[Debian-med-packaging] Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

[Lincoln Stein]

Hi,

Unfortunately I can't reproduce the testing failures, and the build got all
the way to the signature generation, at which point it aborted because I do
not have the proper gpg signing key.

Bear with me, because I am new at this. Here is what I did:

   1. git clone https://anonscm.debian.org/git/debian-med/gbrowse.git
   2. Created a tarball of the current 2.56 GBrowse distribution
   named gbrowse_2.56+dfsg.orig.tar.gz and located in the parent directory of
   the just-cloned directory.
   3. ran debuild

So there are apparently differences in the environment that are causing
Gregor's build to fail. Here is my build environment:

Linux Mint 18.1 Serena

Perl v5.22.1 (debian package)

Bioperl 1.007001 (built from source)

Bio::Graphics 2.39-4 (debian package)


My guess is that I should be using the Bioperl 1.007001 debian package, or
possibly a newer version of the libbio-graphics package? In any case, I'm
stuck in the "works for me" phase.

Lincoln

On Tue, Jan 17, 2017 at 2:07 AM, Andreas Tille <andreas at an3as.eu> wrote:

> Hi Lincoln,
>
> On Mon, Jan 16, 2017 at 06:14:34PM -0500, Lincoln Stein wrote:
> > I need a little help to reproduce Gregor's failed tests, given that I'm a
> > complete newbie wrt the Debian packaging system. I have cloned gbrowse
> > 2.56+dfsg-1 from the Debian Med repository, but I don't know what command
> > line to use to attempt the build. What is the next step? I'm guessing it
> is
> > some form of dpkg-buildpackage, but the number of options is pretty
> > overwhelming!
>
> If you have installed the devscripts package you can try
>
>     debuild
>
> which is a wrapper around dpkg-buildpackage and in principle needs no
> options to reproduce the issue.  Debuild will inform you about missing
> Build-Dependencies you need to install - simply use apt-get install what
> is listed if anything is missing.  When doing so I get
>
> ...
> Test Summary Report
> -------------------
> t/00.compile.t          (Wstat: 3840 Tests: 90 Failed: 15)
>   Failed tests:  1, 3, 5, 7, 10, 15, 17-18, 29, 31, 33, 35
>                 41, 45, 47
>   Non-zero exit status: 15
> t/02.rearchitecture.t   (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 90 tests but ran 0.
> t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 150 tests but ran 0.
> t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 43 tests but ran 0.
> t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 19 tests but ran 0.
> t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 26 tests but ran 0.
> t/07.karyotype.t        (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 3 tests but ran 0.
> Files=10, Tests=103,  5 wallclock secs ( 0.05 usr  0.01 sys +  4.19 cusr
> 0.30 csys =  4.55 CPU)
> Result: FAIL
> Failed 7/10 test programs. 15/103 subtests failed.
> dh_auto_test: perl Build test --verbose 1 TEST_FILES=t/02.rearchitecture.t
> t/05.deferredrendering.t t/00.compile.t t/01.yeast.t t/07.balancer.t
> t/08.calign.t returned exit code 255
>
>
> Kind regards
>
>        Andreas.
>
> --
> http://fam-tille.de
>



-- 
*Lincoln Stein*

Scientific Director (Interim), Ontario Institute for Cancer Research
Director, Informatics and Bio-computing Program, OICR
Senior Principal Investigator, OICR
Professor, Department of Molecular Genetics, University of Toronto

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