<div dir="ltr">Ok, here is the last key piece of information. Replacing source-built Bioperl with the debian bioperl-1.7.1-1 package from <a href="https://packages.debian.org/sid/bioperl">https://packages.debian.org/sid/bioperl</a> reproduced Gregor's test errors exactly. <div><br></div><div>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.</div><div><br></div><div>Conclusion: something in the bioperl debian 1.7.1-1 package is causing the test failures.</div><div><br></div><div>Lincoln</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 18, 2017 at 6:43 AM, Lincoln Stein <span dir="ltr"><<a href="mailto:lincoln.stein@gmail.com" target="_blank">lincoln.stein@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>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.</div><div><br></div><div>Bear with me, because I am new at this. Here is what I did:</div><div><ol><li>git clone <a href="https://anonscm.debian.org/git/debian-med/gbrowse.git" target="_blank">https://anonscm.debian.org/<wbr>git/debian-med/gbrowse.git</a><br></li><li>Created a tarball of the current 2.56 GBrowse distribution named gbrowse_2.56+dfsg.orig.<wbr>tar.gz and located in the parent directory of the just-cloned directory.</li><li>ran debuild</li></ol><div>So there are apparently differences in the environment that are causing Gregor's build to fail. Here is my build environment:</div></div><div><br></div><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>Linux Mint 18.1 Serena</div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>Perl v5.22.1 (debian package)</div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>Bioperl 1.007001 (built from source)</div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>Bio::Graphics 2.39-4 (debian package)</div></blockquote></div><div><br></div><div>My guess is that I should be using the Bioperl 1.007001 debian package, or possibly a newer version of the libbio-graphics package?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.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Lincoln</div></font></span></div><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On Tue, Jan 17, 2017 at 2:07 AM, Andreas Tille <span dir="ltr"><<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>></span> wrote:<br></span><div><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Lincoln,<br>
<span><br>
On Mon, Jan 16, 2017 at 06:14:34PM -0500, Lincoln Stein wrote:<br>
> I need a little help to reproduce Gregor's failed tests, given that I'm a<br>
> complete newbie wrt the Debian packaging system. I have cloned gbrowse<br>
> 2.56+dfsg-1 from the Debian Med repository, but I don't know what command<br>
> line to use to attempt the build. What is the next step? I'm guessing it is<br>
> some form of dpkg-buildpackage, but the number of options is pretty<br>
> overwhelming!<br>
<br>
</span>If you have installed the devscripts package you can try<br>
<br>
  debuild<br>
<br>
which is a wrapper around dpkg-buildpackage and in principle needs no<br>
options to reproduce the issue. Debuild will inform you about missing<br>
Build-Dependencies you need to install - simply use apt-get install what<br>
is listed if anything is missing. When doing so I get<br>
<br>
...<br>
<span>Test Summary Report<br>
-------------------<br>
t/00.compile.t     (Wstat: 3840 Tests: 90 Failed: 15)<br>
 Failed tests: 1, 3, 5, 7, 10, 15, 17-18, 29, 31, 33, 35<br>
        41, 45, 47<br>
 Non-zero exit status: 15<br>
</span>t/02.rearchitecture.t  (Wstat: 512 Tests: 0 Failed: 0)<br>
 Non-zero exit status: 2<br>
<span> Parse errors: Bad plan. You planned 90 tests but ran 0.<br>
</span>t/03.render.t      (Wstat: 512 Tests: 0 Failed: 0)<br>
 Non-zero exit status: 2<br>
<span> Parse errors: Bad plan. You planned 150 tests but ran 0.<br>
</span>t/04.remoteserver.t   (Wstat: 512 Tests: 0 Failed: 0)<br>
 Non-zero exit status: 2<br>
<span> Parse errors: Bad plan. You planned 43 tests but ran 0.<br>
</span>t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)<br>
 Non-zero exit status: 2<br>
<span> Parse errors: Bad plan. You planned 19 tests but ran 0.<br>
</span>t/06.featuresearch.t  (Wstat: 512 Tests: 0 Failed: 0)<br>
 Non-zero exit status: 2<br>
<span> Parse errors: Bad plan. You planned 26 tests but ran 0.<br>
</span>t/07.karyotype.t    (Wstat: 512 Tests: 0 Failed: 0)<br>
 Non-zero exit status: 2<br>
<span> Parse errors: Bad plan. You planned 3 tests but ran 0.<br>
</span>Files=10, Tests=103, 5 wallclock secs ( 0.05 usr 0.01 sys + 4.19 cusr 0.30 csys = 4.55 CPU)<br>
<span>Result: FAIL<br>
Failed 7/10 test programs. 15/103 subtests failed.<br>
</span>dh_auto_test: perl Build test --verbose 1 TEST_FILES=t/02.rearchitecture<wbr>.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<br>
<div class="m_-5545495485248463725HOEnZb"><div class="m_-5545495485248463725h5"><br>
<br>
Kind regards<br>
<br>
    Andreas.<br>
<br>
--<br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</div></div></blockquote></div></div></div><br><br clear="all"><span class=""><div><br></div>-- <br><div class="m_-5545495485248463725gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><b><font color="#38761d">Lincoln Stein</font></b></div><div><span style="font-size:x-small"><br></span></div><div><span style="font-size:x-small">Scientific Director (Interim), Ontario Institute for Cancer Research</span><br></div><div><span style="font-size:x-small">Director, Informatics and Bio-computing Program, OICR</span></div><div><span style="font-size:x-small">Senior Principal Investigator, OICR</span><br></div><div><font size="1">Professor, Department of Molecular Genetics, University of Toronto</font></div><div><font size="1"><a href="http://goog_1828306398" target="_blank"><br></a></font></div><div><b style="color:rgb(56,118,29);font-size:small">Ontario Institute for Cancer Research</b><br></div><div><font size="1">MaRS Centre</font></div><div><font size="1">661 University Avenue</font></div><div><font size="1">Suite 510</font></div><div><font size="1">Toronto, Ontario</font></div><div><font size="1">Canada M5G 0A3</font></div><div><font size="1"><br></font></div><div><font size="1">Tel: <a href="tel:(416)%20673-8514" value="+14166738514" target="_blank">416-673-8514</a></font></div><div><font size="1">Mobile: <a href="tel:(416)%20817-8240" value="+14168178240" target="_blank">416-817-8240</a></font></div><div><font size="1">Email: <a href="mailto:lincoln.stein@gmail.com" target="_blank">lincoln.stein@gmail.com</a></font></div><div><font size="1">Toll-free: <a href="tel:(866)%20678-6427" value="+18666786427" target="_blank">1-866-678-6427</a></font></div><div><font size="1">Twitter: @OICR_news</font></div><div><br></div><div><b><font color="#38761d">Executive Assistant</font></b></div><div><b><font color="#38761d">Lisa Duncan</font></b></div><div><font size="1">Tel:Â </font><a href="tel:(647)%20260-7970" value="+16472607970" style="color:rgb(17,85,204);font-family:Verdana,sans-serif;font-size:10.6667px" target="_blank">647-260-7970</a></div><div><span style="font-size:x-small">Email: lisa.duncan</span><a href="mailto:stacey.quinn@oicr.on.ca" style="font-size:x-small" target="_blank">@oicr.on.ca</a></div><div><font size="1"><a href="http://www.oicr.on.ca" target="_blank">www.oicr.on.ca</a><br></font></div><div><br></div><div><font size="1">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.<br></font></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
</span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><b><font color="#38761d">Lincoln Stein</font></b></div><div><span style="font-size:x-small"><br></span></div><div><span style="font-size:x-small">Scientific Director (Interim), Ontario Institute for Cancer Research</span><br></div><div><span style="font-size:x-small">Director, Informatics and Bio-computing Program, OICR</span></div><div><span style="font-size:x-small">Senior Principal Investigator, OICR</span><br></div><div><font size="1">Professor, Department of Molecular Genetics, University of Toronto</font></div><div><font size="1"><a href="http://goog_1828306398" target="_blank"><br></a></font></div><div><b style="color:rgb(56,118,29);font-size:small">Ontario Institute for Cancer Research</b><br></div><div><font size="1">MaRS Centre</font></div><div><font size="1">661 University Avenue</font></div><div><font size="1">Suite 510</font></div><div><font size="1">Toronto, Ontario</font></div><div><font size="1">Canada M5G 0A3</font></div><div><font size="1"><br></font></div><div><font size="1">Tel: 416-673-8514</font></div><div><font size="1">Mobile: 416-817-8240</font></div><div><font size="1">Email: <a href="mailto:lincoln.stein@gmail.com" target="_blank">lincoln.stein@gmail.com</a></font></div><div><font size="1">Toll-free: 1-866-678-6427</font></div><div><font size="1">Twitter: @OICR_news</font></div><div><br></div><div><b><font color="#38761d">Executive Assistant</font></b></div><div><b><font color="#38761d">Lisa Duncan</font></b></div><div><font size="1">Tel:Â </font><a href="tel:(647)%20260-7970" value="+16472607970" style="color:rgb(17,85,204);font-family:Verdana,sans-serif;font-size:10.6667px" target="_blank">647-260-7970</a></div><div><span style="font-size:x-small">Email: lisa.duncan</span><a href="mailto:stacey.quinn@oicr.on.ca" style="font-size:x-small" target="_blank">@oicr.on.ca</a></div><div><font size="1"><a href="http://www.oicr.on.ca" target="_blank">www.oicr.on.ca</a><br></font></div><div><br></div><div><font size="1">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.<br></font></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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