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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(biosys) > > test_check("biosys") Running command d:\rtools44\usr\bin\perl.exe --help Usage: /usr/bin/perl [switches] [--] [programfile] [arguments] -0[octal/hexadecimal] specify record separator (\0, if no argument) -a autosplit mode with -n or -p (splits $_ into @F) -C[number/list] enables the listed Unicode features -c check syntax only (runs BEGIN and CHECK blocks) -d[t][:MOD] run program under debugger or module Devel::MOD -D[number/letters] set debugging flags (argument is a bit mask or alphabets) -e commandline one line of program (several -e's allowed, omit programfile) -E commandline like -e, but enables all optional features -f don't do $sitelib/sitecustomize.pl at startup -F/pattern/ split() pattern for -a switch (//'s are optional) -g read all input in one go (slurp), rather than line-by-line (alias for -0777) -i[extension] edit <> files in place (makes backup if extension supplied) -Idirectory specify @INC/#include directory (several -I's allowed) -l[octnum] enable line ending processing, specifies line terminator -[mM][-]module execute "use/no module..." before executing program -n assume "while (<>) { ... }" loop around program -p assume loop like -n but print line also, like sed -s enable rudimentary parsing for switches after programfile -S look for programfile using PATH environment variable -t enable tainting warnings -T enable tainting checks -u dump core after parsing program -U allow unsafe operations -v print version, patchlevel and license -V[:configvar] print configuration summary (or a single Config.pm variable) -w enable many useful warnings -W enable all warnings -x[directory] ignore text before #!perl line (optionally cd to directory) -X disable all warnings Run 'perldoc perl' for more help with Perl. Running command d:\rtools44\usr\bin\gzip.exe -c D:\temp\RtmpOK1svE\file177745aef4cae | d:\rtools44\usr\bin\gzip.exe -d > D:\temp\RtmpOK1svE\file1777461284e48 gzip: D:\temp\RtmpOK1svE\file177745aef4cae: not in gzip format gzip: |.gz: No such file or directory gzip: d:\rtools44\usr\bin\gzip.exe: not in gzip format gzip: >.gz: No such file or directory gzip: D:\temp\RtmpOK1svE\file1777461284e48.gz: No such file or directory Running command d:\rtools44\usr\bin\gzip.exe -c D:\temp\RtmpOK1svE\file1777466565978 > D:\temp\RtmpOK1svE\file1777466565978.gz ‹QŽffile1777466565978ÁÇ€ ÁÿÍ\‘b@ 1Uïn%Aji¤•N¢ô’dQ&™%Ë"«l²Ë!§¹ä–G^ùäàõ¾$Ngzip: >: No such file or directory gzip: D:\temp\RtmpOK1svE\file1777466565978.gz: No such file or directory [ FAIL 2 | WARN 3 | SKIP 10 | PASS 9 ] â•â• Skipped tests (10) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• • empty test (1): 'test-exec.R:35:1' • nzchar(Sys.which("alleleCounter")) is not TRUE (1): 'test-exec.R:2:5' • nzchar(Sys.which("cellranger")) is not TRUE (1): 'test-exec.R:7:5' • nzchar(Sys.which("fastq_pair")) is not TRUE (1): 'test-exec.R:12:5' • nzchar(Sys.which("gistic2")) is not TRUE (1): 'test-exec.R:17:5' • nzchar(Sys.which("kraken2")) is not TRUE (1): 'test-exec.R:31:5' • nzchar(Sys.which("python2")) || nzchar(Sys.which("python3")) is not TRUE (2): 'test-exec.R:22:5', 'test-exec.R:41:5' • nzchar(Sys.which("run-trust4")) is not TRUE (1): 'test-exec.R:53:5' • nzchar(Sys.which("seqkit")) is not TRUE (1): 'test-exec.R:48:5' â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Error ('test-exec.R:67:5'): `pipe()` method works well ────────────────────── Error in `file(con, "rb")`: cannot open the connection Backtrace: â–† 1. ├─testthat::expect_identical(read_lines(file), read_lines(file2)) at test-exec.R:67:5 2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─biosys:::read_lines(file2) 5. └─biosys:::is_gzip_signature(file) 6. └─biosys:::match_file_signature(...) 7. ├─file_signature %||% readBin(file, raw(), n) 8. └─base::readBin(file, raw(), n) 9. └─base::file(con, "rb") ── Error ('test-utils.R:27:5'): `read_lines()` workds as expected ────────────── Error in `gzfile(file, open = "r")`: cannot open the connection Backtrace: â–† 1. ├─testthat::expect_identical(read_lines(gzip_file), letters) at test-utils.R:27:5 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─biosys:::read_lines(gzip_file) 5. └─base::gzfile(file, open = "r") [ FAIL 2 | WARN 3 | SKIP 10 | PASS 9 ] Error: Test failures Execution halted