* using log directory 'd:/RCompile/CRANincoming/R-devel/biosys.Rcheck'
* using R Under development (unstable) (2024-07-08 r86886 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'biosys/DESCRIPTION' ... OK
* this is package 'biosys' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Yun Peng <yunyunp96@163.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  Bioinformatics (2:36, 6:42)

The Title field should be in title case. Current version is:
  'System Command function for Bioinformatics'
In title case that is:
  'System Command Function for Bioinformatics'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'biosys' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... 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 examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # 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
  ‹QŽf
  gzip: D:\temp\RtmpOK1svE\file1777466565978.gz: No such file or directory
  [ FAIL 2 | WARN 3 | SKIP 10 | PASS 9 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  β€’ empty test (1): 'test-exec.R:35:1'
  β€’ nzchar(Sys.which("alleleCounter")) is not TRUE (1): 'test-exec.R:2:5'
  β€’ nzchar(Sys.which("cellranger")) is not TRUE (1): 'test-exec.R:7:5'
  β€’ nzchar(Sys.which("fastq_pair")) is not TRUE (1): 'test-exec.R:12:5'
  β€’ nzchar(Sys.which("gistic2")) is not TRUE (1): 'test-exec.R:17:5'
  β€’ nzchar(Sys.which("kraken2")) is not TRUE (1): 'test-exec.R:31:5'
  β€’ nzchar(Sys.which("python2")) || nzchar(Sys.which("python3")) is not TRUE (2):
    'test-exec.R:22:5', 'test-exec.R:41:5'
  β€’ nzchar(Sys.which("run-trust4")) is not TRUE (1): 'test-exec.R:53:5'
  β€’ nzchar(Sys.which("seqkit")) is not TRUE (1): 'test-exec.R:48:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-exec.R:67:5'): `pipe()` method works well ──────────────────────
  Error in `file(con, "rb")`: cannot open the connection
  Backtrace:
      β–†
   1. β”œβ”€testthat::expect_identical(read_lines(file), read_lines(file2)) at test-exec.R:67:5
   2. β”‚ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. β”‚   └─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.       β”œβ”€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:
      β–†
   1. β”œβ”€testthat::expect_identical(read_lines(gzip_file), letters) at test-utils.R:27:5
   2. β”‚ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. β”‚   └─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
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE