* using log directory ‘/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck’ * using R Under development (unstable) (2026-10-20 r90728) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-10-21 07:52:51 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘Rduckhts/DESCRIPTION’ ... OK * this is package ‘Rduckhts’ version ‘2.0.0.0.1.9’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rduckhts’ can be installed ... [172s/175s] OK * used C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’ * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [12s/12s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.R’ [272s/229s] [272s/229s] ERROR 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 10.4s test_ancestry_contracts.R..... 0 tests test_ancestry_contracts.R..... 0 tests test_ancestry_contracts.R..... 0 tests test_ancestry_contracts.R..... 54 tests OK 3.6s 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 0.2s 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 test_bam_file_offset.R........ 280 tests OK 1.3s 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 0.2s 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 0.3s 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 0.3s 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 1.5s 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 0.6s 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 test_bcf.R.................... 1800 tests OK test_bcf.R.................... 1810 tests OK test_bcf.R.................... 1833 tests OK [W::vcf_parse] Contig '22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Missing headers may cause later processing to fail test_bcf.R.................... 1858 tests OK test_bcf.R.................... 1862 tests OK 8.2s test_bcf_file_offset.R........ 0 tests test_bcf_file_offset.R........ 0 tests test_bcf_file_offset.R........ 0 tests test_bcf_file_offset.R........ 0 tests test_bcf_file_offset.R........ 0 tests test_bcf_file_offset.R........ 1 tests OK test_bcf_file_offset.R........ 2 tests OK test_bcf_file_offset.R........ 3 tests OK test_bcf_file_offset.R........ 4 tests OK test_bcf_file_offset.R........ 4 tests OK test_bcf_file_offset.R........ 5 tests OK test_bcf_file_offset.R........ 17 tests OK test_bcf_file_offset.R........ 18 tests OK test_bcf_file_offset.R........ 18 tests OK test_bcf_file_offset.R........ 19 tests OK test_bcf_file_offset.R........ 20 tests OK test_bcf_file_offset.R........ 21 tests OK test_bcf_file_offset.R........ 21 tests OK test_bcf_file_offset.R........ 22 tests OK test_bcf_file_offset.R........ 23 tests OK test_bcf_file_offset.R........ 27 tests OK test_bcf_file_offset.R........ 28 tests OK test_bcf_file_offset.R........ 28 tests OK 0.3s test_bcf_regression.R......... 0 tests test_bcf_regression.R......... 0 tests test_bcf_regression.R......... 0 tests test_bcf_regression.R......... 0 tests test_bcf_regression.R......... 0 tests test_bcf_regression.R......... 0 tests test_bcf_regression.R......... 6 tests OK [E::vcf_parse] Could not parse the position 'bad' [E::vcf_parse] Could not parse the position 'bad' [E::vcf_parse] Could not parse the position 'bad' test_bcf_regression.R......... 11 tests OK [W::accept_mismatch] read_bcf: FORMAT/XX encoded BCF type CHAR does not match header Type=Integer at chr1:10 test_bcf_regression.R......... 23 tests OK [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:20 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:30 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_bcf: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/II has 2 values for header Number=1 at chrS:60 [W::bcf_handle_decode_diagnostic] read_bcf: INFO/IF has 2 values for header Number=1 at chrS:60 test_bcf_regression.R......... 60 tests OK 1.7s test_bcftools_norm.R.......... 0 tests test_bcftools_norm.R.......... 0 tests test_bcftools_norm.R.......... 0 tests test_bcftools_norm.R.......... 146 tests OK 4.9s test_bigwig.R................. 0 tests test_bigwig.R................. 0 tests test_bigwig.R................. 0 tests [bwGetOverlappingIntervalsCore] Got an error [bwGetOverlappingIntervalsCore] Got an error [bwGetOverlappingIntervalsCore] Got an error [bwGetOverlappingIntervalsCore] Got an error test_bigwig.R................. 17 tests OK 0.4s test_bin_counts.R............. 0 tests test_bin_counts.R............. 0 tests test_bin_counts.R............. 0 tests test_bin_counts.R............. 39 tests OK 0.3s test_cgranges_api.R........... 0 tests test_cgranges_api.R........... 0 tests test_cgranges_api.R........... 0 tests test_cgranges_api.R........... 76 tests OK 0.3s test_cigar_utils.R............ 0 tests test_cigar_utils.R............ 0 tests test_cigar_utils.R............ 0 tests test_cigar_utils.R............ 0 tests test_cigar_utils.R............ 0 tests test_cigar_utils.R............ 582 tests OK test_cigar_utils.R............ 617 tests OK 5.7s test_connection.R............. 0 tests test_connection.R............. 0 tests test_connection.R............. 1 tests OK test_connection.R............. 2 tests OK test_connection.R............. 2 tests OK test_connection.R............. 2 tests OK test_connection.R............. 2 tests OK test_connection.R............. 2 tests OK test_connection.R............. 2 tests OK test_connection.R............. 2 tests OK test_connection.R............. 10 tests OK test_connection.R............. 15 tests OK test_connection.R............. 17 tests OK test_connection.R............. 18 tests OK 0.6s test_convert_parquet.R........ 0 tests test_convert_parquet.R........ 0 tests test_convert_parquet.R........ 0 tests test_convert_parquet.R........ 0 tests test_convert_parquet.R........ 0 tests test_convert_parquet.R........ 0 tests test_convert_parquet.R........ 1 tests OK test_convert_parquet.R........ 2 tests OK test_convert_parquet.R........ 3 tests OK test_convert_parquet.R........ 4 tests OK test_convert_parquet.R........ 20 tests OK test_convert_parquet.R........ 26 tests OK test_convert_parquet.R........ 33 tests OK test_convert_parquet.R........ 39 tests OK 1.0s test_count_error_fit.R........ 0 tests test_count_error_fit.R........ 0 tests test_count_error_fit.R........ 0 tests test_count_error_fit.R........ 0 tests test_count_error_fit.R........ 0 tests test_count_error_fit.R........ 28 tests OK 1.8s test_count_mixture_lowpass.R.. 0 tests test_count_mixture_lowpass.R.. 0 tests test_count_mixture_lowpass.R.. 0 tests test_count_mixture_lowpass.R.. 0 tests test_count_mixture_lowpass.R.. 0 tests test_count_mixture_lowpass.R.. 0 tests test_count_mixture_lowpass.R.. 135 tests OK 5.7s test_database_lifetime.R...... 0 tests test_database_lifetime.R...... 0 tests test_database_lifetime.R...... 6 tests OK 0.7s test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 0 tests test_depth_fraction.R......... 1 tests OK test_depth_fraction.R......... 2 tests OK test_depth_fraction.R......... 2 tests OK test_depth_fraction.R......... 2 tests OK test_depth_fraction.R......... 2 tests OK test_depth_fraction.R......... 3 tests OK test_depth_fraction.R......... 4 tests OK test_depth_fraction.R......... 5 tests OK test_depth_fraction.R......... 6 tests OK test_depth_fraction.R......... 7 tests OK test_depth_fraction.R......... 7 tests OK test_depth_fraction.R......... 8 tests OK test_depth_fraction.R......... 29 tests OK test_depth_fraction.R......... 29 tests OK test_depth_fraction.R......... 30 tests OK test_depth_fraction.R......... 30 tests OK test_depth_fraction.R......... 30 tests OK test_depth_fraction.R......... 31 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 32 tests OK test_depth_fraction.R......... 33 tests OK test_depth_fraction.R......... 45 tests OK test_depth_fraction.R......... 45 tests OK test_depth_fraction.R......... 46 tests OK test_depth_fraction.R......... 47 tests OK test_depth_fraction.R......... 47 tests OK test_depth_fraction.R......... 47 tests OK test_depth_fraction.R......... 47 tests OK test_depth_fraction.R......... 47 tests OK test_depth_fraction.R......... 48 tests OK test_depth_fraction.R......... 49 tests OK test_depth_fraction.R......... 50 tests OK test_depth_fraction.R......... 50 tests OK test_depth_fraction.R......... 51 tests OK test_depth_fraction.R......... 52 tests OK test_depth_fraction.R......... 52 tests OK test_depth_fraction.R......... 52 tests OK test_depth_fraction.R......... 53 tests OK test_depth_fraction.R......... 65 tests OK test_depth_fraction.R......... 65 tests OK test_depth_fraction.R......... 68 tests OK test_depth_fraction.R......... 69 tests OK test_depth_fraction.R......... 69 tests OK test_depth_fraction.R......... 70 tests OK test_depth_fraction.R......... 71 tests OK test_depth_fraction.R......... 71 tests OK test_depth_fraction.R......... 71 tests OK test_depth_fraction.R......... 72 tests OK test_depth_fraction.R......... 72 tests OK test_depth_fraction.R......... 73 tests OK test_depth_fraction.R......... 74 tests OK test_depth_fraction.R......... 74 tests OK test_depth_fraction.R......... 74 tests OK test_depth_fraction.R......... 74 tests OK test_depth_fraction.R......... 75 tests OK test_depth_fraction.R......... 76 tests OK test_depth_fraction.R......... 77 tests OK test_depth_fraction.R......... 78 tests OK test_depth_fraction.R......... 79 tests OK test_depth_fraction.R......... 79 tests OK test_depth_fraction.R......... 80 tests OK test_depth_fraction.R......... 81 tests OK test_depth_fraction.R......... 82 tests OK test_depth_fraction.R......... 83 tests OK test_depth_fraction.R......... 84 tests OK test_depth_fraction.R......... 85 tests OK test_depth_fraction.R......... 86 tests OK test_depth_fraction.R......... 87 tests OK test_depth_fraction.R......... 87 tests OK test_depth_fraction.R......... 88 tests OK test_depth_fraction.R......... 88 tests OK test_depth_fraction.R......... 89 tests OK test_depth_fraction.R......... 89 tests OK test_depth_fraction.R......... 90 tests OK test_depth_fraction.R......... 90 tests OK test_depth_fraction.R......... 91 tests OK test_depth_fraction.R......... 91 tests OK 1.7s test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 0 tests test_depth_state_model.R...... 1 tests OK test_depth_state_model.R...... 2 tests OK test_depth_state_model.R...... 3 tests OK test_depth_state_model.R...... 3 tests OK test_depth_state_model.R...... 3 tests OK test_depth_state_model.R...... 3 tests OK test_depth_state_model.R...... 4 tests OK test_depth_state_model.R...... 5 tests OK test_depth_state_model.R...... 6 tests OK test_depth_state_model.R...... 7 tests OK test_depth_state_model.R...... 8 tests OK test_depth_state_model.R...... 9 tests OK test_depth_state_model.R...... 10 tests OK test_depth_state_model.R...... 11 tests OK test_depth_state_model.R...... 11 tests OK test_depth_state_model.R...... 12 tests OK test_depth_state_model.R...... 12 tests OK test_depth_state_model.R...... 13 tests OK test_depth_state_model.R...... 13 tests OK test_depth_state_model.R...... 13 tests OK test_depth_state_model.R...... 14 tests OK test_depth_state_model.R...... 14 tests OK test_depth_state_model.R...... 15 tests OK test_depth_state_model.R...... 16 tests OK test_depth_state_model.R...... 17 tests OK test_depth_state_model.R...... 18 tests OK test_depth_state_model.R...... 18 tests OK test_depth_state_model.R...... 18 tests OK test_depth_state_model.R...... 19 tests OK test_depth_state_model.R...... 20 tests OK test_depth_state_model.R...... 21 tests OK test_depth_state_model.R...... 21 tests OK test_depth_state_model.R...... 22 tests OK test_depth_state_model.R...... 23 tests OK test_depth_state_model.R...... 24 tests OK test_depth_state_model.R...... 25 tests OK test_depth_state_model.R...... 26 tests OK test_depth_state_model.R...... 27 tests OK test_depth_state_model.R...... 28 tests OK test_depth_state_model.R...... 29 tests OK test_depth_state_model.R...... 30 tests OK test_depth_state_model.R...... 30 tests OK 15.7s test_fastq_qc.R............... 0 tests test_fastq_qc.R............... 0 tests test_fastq_qc.R............... 0 tests test_fastq_qc.R............... 22 tests OK 0.3s test_genbank.R................ 0 tests test_genbank.R................ 0 tests test_genbank.R................ 0 tests test_genbank.R................ 0 tests test_genbank.R................ 0 tests test_genbank.R................ 28 tests OK test_genbank.R................ 36 tests OK test_genbank.R................ 59 tests OK 1.2s test_geno.R................... 0 tests test_geno.R................... 0 tests test_geno.R................... 0 tests test_geno.R................... 0 tests [W::bcf_hdr_check_sanity] PS should be declared as Type=Integer [W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer [W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer [W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1 [W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1 [W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer [W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer [W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1 [W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1 [W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer [W::accept_mismatch] read_geno: FORMAT/PS must have Number=1,Type=Integer [W::accept_mismatch] read_geno: FORMAT/PS has 2 values for header Number=1 at chrG:10 sample S1 [W::accept_mismatch] read_geno: invalid FORMAT/GT allele at chrG:10 sample S1 slot 1 [W::accept_mismatch] read_geno: FORMAT/PS encoded BCF type CHAR does not match header Type=Integer at chrG:10 [E::vcf_parse] Could not parse the position 'bad' test_geno.R................... 145 tests OK test_geno.R................... 145 tests OK test_geno.R................... 145 tests OK [W::accept_mismatch] read_geno: FORMAT/XX encoded BCF type CHAR does not match header Type=Integer at chr1:10 test_geno.R................... 211 tests OK [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:40 sample S2 [W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:50 sample S1 [W::accept_mismatch] read_geno: FORMAT/SI has 2 values for header Number=1 at chrS:60 sample S1 [W::accept_mismatch] read_geno: FORMAT/SF has 2 values for header Number=1 at chrS:60 sample S1 test_geno.R................... 232 tests OK test_geno.R................... 331 tests OK 4.3s test_geno_sites.R............. 0 tests test_geno_sites.R............. 0 tests test_geno_sites.R............. 0 tests test_geno_sites.R............. 179 tests OK 2.0s test_gxf_named_attributes.R... 0 tests test_gxf_named_attributes.R... 0 tests test_gxf_named_attributes.R... 60 tests OK 1.1s test_htslib_contract.R........ 0 tests test_htslib_contract.R........ 0 tests test_htslib_contract.R........ 28 tests OK 0.7s test_indexes_bgzip.R.......... 0 tests test_indexes_bgzip.R.......... 0 tests test_indexes_bgzip.R.......... 0 tests [E::bgzf_uncompress] CRC32 checksum mismatch [E::bgzf_read_block] BGZF decode jobs returned error 1 for block offset 0 [E::bgzf_read] Read block operation failed with error 1 after 0 of 65536 bytes [E::bgzf_uncompress] CRC32 checksum mismatch [E::bgzf_read] Read block operation failed with error 33 after 0 of 65536 bytes test_indexes_bgzip.R.......... 67 tests OK 0.4s test_insert_size.R............ 0 tests test_insert_size.R............ 0 tests test_insert_size.R............ 0 tests [E::hts_open_format] Failed to open file "missing.bam" : No such file or directory [E::hts_open_format] Failed to open file "missing.bam" : No such file or directory test_insert_size.R............ 484 tests OK 3.8s test_integration.R............ 0 tests test_integration.R............ 0 tests test_integration.R............ 0 tests [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_valid.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_valid.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_invalid.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_invalid.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_invalid_attr.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_invalid_attr.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_extra_field.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_extra_field.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_invalid_end.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_strict_invalid_end.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_attrs.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gff_attrs.gff3' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gtf_attrs.gtf' [E::idx_find_and_load] Could not retrieve index file for '/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/Rduckhts/extdata/gtf_attrs.gtf' GFF schema with attributes_map=TRUE: column_name column_type null key default extra 1 seqname VARCHAR YES 2 source VARCHAR YES 3 feature VARCHAR YES 4 start BIGINT YES 5 end BIGINT YES 6 score DOUBLE YES 7 strand VARCHAR YES 8 frame VARCHAR YES 9 attributes VARCHAR YES 10 attributes_map MAP(VARCHAR, VARCHAR) YES Attributes column type: VARCHAR Sample MAP content: attributes 1 Name=OTTHUME00001604789;Parent=OTTHUMT00000055643 Table creation pattern tests passed! test_integration.R............ 120 tests OK Integration tests completed! test_integration.R............ 120 tests OK 0.7s test_intervals.R.............. 0 tests test_intervals.R.............. 0 tests test_intervals.R.............. 0 tests [E::fai_retrieve_buffer] FASTA/Q index seek position exceeds the signed offset limit [E::fai_retrieve_buffer] Failed to retrieve block: unexpected end of file [E::fai_retrieve_buffer] FASTA/Q index seek position exceeds the signed offset limit test_intervals.R.............. 45 tests OK test_intervals.R.............. 45 tests OK test_intervals.R.............. 59 tests OK 0.8s test_liftover.R............... 0 tests test_liftover.R............... 0 tests test_liftover.R............... 0 tests [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/duckhts_liftover_ac8824c58813/missing.chain" : No such file or directory [E::fai_build3_core] Failed to open the file /tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/duckhts_liftover_ac8824c58813/missing.fa : No such file or directory test_liftover.R............... 264 tests OK 0.8s test_liftover_stress.R........ 0 tests test_liftover_stress.R........ 0 tests test_liftover_stress.R........ 0 tests test_liftover_stress.R........ 14 tests OK 1.2s test_macro_installation.R..... 0 tests test_macro_installation.R..... 0 tests test_macro_installation.R..... 0 tests test_macro_installation.R..... 0 tests test_macro_installation.R..... 0 tests test_macro_installation.R..... 1 tests OK test_macro_installation.R..... 2 tests OK test_macro_installation.R..... 3 tests OK test_macro_installation.R..... 4 tests OK test_macro_installation.R..... 5 tests OK test_macro_installation.R..... 6 tests OK test_macro_installation.R..... 7 tests OK test_macro_installation.R..... 8 tests OK test_macro_installation.R..... 9 tests OK test_macro_installation.R..... 10 tests OK test_macro_installation.R..... 10 tests OK test_macro_installation.R..... 10 tests OK test_macro_installation.R..... 11 tests OK test_macro_installation.R..... 12 tests OK test_macro_installation.R..... 13 tests OK test_macro_installation.R..... 14 tests OK test_macro_installation.R..... 14 tests OK test_macro_installation.R..... 15 tests OK test_macro_installation.R..... 16 tests OK test_macro_installation.R..... 17 tests OK test_macro_installation.R..... 18 tests OK test_macro_installation.R..... 18 tests OK 4.8s test_mosdepth.R............... 0 tests test_mosdepth.R............... 0 tests test_mosdepth.R............... 0 tests test_mosdepth.R............... 60 tests OK 8.4s test_multi.R.................. 0 tests test_multi.R.................. 0 tests test_multi.R.................. 0 tests Multi-file reading tests passed! test_multi.R.................. 41 tests OK 0.8s test_munge.R.................. 0 tests test_munge.R.................. 0 tests test_munge.R.................. 0 tests [E::fai_build3_core] Failed to open the file /tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/duckhts_munge_ac882264525e3/missing.fa : No such file or directory test_munge.R.................. 79 tests OK 2.1s test_munge_threading.R........ 0 tests test_munge_threading.R........ 0 tests test_munge_threading.R........ 0 tests test_munge_threading.R........ 5 tests OK 0.5s test_native_marker.R.......... 0 tests test_native_marker.R.......... 1 tests OK test_native_marker.R.......... 1 tests OK test_native_marker.R.......... 2 tests OK test_native_marker.R.......... 3 tests OK 2ms test_parallel_empty_contigs.R. 0 tests test_parallel_empty_contigs.R. 0 tests test_parallel_empty_contigs.R. 0 tests [W::hts_reglist_create] Region 'empty1' specifies an unknown reference name. Continue anyway [W::hts_reglist_create] Region 'empty2' specifies an unknown reference name. Continue anyway [W::hts_reglist_create] Region 'empty3' specifies an unknown reference name. Continue anyway [W::hts_reglist_create] Region 'empty4' specifies an unknown reference name. Continue anyway [W::hts_reglist_create] Region 'empty5' specifies an unknown reference name. Continue anyway [W::hts_reglist_create] Region 'empty6' specifies an unknown reference name. Continue anyway [W::hts_reglist_create] Region 'empty7' specifies an unknown reference name. Continue anyway [W::hts_reglist_create] Region 'empty8' specifies an unknown reference name. Continue anyway test_parallel_empty_contigs.R. 15 tests OK 0.3s test_pileup.R................. 0 tests test_pileup.R................. 0 tests test_pileup.R................. 0 tests test_pileup.R................. 20 tests OK 0.2s test_quality_encoding.R....... 0 tests test_quality_encoding.R....... 0 tests test_quality_encoding.R....... 0 tests test_quality_encoding.R....... 14 tests OK Quality encoding tests passed! test_quality_encoding.R....... 14 tests OK 0.3s test_reference_cache.R........ 0 tests test_reference_cache.R........ 0 tests test_reference_cache.R........ 0 tests test_reference_cache.R........ 28 tests OK 2.7s test_region_lists.R........... 0 tests test_region_lists.R........... 0 tests test_region_lists.R........... 0 tests [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Missing headers may cause later processing to fail test_region_lists.R........... 73 tests OK 0.8s test_roh.R.................... 0 tests test_roh.R.................... 0 tests test_roh.R.................... 0 tests test_roh.R.................... 0 tests test_roh.R.................... 0 tests test_roh.R.................... 0 tests test_roh.R.................... 76 tests OK test_roh.R.................... 76 tests OK test_roh.R.................... 83 tests OK test_roh.R.................... 83 tests OK test_roh.R.................... 100 tests 1 fails test_roh.R.................... 100 tests 1 fails test_roh.R.................... 100 tests 1 fails test_roh.R.................... 129 tests 1 fails test_roh.R.................... 129 tests 1 fails test_roh.R.................... 158 tests 1 fails test_roh.R.................... 158 tests 1 fails test_roh.R.................... 185 tests 1 fails test_roh.R.................... 185 tests 1 fails test_roh.R.................... 204 tests 1 fails 4.2s test_samtools_idxstats.R...... 0 tests test_samtools_idxstats.R...... 0 tests test_samtools_idxstats.R...... 0 tests [W::sam_read1_sam] Parse error at line 4 test_samtools_idxstats.R...... 14 tests OK 0.3s test_score.R.................. 0 tests test_score.R.................. 0 tests test_score.R.................. 0 tests test_score.R.................. 0 tests test_score.R.................. 129 tests OK 0.5s test_seq_ops.R................ 0 tests test_seq_ops.R................ 0 tests test_seq_ops.R................ 0 tests [E::fai_load3_core] Failed to open FASTA index /tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/duckhts_ce_bgz_ac8826b118ac8.fa.gz.gzi: No such file or directory Sequence operation tests passed! test_seq_ops.R................ 129 tests OK All sequence operation tests completed! test_seq_ops.R................ 129 tests OK 0.7s test_somalier.R............... 0 tests test_somalier.R............... 0 tests test_somalier.R............... 0 tests test_somalier.R............... 0 tests test_somalier.R............... 55 tests OK test_somalier.R............... 95 tests OK 2.7s test_somalier_extraction.R.... 0 tests test_somalier_extraction.R.... 0 tests test_somalier_extraction.R.... 0 tests test_somalier_extraction.R.... 0 tests test_somalier_extraction.R.... 0 tests test_somalier_extraction.R.... 0 tests test_somalier_extraction.R.... 13 tests OK test_somalier_extraction.R.... 23 tests OK test_somalier_extraction.R.... 41 tests OK test_somalier_extraction.R.... 57 tests OK 4.0s test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 0 tests test_somalier_find_sites.R.... 12 tests OK test_somalier_find_sites.R.... 14 tests OK test_somalier_find_sites.R.... 17 tests OK test_somalier_find_sites.R.... 22 tests OK test_somalier_find_sites.R.... 30 tests OK test_somalier_find_sites.R.... 38 tests OK test_somalier_find_sites.R.... 40 tests OK [W::bcf_hdr_check_sanity] AD should be declared as Number=R [W::bcf_hdr_check_sanity] GQ should be declared as Type=Integer [W::bcf_hdr_check_sanity] GT should be declared as Number=1 test_somalier_find_sites.R.... 44 tests OK 3.1s test_somalier_sex.R........... 0 tests test_somalier_sex.R........... 0 tests test_somalier_sex.R........... 0 tests test_somalier_sex.R........... 0 tests test_somalier_sex.R........... 0 tests test_somalier_sex.R........... 0 tests test_somalier_sex.R........... 17 tests OK test_somalier_sex.R........... 26 tests OK test_somalier_sex.R........... 31 tests OK 1.1s test_sql_quoting.R............ 0 tests test_sql_quoting.R............ 0 tests test_sql_quoting.R............ 0 tests test_sql_quoting.R............ 11 tests OK 0.4s test_table_overwrite_failure.R 0 tests [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory [E::hts_open_format] Failed to open file "/tmp/RtmpjzRV5p/working_dir/Rtmp2xErX6/fileac8826a40f273.bed" : No such file or directory test_table_overwrite_failure.R 126 tests OK 1.2s test_type_mappings.R.......... 0 tests test_type_mappings.R.......... 0 tests test_type_mappings.R.......... 0 tests test_type_mappings.R.......... 0 tests test_type_mappings.R.......... 0 tests Testing effective DuckDB to R type mappings... STRUCT type not available in this DuckDB version UNION type not available in this DuckDB version Testing basic types... duckdb_type column_name r_type 1 BIGINT bigint_col double 2 DOUBLE double_col double 3 VARCHAR varchar_col character 4 BOOLEAN boolean_col logical 5 DATE date_col double 6 TIMESTAMP timestamp_col double 7 TIME time_col double 8 BLOB blob_col list 9 INTEGER integer_col integer 10 FLOAT float_col double 11 SMALLINT smallint_col integer 12 USMALLINT usmallint_col integer 13 UBIGINT ubigint_col double Testing array types... duckdb_type column_name r_type 1 VARCHAR[] varchar_array list 2 BIGINT[] bigint_array list 3 INTEGER[] integer_array list 4 DOUBLE[] double_array list 5 FLOAT[] float_array list 6 BOOLEAN[] boolean_array list Testing map types... MAP structure for varchar_map: 2 elements MAP structure for bigint_map: 2 elements MAP structure for double_map: 2 elements duckdb_type column_name 1 MAP(VARCHAR, VARCHAR) varchar_map 2 MAP(VARCHAR, BIGINT) bigint_map 3 MAP(VARCHAR, DOUBLE) double_map r_type 1 data.frame (keys: character, values: character) 2 data.frame (keys: character, values: double) 3 data.frame (keys: character, values: double) Comparing with theoretical mappings... Basic type mappings: MATCH: BIGINT -> double MATCH: DOUBLE -> double MATCH: VARCHAR -> character MATCH: BOOLEAN -> logical MATCH: DATE -> double MATCH: TIMESTAMP -> double MATCH: TIME -> double MATCH: BLOB -> list MATCH: INTEGER -> integer MATCH: FLOAT -> double MATCH: SMALLINT -> integer MATCH: USMALLINT -> integer MATCH: UBIGINT -> double Array type mappings: MATCH: VARCHAR[] -> list MATCH: BIGINT[] -> list MATCH: INTEGER[] -> list MATCH: DOUBLE[] -> list MATCH: FLOAT[] -> list MATCH: BOOLEAN[] -> list MAP type mappings: MATCH: MAP -> data.frame MATCH: MAP -> data.frame MATCH: MAP -> data.frame test_type_mappings.R.......... 0 tests Testing type mapping function assertions... Type mapping function assertions passed! test_type_mappings.R.......... 13 tests OK Type mapping test completed! Check output above for effective type mappings. test_type_mappings.R.......... 13 tests OK 0.1s test_variantkey_regionkey.R... 0 tests test_variantkey_regionkey.R... 0 tests test_variantkey_regionkey.R... 0 tests test_variantkey_regionkey.R... 48 tests OK 0.3s ----- FAILED[xcpt]: test_roh.R<193--193> call| test_roh_validation() call| -->c("expect_error(rduckhts_roh(con, vcf, reference_table = \"x\", proportions_table = \"y\", ", " af_clamp = 0.5), \"af_clamp must be\")") diff| The error message: diff| 'Catalog Error: Table with name x does not exist! diff| diff| LINE 1: SELECT * FROM duckhts_roh_ancestry('/data/localhost/ripley/R/packages... diff| ^ diff| ℹ Context: rapi_prepare diff| ℹ Error type: CATALOG' diff| does not match pattern 'af_clamp must be' Error: 1 out of 7518 tests failed Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-noLD/Rduckhts.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 7:35.05, 468.93 + 24.45