CRAN Package Check Results for Package Rduckhts

Last updated on 2026-10-25 13:51:20 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.0.0.0.1.9	147.08	821.41	968.49	OK
r-devel-linux-x86_64-debian-gcc	2.0.0.0.1.9	160.69	126.71	287.40	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	2.0.0.0.1.9	189.00	105.91	294.91	ERROR
r-devel-windows-x86_64	2.0.1.0.1.0	183.00	813.00	996.00	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	2.0.0.0.1.9	268.00	637.00	905.00	OK
r-oldrel-macos-arm64	2.0.1.0.1.0	53.00	170.00	223.00	OK
r-oldrel-macos-x86_64	2.0.1.0.1.0	120.00	706.00	826.00	OK
r-oldrel-windows-x86_64	2.0.0.0.1.9	307.00	679.00	986.00	OK

Check Details

Version: 2.0.0.0.1.9
Check: tests
Result: ERROR Running ‘tinytest.R’ [54s/58s] 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 28.7s 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 9.4s 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 0.8s 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 1.0s 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 5.2s 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 1.3s 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-devel-linux-x86_64-debian-gcc

Version: 2.0.0.0.1.9
Check: tests
Result: ERROR Running ‘tinytest.R’ [44s/60s] 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 30.1s 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 11.6s 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 0.8s 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 2.9s 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 0.9s 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 1.0s 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 4.0s 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 1.4s 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 in `duckdb_result()`: ! Invalid Input Error: read_bcf: failed to read or parse BCF/VCF record ℹ Context: rapi_execute ℹ Error type: INVALID_INPUT Backtrace: ▆ 1. ├─tinytest::test_package("Rduckhts") 2. │ └─tinytest::run_test_dir(...) 3. │ └─base::lapply(...) 4. │ └─tinytest (local) FUN(X[[i]], ...) 5. │ └─base::eval(expr, envir = e) 6. │ └─base::eval(expr, envir = e) 7. │ └─test_bcf_index_snapshot() 8. │ ├─tinytest::expect_equal(...) at test_bcf.R:423:9 9. │ │ └─tinytest (local) fun(...) 10. │ │ ├─base::all.equal(target, current, tolerance = tolerance, ...) 11. │ │ └─base::all.equal.default(...) 12. │ ├─DBI::dbGetQuery(con, "EXECUTE index_scan") 13. │ └─DBI::dbGetQuery(con, "EXECUTE index_scan") 14. │ └─DBI (local) .local(conn, statement, ...) 15. │ ├─DBI::dbSendQuery(conn, statement, ...) 16. │ └─duckdb::dbSendQuery(conn, statement, ...) 17. │ └─duckdb (local) .local(conn, statement, ...) 18. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 19. │ └─duckdb:::duckdb_execute(res) 20. │ └─duckdb:::rethrow_rapi_execute(...) 21. │ ├─rlang::try_fetch(...) 22. │ │ ├─base::tryCatch(...) 23. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 24. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 25. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 26. │ │ └─base::withCallingHandlers(...) 27. │ └─duckdb:::rapi_execute(stmt, convert_opts) 28. ├─duckdb (local) `<fn>`(...) 29. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields) 30. │ └─rlang:::signal_abort(cnd, .file) 31. │ └─base::signalCondition(cnd) 32. └─rlang (local) `<fn>`(`<dckdb_rr>`) 33. └─handlers[[1L]](cnd) 34. └─duckdb:::rethrow_error_from_rapi(e, call) 35. └─rlang::abort(msg, class = "duckdb_error", call = call, !!!fields) Execution halted Flavor: r-devel-linux-x86_64-fedora-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