在 Linux 的 Windows 子系统上安装 Bio::Grep 失败



我已经在WSL Ubuntu 18.04上安装了bioperl,sudo apt-get install bioperl bioperl-run。我试图用cpanm安装Bio::Grep,但它失败了。从build.log文件中可以看出测试过程中似乎有些失败:

# 
# *****************************************************************************
# * 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

似乎有人创建了票证并遇到了类似的问题,但我没有找到解决方案。

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

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