[Debian-med-packaging] Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)
Lincoln Stein
lincoln.stein at gmail.com
Wed Jan 18 12:00:48 UTC 2017
Ok, here is the last key piece of information. Replacing source-built
Bioperl with the debian bioperl-1.7.1-1 package from
https://packages.debian.org/sid/bioperl reproduced Gregor's test errors
exactly.
I also tried swapping in libbio-graphics-perl 2.40-1 from the same
repository (with both versions of bioperl), but this has no effect one way
or another.
Conclusion: something in the bioperl debian 1.7.1-1 package is causing the
test failures.
Lincoln
On Wed, Jan 18, 2017 at 6:43 AM, Lincoln Stein <lincoln.stein at gmail.com>
wrote:
> 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 possibly a newer version of the libbio-graphics package?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
>
> <http://goog_1828306398>
> *Ontario Institute for Cancer Research*
> MaRS Centre
> 661 University Avenue
> Suite 510
> Toronto, Ontario
> Canada M5G 0A3
>
> Tel: 416-673-8514 <(416)%20673-8514>
> Mobile: 416-817-8240 <(416)%20817-8240>
> Email: lincoln.stein at gmail.com
> Toll-free: 1-866-678-6427 <(866)%20678-6427>
> Twitter: @OICR_news
>
> *Executive Assistant*
> *Lisa Duncan*
> Tel: 647-260-7970 <(647)%20260-7970>
> Email: lisa.duncan at oicr.on.ca <stacey.quinn at oicr.on.ca>
> www.oicr.on.ca
>
> This message and any attachments may contain confidential and/or
> privileged information for the sole use of the intended recipient. Any
> review or distribution by anyone other than the person for whom it was
> originally intended is strictly prohibited. If you have received this
> message in error, please contact the sender and delete all copies.
> Opinions, conclusions or other information contained in this message may
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>
--
*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
<http://goog_1828306398>
*Ontario Institute for Cancer Research*
MaRS Centre
661 University Avenue
Suite 510
Toronto, Ontario
Canada M5G 0A3
Tel: 416-673-8514
Mobile: 416-817-8240
Email: lincoln.stein at gmail.com
Toll-free: 1-866-678-6427
Twitter: @OICR_news
*Executive Assistant*
*Lisa Duncan*
Tel: 647-260-7970 <(647)%20260-7970>
Email: lisa.duncan at oicr.on.ca <stacey.quinn at oicr.on.ca>
www.oicr.on.ca
This message and any attachments may contain confidential and/or privileged
information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was originally
intended is strictly prohibited. If you have received this message in
error, please contact the sender and delete all copies. Opinions,
conclusions or other information contained in this message may not be that
of the organization.
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