... 0 tests
test_mosdepth.R............... 60 tests OK 16.5s
test_multi.R.................. 0 tests
test_multi.R.................. 0 tests
test_multi.R.................. 0 tests Multi-file reading tests passed!
test_multi.R.................. 41 tests OK 1.5s
test_munge.R.................. 0 tests
test_munge.R.................. 0 tests
test_munge.R.................. 0 tests [E::fai_build3_core] Failed to open the file /home/hornik/tmp/scratch/RtmpfRPjjO/duckhts_munge_4b27e6555ad6f/missing.fa : No such file or directory
[E::fai_build3_core] Failed to open the file /home/hornik/tmp/scratch/RtmpfRPjjO/duckhts_munge_4b27e6555ad6f/missing.fa : No such file or directory
test_munge.R.................. 79 tests OK 4.3s
test_munge_threading.R........ 0 tests
test_munge_threading.R........ 0 tests
test_munge_threading.R........ 0 tests
test_munge_threading.R........ 5 tests OK 1.4s
test_native_marker.R.......... 0 tests
test_native_marker.R.......... 1 tests OK
test_native_marker.R.......... 1 tests OK
test_native_marker.R.......... 2 tests OK
test_native_marker.R.......... 3 tests OK 5ms
test_parallel_empty_contigs.R. 0 tests
test_parallel_empty_contigs.R. 0 tests
test_parallel_empty_contigs.R. 0 tests [W::hts_reglist_create] Region 'empty1' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty2' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty3' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty4' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty5' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty6' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty7' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty8' specifies an unknown reference name. Continue anyway
test_parallel_empty_contigs.R. 15 tests OK 0.9s
test_pileup.R................. 0 tests
test_pileup.R................. 0 tests
test_pileup.R................. 0 tests
test_pileup.R................. 20 tests OK 1.0s
test_quality_encoding.R....... 0 tests
test_quality_encoding.R....... 0 tests
test_quality_encoding.R....... 0 tests
test_quality_encoding.R....... 14 tests OK Quality encoding tests passed!
test_quality_encoding.R....... 14 tests OK 0.8s
test_reference_cache.R........ 0 tests
test_reference_cache.R........ 0 tests
test_reference_cache.R........ 0 tests
test_reference_cache.R........ 28 tests OK 5.3s
test_region_lists.R........... 0 tests
test_region_lists.R........... 0 tests
test_region_lists.R........... 0 tests [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
test_region_lists.R........... 73 tests OK 1.0s
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 76 tests OK
test_roh.R.................... 76 tests OK
test_roh.R.................... 83 tests OK
test_roh.R.................... 83 tests OK
test_roh.R.................... 100 tests OK
test_roh.R.................... 100 tests OK
test_roh.R.................... 100 tests OK
test_roh.R.................... 129 tests OK
test_roh.R.................... 129 tests OK
test_roh.R.................... 158 tests OK
test_roh.R.................... 158 tests OK
test_roh.R.................... 185 tests OK
test_roh.R.................... 185 tests OK
test_roh.R.................... 204 tests OK 10.0s
test_samtools_idxstats.R...... 0 tests
test_samtools_idxstats.R...... 0 tests
test_samtools_idxstats.R...... 0 tests [W::sam_read1_sam] Parse error at line 4
test_samtools_idxstats.R...... 14 tests OK 0.9s
test_score.R.................. 0 tests
test_score.R.................. 0 tests
test_score.R.................. 0 tests
test_score.R.................. 0 tests
test_score.R.................. 129 tests OK 1.5s
test_seq_ops.R................ 0 tests
test_seq_ops.R................ 0 tests
test_seq_ops.R................ 0 tests [E::fai_load3_core] Failed to open FASTA index /home/hornik/tmp/scratch/RtmpfRPjjO/duckhts_ce_bgz_4b27e7ec841af.fa.gz.gzi: No such file or directory
Sequence operation tests passed!
test_seq_ops.R................ 129 tests OK All sequence operation tests completed!
test_seq_ops.R................ 129 tests OK 1.7s
test_somalier.R............... 0 tests
test_somalier.R............... 0 tests
test_somalier.R............... 0 tests
test_somalier.R............... 0 tests
test_somalier.R............... 55 tests OK
test_somalier.R............... 95 tests OK 7.7s
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 13 tests OK
test_somalier_extraction.R.... 23 tests OK
test_somalier_extraction.R.... 41 tests 1 fails
test_somalier_extraction.R.... 57 tests 1 fails 8.8s
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 12 tests OK
test_somalier_find_sites.R.... 14 tests OK
test_somalier_find_sites.R.... 17 tests OK
test_somalier_find_sites.R.... 22 tests OK
test_somalier_find_sites.R.... 30 tests OK
test_somalier_find_sites.R.... 38 tests OK
test_somalier_find_sites.R.... 40 tests OK [W::bcf_hdr_check_sanity] AD should be declared as Number=R
[W::bcf_hdr_check_sanity] GQ should be declared as Type=Integer
[W::bcf_hdr_check_sanity] GT should be declared as Number=1
test_somalier_find_sites.R.... 44 tests OK 12.5s
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 17 tests OK
test_somalier_sex.R........... 26 tests OK
test_somalier_sex.R........... 31 tests OK 4.1s
test_sql_quoting.R............ 0 tests
test_sql_quoting.R............ 0 tests
test_sql_quoting.R............ 0 tests
test_sql_quoting.R............ 11 tests OK 0.9s
test_table_overwrite_failure.R 0 tests [E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
[E::hts_open_format] Failed to open file "/home/hornik/tmp/scratch/RtmpfRPjjO/file4b27e116ef146.bed" : No such file or directory
test_table_overwrite_failure.R 126 tests OK 1.7s
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests Testing effective DuckDB to R type mappings...
STRUCT type not available in this DuckDB version
UNION type not available in this DuckDB version
Testing basic types...
duckdb_type column_name r_type
1 BIGINT bigint_col double
2 DOUBLE double_col double
3 VARCHAR varchar_col character
4 BOOLEAN boolean_col logical
5 DATE date_col double
6 TIMESTAMP timestamp_col double
7 TIME time_col double
8 BLOB blob_col list
9 INTEGER integer_col integer
10 FLOAT float_col double
11 SMALLINT smallint_col integer
12 USMALLINT usmallint_col integer
13 UBIGINT ubigint_col double
Testing array types...
duckdb_type column_name r_type
1 VARCHAR[] varchar_array list
2 BIGINT[] bigint_array list
3 INTEGER[] integer_array list
4 DOUBLE[] double_array list
5 FLOAT[] float_array list
6 BOOLEAN[] boolean_array list
Testing map types...
MAP structure for varchar_map: 2 elements
MAP structure for bigint_map: 2 elements
MAP structure for double_map: 2 elements
duckdb_type column_name
1 MAP(VARCHAR, VARCHAR) varchar_map
2 MAP(VARCHAR, BIGINT) bigint_map
3 MAP(VARCHAR, DOUBLE) double_map
r_type
1 data.frame (keys: character, values: character)
2 data.frame (keys: character, values: double)
3 data.frame (keys: character, values: double)
Comparing with theoretical mappings...
Basic type mappings:
MATCH: BIGINT -> double
MATCH: DOUBLE -> double
MATCH: VARCHAR -> character
MATCH: BOOLEAN -> logical
MATCH: DATE -> double
MATCH: TIMESTAMP -> double
MATCH: TIME -> double
MATCH: BLOB -> list
MATCH: INTEGER -> integer
MATCH: FLOAT -> double
MATCH: SMALLINT -> integer
MATCH: USMALLINT -> integer
MATCH: UBIGINT -> double
Array type mappings:
MATCH: VARCHAR[] -> list
MATCH: BIGINT[] -> list
MATCH: INTEGER[] -> list
MATCH: DOUBLE[] -> list
MATCH: FLOAT[] -> list
MATCH: BOOLEAN[] -> list
MAP type mappings:
MATCH: MAP -> data.frame
MATCH: MAP -> data.frame
MATCH: MAP -> data.frame
test_type_mappings.R.......... 0 tests Testing type mapping function assertions...
Type mapping function assertions passed!
test_type_mappings.R.......... 13 tests OK Type mapping test completed! Check output above for effective type mappings.
test_type_mappings.R.......... 13 tests OK 0.2s
test_variantkey_regionkey.R... 0 tests
test_variantkey_regionkey.R... 0 tests
test_variantkey_regionkey.R... 0 tests
test_variantkey_regionkey.R... 48 tests OK 0.8s
----- FAILED[xcpt]: test_somalier_extraction.R<504--504>
call| test_somalier_vcf_count_contract_edges()
call| -->c("expect_error(rduckhts_somalier_vcf_counts(con, stress_source, ", " panel_table = \"count_edge_offpanel\", samples = \"S1\"), pattern = \"multiple source records occur at a panel site\")")
diff| The error message:
diff| 'rapi_execute: Out of Memory Error: could not allocate block of size 256.0 KiB (121.9 MiB/122.0 MiB used)
diff|
diff| Possible solutions:
diff| * Reducing the number of threads (SET threads=X)
diff| * Disabling insertion-order preservation (SET preserve_insertion_order=false)
diff| * Increasing the memory limit (SET memory_limit='...GB')
diff|
diff| See also https://duckdb.org/docs/current/guides/performance/how_to_tune_workloads (error_type: OUT_OF_MEMORY)'
diff| does not match pattern 'multiple source records occur at a panel site'
Error: 1 out of 8292 tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.0.0.1.9
Check: tests
Result: ERROR
Running ‘tinytest.R’ [61s/70s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
> if (requireNamespace("tinytest", quietly = TRUE)) {
+ tinytest::test_package("Rduckhts")
+ } else {
+ message("tinytest not available; skipping tests")
+ }
test_ancestry.R............... 0 tests
test_ancestry.R............... 0 tests
test_ancestry.R............... 0 tests
test_ancestry.R............... 156 tests OK
test_ancestry.R............... 156 tests OK
test_ancestry.R............... 170 tests OK 33.1s
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 54 tests OK 14.4s
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 37 tests OK 1.2s
test_bam_file_offset.R........ 0 tests
test_bam_file_offset.R........ 0 tests
test_bam_file_offset.R........ 0 tests [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
test_bam_file_offset.R........ 280 tests OK 3.2s
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 18 tests OK 1.3s
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 39 tests OK 1.3s
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 18 tests OK 1.2s
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests [W::sam_read1_sam] Parse error at line 4
test_bam_scan.R............... 186 tests OK
test_bam_scan.R............... 194 tests OK
test_bam_scan.R............... 208 tests OK
test_bam_scan.R............... 241 tests OK 5.8s
test_basic.R.................. 0 tests
test_basic.R.................. 1 tests OK
test_basic.R.................. 2 tests OK
test_basic.R.................. 3 tests OK
test_basic.R.................. 4 tests OK
test_basic.R.................. 5 tests OK
test_basic.R.................. 6 tests OK
test_basic.R.................. 7 tests OK
test_basic.R.................. 8 tests OK
test_basic.R.................. 9 tests OK
test_basic.R.................. 10 tests OK
test_basic.R.................. 11 tests OK
test_basic.R.................. 12 tests OK
test_basic.R.................. 13 tests OK
test_basic.R.................. 14 tests OK
test_basic.R.................. 15 tests OK
test_basic.R.................. 16 tests OK
test_basic.R.................. 17 tests OK
test_basic.R.................. 18 tests OK
test_basic.R.................. 19 tests OK
test_basic.R.................. 20 tests OK
test_basic.R.................. 21 tests OK
test_basic.R.................. 22 tests OK
test_basic.R.................. 23 tests OK
test_basic.R.................. 24 tests OK
test_basic.R.................. 25 tests OK
test_basic.R.................. 26 tests OK
test_basic.R.................. 27 tests OK
test_basic.R.................. 28 tests OK
test_basic.R.................. 29 tests OK
test_basic.R.................. 30 tests OK
test_basic.R.................. 31 tests OK
test_basic.R.................. 32 tests OK
test_basic.R.................. 33 tests OK
test_basic.R.................. 34 tests OK
test_basic.R.................. 35 tests OK
test_basic.R.................. 36 tests OK
test_basic.R.................. 37 tests OK
test_basic.R.................. 38 tests OK
test_basic.R.................. 39 tests OK
test_basic.R.................. 40 tests OK
test_basic.R.................. 41 tests OK
test_basic.R.................. 42 tests OK
test_basic.R.................. 43 tests OK
test_basic.R.................. 44 tests OK
test_basic.R.................. 45 tests OK
test_basic.R.................. 46 tests OK
test_basic.R.................. 47 tests OK
test_basic.R.................. 48 tests OK
test_basic.R.................. 49 tests OK
test_basic.R.................. 50 tests OK
test_basic.R.................. 51 tests OK
test_basic.R.................. 52 tests OK
test_basic.R.................. 53 tests OK
test_basic.R.................. 54 tests OK
test_basic.R.................. 55 tests OK
test_basic.R.................. 56 tests OK
test_basic.R.................. 57 tests OK
test_basic.R.................. 58 tests OK
test_basic.R.................. 59 tests OK
test_basic.R.................. 60 tests OK
test_basic.R.................. 61 tests OK
test_basic.R.................. 62 tests OK
test_basic.R.................. 63 tests OK
test_basic.R.................. 64 tests OK
test_basic.R.................. 65 tests OK
test_basic.R.................. 66 tests OK
test_basic.R.................. 67 tests OK
test_basic.R.................. 68 tests OK
test_basic.R.................. 69 tests OK
test_basic.R.................. 70 tests OK
test_basic.R.................. 71 tests OK
test_basic.R.................. 72 tests OK
test_basic.R.................. 73 tests OK
test_basic.R.................. 74 tests OK
test_basic.R.................. 75 tests OK
test_basic.R.................. 76 tests OK
test_basic.R.................. 77 tests OK
test_basic.R.................. 78 tests OK
test_basic.R.................. 78 tests OK
test_basic.R.................. 79 tests OK
test_basic.R.................. 80 tests OK
test_basic.R.................. 81 tests OK
test_basic.R.................. 82 tests OK
test_basic.R.................. 83 tests OK
test_basic.R.................. 84 tests OK
test_basic.R.................. 85 tests OK
test_basic.R.................. 86 tests OK
test_basic.R.................. 87 tests OK
test_basic.R.................. 88 tests OK
test_basic.R.................. 89 tests OK
test_basic.R.................. 89 tests OK
test_basic.R.................. 90 tests OK
test_basic.R.................. 91 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 93 tests OK
test_basic.R.................. 94 tests OK
test_basic.R.................. 95 tests OK
test_basic.R.................. 96 tests OK
test_basic.R.................. 96 tests OK
test_basic.R.................. 97 tests OK
test_basic.R.................. 98 tests OK
test_basic.R.................. 99 tests OK
test_basic.R.................. 100 tests OK
test_basic.R.................. 101 tests OK
test_basic.R.................. 102 tests OK
test_basic.R.................. 103 tests OK
test_basic.R.................. 104 tests OK
test_basic.R.................. 104 tests OK
test_basic.R.................. 105 tests OK
test_basic.R.................. 106 tests OK
test_basic.R.................. 106 tests OK
test_basic.R.................. 107 tests OK
test_basic.R.................. 108 tests OK
test_basic.R.................. 109 tests OK
test_basic.R.................. 110 tests OK
test_basic.R.................. 111 tests OK
test_basic.R.................. 112 tests OK
test_basic.R.................. 113 tests OK
test_basic.R.................. 114 tests OK
test_basic.R.................. 115 tests OK
test_basic.R.................. 116 tests OK
test_basic.R.................. 117 tests OK
test_basic.R.................. 118 tests OK
test_basic.R.................. 119 tests OK
test_basic.R.................. 120 tests OK
test_basic.R.................. 121 tests OK
test_basic.R.................. 122 tests OK
test_basic.R.................. 123 tests OK
test_basic.R.................. 124 tests OK
test_basic.R.................. 125 tests OK
test_basic.R.................. 126 tests OK
test_basic.R.................. 127 tests OK
test_basic.R.................. 128 tests OK
test_basic.R.................. 129 tests OK
test_basic.R.................. 130 tests OK
test_basic.R.................. 131 tests OK
test_basic.R.................. 483 tests OK
test_basic.R.................. 484 tests OK
test_basic.R.................. 485 tests OK
test_basic.R.................. 486 tests OK
test_basic.R.................. 487 tests OK
test_basic.R.................. 488 tests OK
test_basic.R.................. 489 tests OK
test_basic.R.................. 490 tests OK
test_basic.R.................. 491 tests OK
test_basic.R.................. 492 tests OK
test_basic.R.................. 493 tests OK
test_basic.R.................. 494 tests OK
test_basic.R.................. 495 tests OK
test_basic.R.................. 496 tests OK
test_basic.R.................. 497 tests OK
test_basic.R.................. 498 tests OK
test_basic.R.................. 499 tests OK
test_basic.R.................. 500 tests OK
test_basic.R.................. 501 tests OK
test_basic.R.................. 502 tests OK
test_basic.R.................. 503 tests OK
test_basic.R.................. 504 tests OK
test_basic.R.................. 505 tests OK
test_basic.R.................. 506 tests OK
test_basic.R.................. 507 tests OK
test_basic.R.................. 508 tests OK
test_basic.R.................. 509 tests OK
test_basic.R.................. 510 tests OK
test_basic.R.................. 511 tests OK
test_basic.R.................. 512 tests OK
test_basic.R.................. 513 tests OK
test_basic.R.................. 514 tests OK
test_basic.R.................. 515 tests OK
test_basic.R.................. 516 tests OK
test_basic.R.................. 517 tests OK
test_basic.R.................. 518 tests OK
test_basic.R.................. 519 tests OK
test_basic.R.................. 520 tests OK
test_basic.R.................. 521 tests OK
test_basic.R.................. 522 tests OK
test_basic.R.................. 523 tests OK
test_basic.R.................. 524 tests OK
test_basic.R.................. 525 tests OK All basic tests passed!
test_basic.R.................. 525 tests OK 2.0s
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
test_bcf.R.................... 64 tests OK [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
test_bcf.R.................... 258 tests OK [E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
Error: rapi_execute: Invalid Input Error: read_bcf: failed to read or parse BCF/VCF record (error_type: INVALID_INPUT)
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.0.1.0.1.0
Check: tests
Result: ERROR
Running 'tinytest.R' [10m]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
> if (requireNamespace("tinytest", quietly = TRUE)) {
+ tinytest::test_package("Rduckhts")
+ } else {
+ message("tinytest not available; skipping tests")
+ }
test_ancestry.R............... 0 tests
test_ancestry.R............... 0 tests
test_ancestry.R............... 0 tests
test_ancestry.R............... 156 tests OK
test_ancestry.R............... 156 tests OK
test_ancestry.R............... 170 tests OK 31.4s
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 0 tests
test_ancestry_contracts.R..... 54 tests OK 12.1s
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 0 tests
test_bam_bed_coverage.R....... 37 tests OK 1.0s
test_bam_file_offset.R........ 0 tests
test_bam_file_offset.R........ 0 tests
test_bam_file_offset.R........ 0 tests [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
test_bam_file_offset.R........ 280 tests OK 2.7s
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 0 tests
test_bam_mate_overlap_counts.R 18 tests OK 1.1s
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 0 tests
test_bam_materialize.R........ 39 tests OK 1.3s
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 0 tests
test_bam_mismatch_counts.R.... 18 tests OK 1.4s
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests
test_bam_scan.R............... 0 tests [W::sam_read1_sam] Parse error at line 4
test_bam_scan.R............... 186 tests OK
test_bam_scan.R............... 194 tests OK
test_bam_scan.R............... 208 tests OK
test_bam_scan.R............... 241 tests OK 5.4s
test_basic.R.................. 0 tests
test_basic.R.................. 1 tests OK
test_basic.R.................. 2 tests OK
test_basic.R.................. 3 tests OK
test_basic.R.................. 4 tests OK
test_basic.R.................. 5 tests OK
test_basic.R.................. 6 tests OK
test_basic.R.................. 7 tests OK
test_basic.R.................. 8 tests OK
test_basic.R.................. 9 tests OK
test_basic.R.................. 10 tests OK
test_basic.R.................. 11 tests OK
test_basic.R.................. 12 tests OK
test_basic.R.................. 13 tests OK
test_basic.R.................. 14 tests OK
test_basic.R.................. 15 tests OK
test_basic.R.................. 16 tests OK
test_basic.R.................. 17 tests OK
test_basic.R.................. 18 tests OK
test_basic.R.................. 19 tests OK
test_basic.R.................. 20 tests OK
test_basic.R.................. 21 tests OK
test_basic.R.................. 22 tests OK
test_basic.R.................. 23 tests OK
test_basic.R.................. 24 tests OK
test_basic.R.................. 25 tests OK
test_basic.R.................. 26 tests OK
test_basic.R.................. 27 tests OK
test_basic.R.................. 28 tests OK
test_basic.R.................. 29 tests OK
test_basic.R.................. 30 tests OK
test_basic.R.................. 31 tests OK
test_basic.R.................. 32 tests OK
test_basic.R.................. 33 tests OK
test_basic.R.................. 34 tests OK
test_basic.R.................. 35 tests OK
test_basic.R.................. 36 tests OK
test_basic.R.................. 37 tests OK
test_basic.R.................. 38 tests OK
test_basic.R.................. 39 tests OK
test_basic.R.................. 40 tests OK
test_basic.R.................. 41 tests OK
test_basic.R.................. 42 tests OK
test_basic.R.................. 43 tests OK
test_basic.R.................. 44 tests OK
test_basic.R.................. 45 tests OK
test_basic.R.................. 46 tests OK
test_basic.R.................. 47 tests OK
test_basic.R.................. 48 tests OK
test_basic.R.................. 49 tests OK
test_basic.R.................. 50 tests OK
test_basic.R.................. 51 tests OK
test_basic.R.................. 52 tests OK
test_basic.R.................. 53 tests OK
test_basic.R.................. 54 tests OK
test_basic.R.................. 55 tests OK
test_basic.R.................. 56 tests OK
test_basic.R.................. 57 tests OK
test_basic.R.................. 58 tests OK
test_basic.R.................. 59 tests OK
test_basic.R.................. 60 tests OK
test_basic.R.................. 61 tests OK
test_basic.R.................. 62 tests OK
test_basic.R.................. 63 tests OK
test_basic.R.................. 64 tests OK
test_basic.R.................. 65 tests OK
test_basic.R.................. 66 tests OK
test_basic.R.................. 67 tests OK
test_basic.R.................. 68 tests OK
test_basic.R.................. 69 tests OK
test_basic.R.................. 70 tests OK
test_basic.R.................. 71 tests OK
test_basic.R.................. 72 tests OK
test_basic.R.................. 73 tests OK
test_basic.R.................. 74 tests OK
test_basic.R.................. 75 tests OK
test_basic.R.................. 76 tests OK
test_basic.R.................. 77 tests OK
test_basic.R.................. 78 tests OK
test_basic.R.................. 78 tests OK
test_basic.R.................. 79 tests OK
test_basic.R.................. 80 tests OK
test_basic.R.................. 81 tests OK
test_basic.R.................. 82 tests OK
test_basic.R.................. 83 tests OK
test_basic.R.................. 84 tests OK
test_basic.R.................. 85 tests OK
test_basic.R.................. 86 tests OK
test_basic.R.................. 87 tests OK
test_basic.R.................. 88 tests OK
test_basic.R.................. 89 tests OK
test_basic.R.................. 89 tests OK
test_basic.R.................. 90 tests OK
test_basic.R.................. 91 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 92 tests OK
test_basic.R.................. 93 tests OK
test_basic.R.................. 94 tests OK
test_basic.R.................. 95 tests OK
test_basic.R.................. 96 tests OK
test_basic.R.................. 96 tests OK
test_basic.R.................. 97 tests OK
test_basic.R.................. 98 tests OK
test_basic.R.................. 99 tests OK
test_basic.R.................. 100 tests OK
test_basic.R.................. 101 tests OK
test_basic.R.................. 102 tests OK
test_basic.R.................. 103 tests OK
test_basic.R.................. 104 tests OK
test_basic.R.................. 104 tests OK
test_basic.R.................. 105 tests OK
test_basic.R.................. 106 tests OK
test_basic.R.................. 106 tests OK
test_basic.R.................. 107 tests OK
test_basic.R.................. 108 tests OK
test_basic.R.................. 109 tests OK
test_basic.R.................. 110 tests OK
test_basic.R.................. 111 tests OK
test_basic.R.................. 112 tests OK
test_basic.R.................. 113 tests OK
test_basic.R.................. 114 tests OK
test_basic.R.................. 115 tests OK
test_basic.R.................. 116 tests OK
test_basic.R.................. 117 tests OK
test_basic.R.................. 118 tests OK
test_basic.R.................. 119 tests OK
test_basic.R.................. 120 tests OK
test_basic.R.................. 121 tests OK
test_basic.R.................. 122 tests OK
test_basic.R.................. 123 tests OK
test_basic.R.................. 124 tests OK
test_basic.R.................. 125 tests OK
test_basic.R.................. 126 tests OK
test_basic.R.................. 127 tests OK
test_basic.R.................. 128 tests OK
test_basic.R.................. 129 tests OK
test_basic.R.................. 130 tests OK
test_basic.R.................. 131 tests OK
test_basic.R.................. 483 tests OK
test_basic.R.................. 484 tests OK
test_basic.R.................. 485 tests OK
test_basic.R.................. 486 tests OK
test_basic.R.................. 487 tests OK
test_basic.R.................. 488 tests OK
test_basic.R.................. 489 tests OK
test_basic.R.................. 490 tests OK
test_basic.R.................. 491 tests OK
test_basic.R.................. 492 tests OK
test_basic.R.................. 493 tests OK
test_basic.R.................. 494 tests OK
test_basic.R.................. 495 tests OK
test_basic.R.................. 496 tests OK
test_basic.R.................. 497 tests OK
test_basic.R.................. 498 tests OK
test_basic.R.................. 499 tests OK
test_basic.R.................. 500 tests OK
test_basic.R.................. 501 tests OK
test_basic.R.................. 502 tests OK
test_basic.R.................. 503 tests OK
test_basic.R.................. 504 tests OK
test_basic.R.................. 505 tests OK
test_basic.R.................. 506 tests OK
test_basic.R.................. 507 tests OK
test_basic.R.................. 508 tests OK
test_basic.R.................. 509 tests OK
test_basic.R.................. 510 tests OK
test_basic.R.................. 511 tests OK
test_basic.R.................. 512 tests OK
test_basic.R.................. 513 tests OK
test_basic.R.................. 514 tests OK
test_basic.R.................. 515 tests OK
test_basic.R.................. 516 tests OK
test_basic.R.................. 517 tests OK
test_basic.R.................. 518 tests OK
test_basic.R.................. 519 tests OK
test_basic.R.................. 520 tests OK
test_basic.R.................. 521 tests OK
test_basic.R.................. 522 tests OK
test_basic.R.................. 523 tests OK
test_basic.R.................. 524 tests OK
test_basic.R.................. 525 tests OK All basic tests passed!
test_basic.R.................. 525 tests OK 1.8s
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests
test_bcf.R.................... 0 tests [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
[E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
test_bcf.R.................... 64 tests OK [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
test_bcf.R.................... 258 tests OK [E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[E::bgzf_read_block] Invalid BGZF header at offset 447
[E::bgzf_read] Read block operation failed with error 2 after 0 of 32 bytes
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] [W::bgzf_read_block] EOF marker is absent. The input may be truncated
EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
[W::bgzf_read_block] EOF marker is absent. The input may be truncated
test_bcf.R.................... 2520 tests OK
test_bcf.R.................... 2530 tests OK
test_bcf.R.................... 2553 tests OK [W::vcf_parse] Contig '22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
test_bcf.R.................... 2578 tests OK
test_bcf.R.................... 2582 tests OK 33.3s
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 0 tests
test_bcf_file_offset.R........ 1 tests OK
test_bcf_file_offset.R........ 2 tests OK
test_bcf_file_offset.R........ 3 tests OK
test_bcf_file_offset.R........ 4 tests OK
test_bcf_file_offset.R........ 4 tests OK
test_bcf_file_offset.R........ 5 tests OK
test_bcf_file_offset.R........ 17 tests OK
test_bcf_file_offset.R........ 18 tests OK
test_bcf_file_offset.R........ 18 tests OK
test_bcf_file_offset.R........ 19 tests OK
test_bcf_file_offset.R........ 20 tests OK
test_bcf_file_offset.R........ 21 tests OK
test_bcf_file_offset.R........ 21 tests OK
test_bcf_file_offset.R........ 22 tests OK
test_bcf_file_offset.R........ 23 tests OK
test_bcf_file_offset.R........ 27 tests OK
test_bcf_file_offset.R........ 28 tests OK
test_bcf_file_offset.R........ 28 tests OK 1.1s
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 0 tests
test_bcf_regression.R......... 6 tests OK [E::vcf_parse] Could not parse the position 'bad'
[E::vcf_parse] Could not parse the position 'bad'
[E::vcf_parse] Could not parse the position 'bad'
test_bcf_regression.R......... 11 tests OK [W::accept_mismatch] read_bcf: FORMAT/XX encoded BCF type CHAR does not match header Type=Integer at chr1:10
test_bcf_regression.R......... 23 tests OK [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60
[W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60
test_bcf_regression.R......... 60 tests OK 4.3s
test_bcftools_norm.R.......... 0 tests
test_bcftools_norm.R.......... 0 tests
test_bcftools_norm.R.......... 0 tests
test_bcftools_norm.R.......... 146 tests OK 2.4s
test_bigwig.R................. 0 tests
test_bigwig.R................. 0 tests
test_bigwig.R................. 0 tests [bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
[bwGetOverlappingIntervalsCore] Got an error
test_bigwig.R................. 17 tests OK 1.0s
test_bin_counts.R............. 0 tests
test_bin_counts.R............. 0 tests
test_bin_counts.R............. 0 tests
test_bin_counts.R............. 39 tests OK 1.1s
test_cgranges_api.R........... 0 tests
test_cgranges_api.R........... 0 tests
test_cgranges_api.R........... 0 tests
test_cgranges_api.R........... 96 tests OK 1.4s
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 0 tests
test_cigar_utils.R............ 582 tests OK
test_cigar_utils.R............ 617 tests OK 3.8s
test_connection.R............. 0 tests
test_connection.R............. 0 tests
test_connection.R............. 1 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 2 tests OK
test_connection.R............. 10 tests OK
test_connection.R............. 15 tests OK
test_connection.R............. 17 tests OK
test_connection.R............. 18 tests OK 2.6s
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 0 tests
test_convert_parquet.R........ 1 tests OK
test_convert_parquet.R........ 2 tests OK
test_convert_parquet.R........ 3 tests OK
test_convert_parquet.R........ 4 tests OK
test_convert_parquet.R........ 23 tests OK
test_convert_parquet.R........ 29 tests OK
test_convert_parquet.R........ 36 tests OK
test_convert_parquet.R........ 42 tests OK 4.5s
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 0 tests
test_count_error_fit.R........ 28 tests OK 5.2s
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 0 tests
test_count_mixture_lowpass.R.. 137 tests OK 9.2s
test_database_lifetime.R...... 0 tests
test_database_lifetime.R...... 0 tests
test_database_lifetime.R...... 5 tests OK 1.7s
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 0 tests
test_depth_fraction.R......... 1 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 2 tests OK
test_depth_fraction.R......... 3 tests OK
test_depth_fraction.R......... 4 tests OK
test_depth_fraction.R......... 5 tests OK
test_depth_fraction.R......... 6 tests OK
test_depth_fraction.R......... 7 tests OK
test_depth_fraction.R......... 7 tests OK
test_depth_fraction.R......... 8 tests OK
test_depth_fraction.R......... 29 tests OK
test_depth_fraction.R......... 29 tests OK
test_depth_fraction.R......... 30 tests OK
test_depth_fraction.R......... 30 tests OK
test_depth_fraction.R......... 30 tests OK
test_depth_fraction.R......... 31 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 32 tests OK
test_depth_fraction.R......... 33 tests OK
test_depth_fraction.R......... 45 tests OK
test_depth_fraction.R......... 45 tests OK
test_depth_fraction.R......... 46 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 47 tests OK
test_depth_fraction.R......... 48 tests OK
test_depth_fraction.R......... 49 tests OK
test_depth_fraction.R......... 50 tests OK
test_depth_fraction.R......... 50 tests OK
test_depth_fraction.R......... 51 tests OK
test_depth_fraction.R......... 52 tests OK
test_depth_fraction.R......... 52 tests OK
test_depth_fraction.R......... 52 tests OK
test_depth_fraction.R......... 53 tests OK
test_depth_fraction.R......... 65 tests OK
test_depth_fraction.R......... 65 tests OK
test_depth_fraction.R......... 68 tests OK
test_depth_fraction.R......... 69 tests OK
test_depth_fraction.R......... 69 tests OK
test_depth_fraction.R......... 70 tests OK
test_depth_fraction.R......... 71 tests OK
test_depth_fraction.R......... 71 tests OK
test_depth_fraction.R......... 71 tests OK
test_depth_fraction.R......... 72 tests OK
test_depth_fraction.R......... 72 tests OK
test_depth_fraction.R......... 73 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 74 tests OK
test_depth_fraction.R......... 75 tests OK
test_depth_fraction.R......... 76 tests OK
test_depth_fraction.R......... 77 tests OK
test_depth_fraction.R......... 78 tests OK
test_depth_fraction.R......... 79 tests OK
test_depth_fraction.R......... 79 tests OK
test_depth_fraction.R......... 80 tests OK
test_depth_fraction.R......... 81 tests OK
test_depth_fraction.R......... 82 tests OK
test_depth_fraction.R......... 83 tests OK
test_depth_fraction.R......... 84 tests OK
test_depth_fraction.R......... 85 tests OK
test_depth_fraction.R......... 86 tests OK
test_depth_fraction.R......... 87 tests OK
test_depth_fraction.R......... 87 tests OK
test_depth_fraction.R......... 88 tests OK
test_depth_fraction.R......... 88 tests OK
test_depth_fraction.R......... 89 tests OK
test_depth_fraction.R......... 89 tests OK
test_depth_fraction.R......... 90 tests OK
test_depth_fraction.R......... 90 tests OK
test_depth_fraction.R......... 91 tests OK
test_depth_fraction.R......... 91 tests OK 3.0s
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 0 tests
test_depth_state_model.R...... 1 tests OK
test_depth_state_model.R...... 2 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 3 tests OK
test_depth_state_model.R...... 4 tests OK
test_depth_state_model.R...... 5 tests OK
test_depth_state_model.R...... 6 tests OK
test_depth_state_model.R...... 7 tests OK
test_depth_state_model.R...... 8 tests OK
test_depth_state_model.R...... 9 tests OK
test_depth_state_model.R...... 10 tests OK
test_depth_state_model.R...... 11 tests OK
test_depth_state_model.R...... 11 tests OK
test_depth_state_model.R...... 12 tests OK
test_depth_state_model.R...... 12 tests OK
test_depth_state_model.R...... 13 tests OK
test_depth_state_model.R...... 13 tests OK
test_depth_state_model.R...... 13 tests OK
test_depth_state_model.R...... 14 tests OK
test_depth_state_model.R...... 14 tests OK
test_depth_state_model.R...... 15 tests OK
test_depth_state_model.R...... 16 tests OK
test_depth_state_model.R...... 17 tests OK
test_depth_state_model.R...... 18 tests OK
test_depth_state_model.R...... 18 tests OK
test_depth_state_model.R...... 18 tests OK
test_depth_state_model.R...... 19 tests OK
test_depth_state_model.R...... 20 tests OK
test_depth_state_model.R...... 21 tests OK
test_depth_state_model.R...... 21 tests OK
test_depth_state_model.R...... 22 tests OK
test_depth_state_model.R...... 23 tests OK
test_depth_state_model.R...... 24 tests OK
test_depth_state_model.R...... 25 tests OK
test_depth_state_model.R...... 26 tests OK
test_depth_state_model.R...... 27 tests OK
test_depth_state_model.R...... 28 tests OK
test_depth_state_model.R...... 29 tests OK
test_depth_state_model.R...... 30 tests OK
test_depth_state_model.R...... 30 tests OK 52.1s
test_fastq_qc.R............... 0 tests
test_fastq_qc.R............... 0 tests
test_fastq_qc.R............... 0 tests
test_fastq_qc.R............... 22 tests OK 0.9s
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 0 tests
test_genbank.R................ 28 tests OK
test_genbank.R................ 36 tests OK
test_genbank.R................ 59 tests OK 2.2s
test_geno.R................... 0 tests
test_geno.R................... 0 tests
test_geno.R................... 0 tests
test_geno.R................... 0 tests [W::bcf_hdr_check_sanity] PS should be declared as Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1
[W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1
[W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer
[W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1
[W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1
[W::accept_mismatch] read_geno: FORMAT/PS encoded BCF type CHAR does not match header Type=Integer at chrG:10
[E::vcf_parse] Could not parse the position 'bad'
test_geno.R................... 145 tests OK
test_geno.R................... 145 tests OK
test_geno.R................... 145 tests OK [W::accept_mismatch] read_geno: FORMAT/XX encoded BCF type CHAR does not match header Type=Integer at chr1:10
test_geno.R................... 211 tests OK [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1
[W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1
[W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1
test_geno.R................... 232 tests OK
test_geno.R................... 331 tests OK 6.4s
test_geno_sites.R............. 0 tests
test_geno_sites.R............. 0 tests
test_geno_sites.R............. 0 tests
test_geno_sites.R............. 182 tests OK 2.5s
test_gxf_named_attributes.R... 0 tests
test_gxf_named_attributes.R... 0 tests
test_gxf_named_attributes.R... 60 tests OK 1.0s
test_htslib_contract.R........ 0 tests
test_htslib_contract.R........ 0 tests
test_htslib_contract.R........ 27 tests OK 1.8s
test_indexes_bgzip.R.......... 0 tests
test_indexes_bgzip.R.......... 0 tests
test_indexes_bgzip.R.......... 0 tests
test_indexes_bgzip.R.......... 0 tests [E::bgzf_uncompress] CRC32 checksum mismatch
[E::bgzf_read_block] BGZF decode jobs returned error 1 for block offset 0
[E::bgzf_read] Read block operation failed with error 1 after 0 of 65536 bytes
test_indexes_bgzip.R.......... 51 tests OK
test_indexes_bgzip.R.......... 77 tests OK 1.4s
test_insert_size.R............ 0 tests
test_insert_size.R............ 0 tests
test_insert_size.R............ 0 tests [E::hts_open_format] Failed to open file "missing.bam" : No such file or directory
[E::hts_open_format] Failed to open file "missing.bam" : No such file or directory
test_insert_size.R............ 484 tests OK 6.5s
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests [E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_valid.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_valid.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_valid.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid_attr.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid_attr.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid_attr.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_extra_field.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_extra_field.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_extra_field.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid_end.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid_end.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_strict_invalid_end.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_attrs.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_attrs.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gff_attrs.gff3'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gtf_attrs.gtf'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gtf_attrs.gtf'
[E::idx_find_and_load] Could not retrieve index file for 'D:/RCompile/CRANpkg/lib/4.5/Rduckhts/extdata/gtf_attrs.gtf'
GFF schema with attributes_map=TRUE:
column_name column_type null key default extra
1 seqname VARCHAR YES <NA> <NA> <NA>
2 source VARCHAR YES <NA> <NA> <NA>
3 feature VARCHAR YES <NA> <NA> <NA>
4 start BIGINT YES <NA> <NA> <NA>
5 end BIGINT YES <NA> <NA> <NA>
6 score DOUBLE YES <NA> <NA> <NA>
7 strand VARCHAR YES <NA> <NA> <NA>
8 frame VARCHAR YES <NA> <NA> <NA>
9 attributes VARCHAR YES <NA> <NA> <NA>
10 attributes_map MAP(VARCHAR, VARCHAR) YES <NA> <NA> <NA>
Attributes column type: VARCHAR
Sample MAP content:
attributes
1 Name=OTTHUME00001604789;Parent=OTTHUMT00000055643
Table creation pattern tests passed!
test_integration.R............ 120 tests OK Integration tests completed!
test_integration.R............ 120 tests OK 1.3s
test_intervals.R.............. 0 tests
test_intervals.R.............. 0 tests
test_intervals.R.............. 0 tests [E::fai_retrieve_buffer] FASTA/Q index seek position exceeds the signed offset limit
[E::fai_retrieve_buffer] Failed to retrieve block: unexpected end of file
[E::fai_retrieve_buffer] FASTA/Q index seek position exceeds the signed offset limit
test_intervals.R.............. 45 tests OK
test_intervals.R.............. 45 tests OK
test_intervals.R.............. 59 tests OK 1.3s
test_liftover.R............... 0 tests
test_liftover.R............... 0 tests
test_liftover.R............... 0 tests [E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\duckhts_liftover_4285c59d68ff/missing.chain" : No such file or directory
[E::fai_build3_core] Failed to open the file D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\duckhts_liftover_4285c59d68ff/missing.fa : No such file or directory
test_liftover.R............... 264 tests OK 2.2s
test_liftover_stress.R........ 0 tests
test_liftover_stress.R........ 0 tests
test_liftover_stress.R........ 0 tests
test_liftover_stress.R........ 14 tests OK 8.6s
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 0 tests
test_macro_installation.R..... 1 tests OK
test_macro_installation.R..... 2 tests OK
test_macro_installation.R..... 3 tests OK
test_macro_installation.R..... 4 tests OK
test_macro_installation.R..... 5 tests OK
test_macro_installation.R..... 6 tests OK
test_macro_installation.R..... 7 tests OK
test_macro_installation.R..... 8 tests OK
test_macro_installation.R..... 9 tests OK
test_macro_installation.R..... 10 tests OK
test_macro_installation.R..... 10 tests OK
test_macro_installation.R..... 10 tests OK
test_macro_installation.R..... 11 tests OK
test_macro_installation.R..... 12 tests OK
test_macro_installation.R..... 13 tests OK
test_macro_installation.R..... 14 tests OK
test_macro_installation.R..... 14 tests OK
test_macro_installation.R..... 15 tests OK
test_macro_installation.R..... 16 tests OK
test_macro_installation.R..... 17 tests OK
test_macro_installation.R..... 18 tests OK
test_macro_installation.R..... 18 tests OK 7.4s
test_mosdepth.R............... 0 tests
test_mosdepth.R............... 0 tests
test_mosdepth.R............... 0 tests
test_mosdepth.R............... 60 tests OK 13.7s
test_multi.R.................. 0 tests
test_multi.R.................. 0 tests
test_multi.R.................. 0 tests Multi-file reading tests passed!
test_multi.R.................. 41 tests OK 0.8s
test_munge.R.................. 0 tests
test_munge.R.................. 0 tests
test_munge.R.................. 0 tests [E::fai_build3_core] Failed to open the file D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\duckhts_munge_4285c74064c95/missing.fa : No such file or directory
[E::fai_build3_core] Failed to open the file D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\duckhts_munge_4285c74064c95/missing.fa : No such file or directory
test_munge.R.................. 79 tests OK 4.6s
test_munge_threading.R........ 0 tests
test_munge_threading.R........ 0 tests
test_munge_threading.R........ 0 tests
test_munge_threading.R........ 5 tests OK 1.1s
test_native_marker.R.......... 0 tests
test_native_marker.R.......... 1 tests OK
test_native_marker.R.......... 1 tests OK
test_native_marker.R.......... 2 tests OK
test_native_marker.R.......... 3 tests OK 5ms
test_parallel_empty_contigs.R. 0 tests
test_parallel_empty_contigs.R. 0 tests
test_parallel_empty_contigs.R. 0 tests [W::hts_reglist_create] Region 'empty1' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty2' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty3' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty4' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty5' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty6' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty7' specifies an unknown reference name. Continue anyway
[W::hts_reglist_create] Region 'empty8' specifies an unknown reference name. Continue anyway
test_parallel_empty_contigs.R. 15 tests OK 0.8s
test_pileup.R................. 0 tests
test_pileup.R................. 0 tests
test_pileup.R................. 0 tests
test_pileup.R................. 20 tests OK 0.7s
test_quality_encoding.R....... 0 tests
test_quality_encoding.R....... 0 tests
test_quality_encoding.R....... 0 tests
test_quality_encoding.R....... 14 tests OK Quality encoding tests passed!
test_quality_encoding.R....... 14 tests OK 0.6s
test_reference_cache.R........ 0 tests
test_reference_cache.R........ 0 tests
test_reference_cache.R........ 0 tests
test_reference_cache.R........ 28 tests OK 7.8s
test_region_lists.R........... 0 tests
test_region_lists.R........... 0 tests
test_region_lists.R........... 0 tests [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Missing headers may cause later processing to fail
test_region_lists.R........... 73 tests OK 1.0s
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 0 tests
test_roh.R.................... 76 tests OK
test_roh.R.................... 76 tests OK
test_roh.R.................... 83 tests OK
test_roh.R.................... 83 tests OK
test_roh.R.................... 100 tests OK
test_roh.R.................... 100 tests OK
test_roh.R.................... 100 tests OK
test_roh.R.................... 129 tests OK
test_roh.R.................... 129 tests OK
test_roh.R.................... 158 tests OK
test_roh.R.................... 158 tests OK
test_roh.R.................... 185 tests OK
test_roh.R.................... 185 tests OK
test_roh.R.................... 204 tests OK 8.4s
test_samtools_idxstats.R...... 0 tests
test_samtools_idxstats.R...... 0 tests
test_samtools_idxstats.R...... 0 tests [W::sam_read1_sam] Parse error at line 4
test_samtools_idxstats.R...... 14 tests OK 0.8s
test_score.R.................. 0 tests
test_score.R.................. 0 tests
test_score.R.................. 0 tests
test_score.R.................. 0 tests
test_score.R.................. 129 tests OK 0.9s
test_seq_ops.R................ 0 tests
test_seq_ops.R................ 0 tests
test_seq_ops.R................ 0 tests [E::fai_load3_core] Failed to open FASTA index D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\duckhts_ce_bgz_4285c504c1d57.fa.gz.gzi: No such file or directory
Sequence operation tests passed!
test_seq_ops.R................ 129 tests OK All sequence operation tests completed!
test_seq_ops.R................ 129 tests OK 1.0s
test_somalier.R............... 0 tests
test_somalier.R............... 0 tests
test_somalier.R............... 0 tests
test_somalier.R............... 0 tests
test_somalier.R............... 55 tests OK
test_somalier.R............... 95 tests OK 6.7s
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 0 tests
test_somalier_extraction.R.... 13 tests OK
test_somalier_extraction.R.... 23 tests OK
test_somalier_extraction.R.... 41 tests 1 fails
test_somalier_extraction.R.... 57 tests 1 fails 9.8s
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 0 tests
test_somalier_find_sites.R.... 12 tests OK
test_somalier_find_sites.R.... 14 tests OK
test_somalier_find_sites.R.... 17 tests OK
test_somalier_find_sites.R.... 22 tests OK
test_somalier_find_sites.R.... 30 tests OK
test_somalier_find_sites.R.... 38 tests OK
test_somalier_find_sites.R.... 40 tests OK [W::bcf_hdr_check_sanity] AD should be declared as Number=R
[W::bcf_hdr_check_sanity] GQ should be declared as Type=Integer
[W::bcf_hdr_check_sanity] GT should be declared as Number=1
test_somalier_find_sites.R.... 44 tests OK 10.6s
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 0 tests
test_somalier_sex.R........... 17 tests OK
test_somalier_sex.R........... 26 tests OK
test_somalier_sex.R........... 31 tests OK 3.1s
test_sql_quoting.R............ 0 tests
test_sql_quoting.R............ 0 tests
test_sql_quoting.R............ 0 tests
test_sql_quoting.R............ 11 tests OK 0.7s
test_table_overwrite_failure.R 0 tests [E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
[E::hts_open_format] Failed to open file "D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\file4285c302143a2.bed" : No such file or directory
test_table_overwrite_failure.R 126 tests OK 1.1s
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests
test_type_mappings.R.......... 0 tests Testing effective DuckDB to R type mappings...
STRUCT type not available in this DuckDB version
UNION type not available in this DuckDB version
Testing basic types...
duckdb_type column_name r_type
1 BIGINT bigint_col double
2 DOUBLE double_col double
3 VARCHAR varchar_col character
4 BOOLEAN boolean_col logical
5 DATE date_col double
6 TIMESTAMP timestamp_col double
7 TIME time_col double
8 BLOB blob_col list
9 INTEGER integer_col integer
10 FLOAT float_col double
11 SMALLINT smallint_col integer
12 USMALLINT usmallint_col integer
13 UBIGINT ubigint_col double
Testing array types...
duckdb_type column_name r_type
1 VARCHAR[] varchar_array list
2 BIGINT[] bigint_array list
3 INTEGER[] integer_array list
4 DOUBLE[] double_array list
5 FLOAT[] float_array list
6 BOOLEAN[] boolean_array list
Testing map types...
MAP structure for varchar_map: 2 elements
MAP structure for bigint_map: 2 elements
MAP structure for double_map: 2 elements
duckdb_type column_name
1 MAP(VARCHAR, VARCHAR) varchar_map
2 MAP(VARCHAR, BIGINT) bigint_map
3 MAP(VARCHAR, DOUBLE) double_map
r_type
1 data.frame (keys: character, values: character)
2 data.frame (keys: character, values: double)
3 data.frame (keys: character, values: double)
Comparing with theoretical mappings...
Basic type mappings:
MATCH: BIGINT -> double
MATCH: DOUBLE -> double
MATCH: VARCHAR -> character
MATCH: BOOLEAN -> logical
MATCH: DATE -> double
MATCH: TIMESTAMP -> double
MATCH: TIME -> double
MATCH: BLOB -> list
MATCH: INTEGER -> integer
MATCH: FLOAT -> double
MATCH: SMALLINT -> integer
MATCH: USMALLINT -> integer
MATCH: UBIGINT -> double
Array type mappings:
MATCH: VARCHAR[] -> list
MATCH: BIGINT[] -> list
MATCH: INTEGER[] -> list
MATCH: DOUBLE[] -> list
MATCH: FLOAT[] -> list
MATCH: BOOLEAN[] -> list
MAP type mappings:
MATCH: MAP -> data.frame
MATCH: MAP -> data.frame
MATCH: MAP -> data.frame
test_type_mappings.R.......... 0 tests Testing type mapping function assertions...
Type mapping function assertions passed!
test_type_mappings.R.......... 13 tests OK Type mapping test completed! Check output above for effective type mappings.
test_type_mappings.R.......... 13 tests OK 0.1s
test_variantkey_regionkey.R... 0 tests
test_variantkey_regionkey.R... 0 tests
test_variantkey_regionkey.R... 0 tests
test_variantkey_regionkey.R... 48 tests OK 0.6s
----- FAILED[xcpt]: test_somalier_extraction.R<504--504>
call| test_somalier_vcf_count_contract_edges()
call| -->c("expect_error(rduckhts_somalier_vcf_counts(con, stress_source, ", " panel_table = \"count_edge_offpanel\", samples = \"S1\"), pattern = \"multiple source records occur at a panel site\")")
diff| The error message:
diff| 'rapi_execute: Out of Memory Error: failed to allocate data of size 32.0 KiB (123.8 MiB/122.0 MiB used)
diff|
diff| Possible solutions:
diff| * Reducing the number of threads (SET threads=X)
diff| * Disabling insertion-order preservation (SET preserve_insertion_order=false)
diff| * Increasing the memory limit (SET memory_limit='...GB')
diff|
diff| See also https://duckdb.org/docs/current/guides/performance/how_to_tune_workloads (error_type: OUT_OF_MEMORY)'
diff| does not match pattern 'multiple source records occur at a panel site'
Error: 1 out of 8274 tests failed
In addition: Warning message:
In file.symlink(config$library_file, relocated_library) :
cannot symlink 'D:\RCompile\CRANpkg\lib\4.5\Rduckhts\duckhts_extension\htslib\lib\libhts.a' to 'D:\temp\2026_10_25_22_59_48_19435\RtmpQh4odH\rduckhts_htslib_4285c7046579c/lib/libhts.a', reason 'Dem Client fehlt ein erforderliches Recht'
Execution halted
Flavor: r-oldrel-windows-x86_64