在 Linux 的 Windows 子系统上安装 Bio::Grep 失败答案

【问题标题】：Failed installation of Bio::Grep on Windows subsystem for Linux在 Linux 的 Windows 子系统上安装 Bio::Grep 失败
【发布时间】：2020-01-15 21:40:45
【问题描述】：

我已经在 WSL Ubuntu 18.04 上使用sudo apt-get install bioperl bioperl-run 安装了 bioperl。我尝试使用 cpanm 安装 Bio::Grep 但失败了。从build.log 文件看来，测试过程中出现了一些问题：

# 
# *****************************************************************************
# * Bioperl    : FOUND                                                        *
# * Bioperl-run: FOUND                                                        *
# * Backend    : No backend found in path. You should install the back-ends   *
# *              before running these tests. This way you make sure that the  *
# *              parsers work with your installed version of the back-end.    *
# * EMBOSS     : FOUND                                                        *
# *****************************************************************************
t/00.checkprereq.t ............ ok

#   Failed test 'use Bio::Grep::Backend::Agrep;'
#   at t/00.load.t line 14.
#     Tried to use 'Bio::Grep::Backend::Agrep'.
#     Error:  UNIVERSAL does not export anything at ...
...

Test Summary Report
-------------------
t/00.load.t                 (Wstat: 1280 Tests: 12 Failed: 5)
  Failed tests:  3-7
  Non-zero exit status: 5
t/10.backends.all.t         (Wstat: 65280 Tests: 133 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 344 tests but ran 133.
t/11.backends.guugle.t      (Wstat: 0 Tests: 1 Failed: 1)
  Failed test:  1
  Parse errors: Bad plan.  You planned 0 tests but ran 1.
t/11.backends.re.t          (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 30 tests but ran 1.
t/20.filter.t               (Wstat: 65280 Tests: 17 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 46 tests but ran 17.
t/30.features.alignments.t  (Wstat: 65280 Tests: 50 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 108 tests but ran 50.
t/30.features.updownstream.t (Wstat: 65280 Tests: 16 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 46 tests but ran 16.
t/40.utils.t                (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 30 tests but ran 1.
t/50.synopsis.t             (Wstat: 512 Tests: 9 Failed: 2)
  Failed tests:  6-7
  Non-zero exit status: 2
Files=13, Tests=242, 10 wallclock secs ( 0.11 usr  0.19 sys +  2.33 cusr  5.13 csys =  7.76 CPU)
Result: FAIL
Failed 9/13 test programs. 8/242 subtests failed.
-> FAIL Installing Bio::Grep failed

似乎有人创建了ticket，之前遇到过类似的problem，但我没有找到解决方案。

【问题讨论】：

cpanm 的输出显示：“在路径中未找到后端。您应该在运行这些测试之前安装后端”您是否尝试安装后端？
@Håkon Hægland，这不是这里的问题。对 Perl 的更改破坏了该模块。缺少后端可能会使大多数测试无用，也许模块本身也无用，但这无关紧要。但是，这可能意味着最好在安装 Bio::Grep 之前安装打算使用的后端模块。
请注意，这与 WSL 无关。

标签： perl windows-subsystem-for-linux bioperl

【解决方案1】：

解决方法很简单：删除 use UNIVERSAL ...; 行。

wget https://cpan.metacpan.org/authors/id/L/LI/LIMAONE/Bio-Grep-v0.10.6.tar.gz
tar xvzf Bio-Grep-v0.10.6.tar.gz
cd Bio-Grep-v0.10.6
perl -pe's/^(?=use UNIVERSAL)/#/' -i~ lib/Bio/Grep/Backend/BackendI.pm
perl Makefile.PL && make test && make install

【讨论】：