Ok, and here is a little command-line test that takes the problem a bit deeper. I'm sending this out because I have to go to work now and can't get back to this again today:
perl -MBio::Perl -MBio::Graphics -MBio::Graphics::Glyph::span Can't locate Bio/Coordinate/Pair.pm in @INC (you may need to install the Bio::Coordinate::Pair module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/share/perl5/Bio/Graphics/Glyph/arrow.pm line 13, <DATA> line 192. BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Graphics/Glyph/ arrow.pm line 13, <DATA> line 192. Compilation failed in require at /usr/share/perl/5.22/base.pm line 97, <DATA> line 192. ...propagated at /usr/share/perl/5.22/base.pm line 106, <DATA> line 192. BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Graphics/Glyph/ anchored_arrow.pm line 5, <DATA> line 192. Compilation failed in require at /usr/share/perl/5.22/base.pm line 97, <DATA> line 192. ...propagated at /usr/share/perl/5.22/base.pm line 106, <DATA> line 192. BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Graphics/Glyph/ span.pm line 4, <DATA> line 192. Compilation failed in require, <DATA> line 192. BEGIN failed--compilation aborted, <DATA> line 192. There appears to be a new dependency on libbio-coordinate. Probably best to add a "use Bio::Coordinate" and the dependency to Bio::Graphics. Then the problem will disappear. Lincoln On Wed, Jan 18, 2017 at 7:00 AM, Lincoln Stein <lincoln.st...@gmail.com> wrote: > 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.st...@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 <andr...@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.st...@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.dun...@oicr.on.ca <stacey.qu...@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. >> > > > > -- > *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.st...@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.dun...@oicr.on.ca <stacey.qu...@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. > -- *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.st...@gmail.com Toll-free: 1-866-678-6427 Twitter: @OICR_news *Executive Assistant* *Lisa Duncan* Tel: 647-260-7970 <(647)%20260-7970> Email: lisa.dun...@oicr.on.ca <stacey.qu...@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.
