Help for Perl script inside test suite of bowtie2 needed

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Help for Perl script inside test suite of bowtie2 needed

Andreas Tille-5
Hi,

the bowtie2 package should be ready in git[1] for Python3 now but its
build time test is failing for a probably unrelated reason:

...
make[2]: Leaving directory '/build/bowtie2-2.3.5.1'
make -j1 test
make[2]: Entering directory '/build/bowtie2-2.3.5.1'
eval `perl -I /build/bowtie2-2.3.5.1/.tmp/lib/perl5 -Mlocal::lib=/build/bowtie2-2.3.5.1/.tmp` ; \
sh ./scripts/test/simple_tests.sh
Attempting to create directory /build/bowtie2-2.3.5.1/.tmp
Can't locate File/Which.pm in @INC (you may need to install the File::Which module) (@INC contains: /build/bowtie2-2.3.5.1/scripts/test /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.1/x86_64-linux-gnu-thread-multi /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.1 /build/bowtie2-2.3.5.1/.tmp/lib/perl5/x86_64-linux-gnu-thread-multi /build/bowtie2-2.3.5.1/.tmp/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/x86_64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.0 /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.0/x86_64-linux-gnu-thread-multi /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at scripts/test/simple_tests.pl line 36.
BEGIN failed--compilation aborted at scripts/test/simple_tests.pl line 36.
make[2]: *** [Makefile:553: simple-test] Error 2


Any help from the Perl team to fix this?

Thanks a lot in advance

     Andreas.


[1] https://salsa.debian.org/med-team/bowtie2

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Re: Help for Perl script inside test suite of bowtie2 needed

Andrius Merkys
Hello,

Looks like there's a missing dependency on libfile-which-perl.

Best,
Andrius


On Wed, 4 Sep 2019, 17:02 Andreas Tille, <[hidden email]> wrote:
Hi,

the bowtie2 package should be ready in git[1] for Python3 now but its
build time test is failing for a probably unrelated reason:

...
make[2]: Leaving directory '/build/bowtie2-2.3.5.1'
make -j1 test
make[2]: Entering directory '/build/bowtie2-2.3.5.1'
eval `perl -I /build/bowtie2-2.3.5.1/.tmp/lib/perl5 -Mlocal::lib=/build/bowtie2-2.3.5.1/.tmp` ; \
sh ./scripts/test/simple_tests.sh
Attempting to create directory /build/bowtie2-2.3.5.1/.tmp
Can't locate File/Which.pm in @INC (you may need to install the File::Which module) (@INC contains: /build/bowtie2-2.3.5.1/scripts/test /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.1/x86_64-linux-gnu-thread-multi /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.1 /build/bowtie2-2.3.5.1/.tmp/lib/perl5/x86_64-linux-gnu-thread-multi /build/bowtie2-2.3.5.1/.tmp/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/x86_64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.0 /build/bowtie2-2.3.5.1/.tmp/lib/perl5/5.28.0/x86_64-linux-gnu-thread-multi /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at scripts/test/simple_tests.pl line 36.
BEGIN failed--compilation aborted at scripts/test/simple_tests.pl line 36.
make[2]: *** [Makefile:553: simple-test] Error 2


Any help from the Perl team to fix this?

Thanks a lot in advance

     Andreas.


[1] https://salsa.debian.org/med-team/bowtie2

--
http://fam-tille.de

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Re: Help for Perl script inside test suite of bowtie2 needed

Andreas Tille-5
Hi,

On Wed, Sep 04, 2019 at 05:16:21PM +0300, Andrius Merkys wrote:
> Looks like there's a missing dependency on libfile-which-perl.

Just to confirm this helped to proceed with this package which
has other issues in the test suite which need to be solved.

Thanks for the hint in any case
     Andreas.

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