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

[Andreas Tille]

On Wed, Jan 18, 2017 at 02:21:04PM -0500, Lincoln Stein wrote:
> Yes, I'll remove it immediately and apply the patches to bio::graphics as
> well.

Fine.  Do you intend to do a micro release (say 2.56.1) after this change
or should I remove the file here locally for the time beeing?  Both would
be fine but I want to know in advance.

Kind regards

 Andreas.

-- 
http://fam-tille.de

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

[Lincoln Stein]

Yes, I'll remove it immediately and apply the patches to bio::graphics as
well.

Lincoln

On Wed, Jan 18, 2017 at 11:58 AM, Andreas Tille  wrote:

> On Wed, Jan 18, 2017 at 05:39:05PM +0100, gregor herrmann wrote:
> > >
> > >https://anonscm.debian.org/cgit/debian-med/gbrowse.git/
> tree/debian/patches
> >
> > Oh, cool, adding the (build)-dep is really enough, no patching
> > required. Nice.
>
> Yes, we needed this for another package ...
>
> > For stretch, I think there's still one thing to do:
> > autopkgtest still fails with
> >
> > pmerror:/tmp/apt-dpkg-install-qeDTFa/103-gbrowse.deb:42.2343:trying to
> overwrite '/usr/share/man/man3/Bio::DB::SeqFeature::Store::LoadHelper.3pm.gz',
> which is also in package libbio-perl-perl 1.7.1-2
>
> Urgs - Lincoln, I guess it makes sense to remove this copy of bioperl
> even in your distribution.  What do you think?
>
> 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


*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 
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.

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

[Andreas Tille]

On Wed, Jan 18, 2017 at 05:39:05PM +0100, gregor herrmann wrote:
> > 
> >
> > https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/patches
> 
> Oh, cool, adding the (build)-dep is really enough, no patching
> required. Nice.

Yes, we needed this for another package ...
  
> For stretch, I think there's still one thing to do:
> autopkgtest still fails with
> 
> pmerror:/tmp/apt-dpkg-install-qeDTFa/103-gbrowse.deb:42.2343:trying to 
> overwrite 
> '/usr/share/man/man3/Bio::DB::SeqFeature::Store::LoadHelper.3pm.gz', which is 
> also in package libbio-perl-perl 1.7.1-2

Urgs - Lincoln, I guess it makes sense to remove this copy of bioperl
even in your distribution.  What do you think?

Kind regards

   Andreas.


-- 
http://fam-tille.de

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

[gregor herrmann]

On Wed, 18 Jan 2017 17:27:21 +0100, Andreas Tille wrote:

> > Cool.  In Debian terminology this means a new "Build-Depends" and after 
> > adding
> > libbio-coordinate-perl package to this the tests succeeded.  Thanks a lot 
> > for
> > your help and patience!
> > 
> > I now need to sort out some other issues with packaging and think I'll 
> > upload
> > soon.
> 
> This is done now.
> 
> I'd recommend you have a look at several patches for the Debian package which
> are available here:
> 
>https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/patches

Oh, cool, adding the (build)-dep is really enough, no patching
required. Nice.
 
For stretch, I think there's still one thing to do:
autopkgtest still fails with

pmerror:/tmp/apt-dpkg-install-qeDTFa/103-gbrowse.deb:42.2343:trying to 
overwrite '/usr/share/man/man3/Bio::DB::SeqFeature::Store::LoadHelper.3pm.gz', 
which is also in package libbio-perl-perl 1.7.1-2

Cheers,
gregor

-- 
 .''`.  https://info.comodo.priv.at/ - Debian Developer https://www.debian.org
 : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D  85FA BB3A 6801 8649 AA06
 `. `'  Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe
   `-   NP: Schmetterlinge: Kommt ihr tausend Haufen


signature.asc
Description: Digital Signature

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

[Andreas Tille]

[droping debian-perl list from CC]

On Wed, Jan 18, 2017 at 02:30:32PM +0100, Andreas Tille wrote:
> Hi Lincoln,
> 
> On Wed, Jan 18, 2017 at 07:07:55AM -0500, Lincoln Stein wrote:
> > 
> > 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.
> 
> Cool.  In Debian terminology this means a new "Build-Depends" and after adding
> libbio-coordinate-perl package to this the tests succeeded.  Thanks a lot for
> your help and patience!
> 
> I now need to sort out some other issues with packaging and think I'll upload
> soon.

This is done now.

I'd recommend you have a look at several patches for the Debian package which
are available here:

   https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/patches

They apply in the sequence of the series file and I guess several of them are
useful also for your upstream code.

Thanks a lot for your help

  Andreas.

-- 
http://fam-tille.de

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

[gregor herrmann]

On Wed, 18 Jan 2017 14:00:47 +, Lincoln Stein wrote:

> Glad to be of help. No source changes to bio::graphics needed then?

Probably that too :)
I'll take a look later today.
 
Thanks for your efforts and your enormous help!


Cheers,
gregor

-- 
 .''`.  https://info.comodo.priv.at/ - Debian Developer https://www.debian.org
 : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D  85FA BB3A 6801 8649 AA06
 `. `'  Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe
   `-   BOFH excuse #267:  The UPS is on strike. 

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

[Lincoln Stein]

Glad to be of help. No source changes to bio::graphics needed then?

At some point in near future I will be making changes to the exception
reporting in bio::graphics so that the error messages are more informative.

Lincoln

On Wed, Jan 18, 2017 at 8:30 AM Andreas Tille  wrote:

> Hi Lincoln,
>
>
>
> On Wed, Jan 18, 2017 at 07:07:55AM -0500, Lincoln Stein wrote:
>
> >
>
> > 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.
>
>
>
> Cool.  In Debian terminology this means a new "Build-Depends" and after
> adding
>
> libbio-coordinate-perl package to this the tests succeeded.  Thanks a lot
> for
>
> your help and patience!
>
>
>
> I now need to sort out some other issues with packaging and think I'll
> upload
>
> soon.
>
>
>
> Kind regards
>
>
>
>Andreas.
>
>
>
> --
>
> http://fam-tille.de
>
> --
Written on my cell phone. Anything that seems odd is the fault of
auto-correct.

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

[Andreas Tille]

Hi Lincoln,

On Wed, Jan 18, 2017 at 07:07:55AM -0500, Lincoln Stein wrote:
> 
> 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.

Cool.  In Debian terminology this means a new "Build-Depends" and after adding
libbio-coordinate-perl package to this the tests succeeded.  Thanks a lot for
your help and patience!

I now need to sort out some other issues with packaging and think I'll upload
soon.

Kind regards

   Andreas.

-- 
http://fam-tille.de

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

[Lincoln Stein]

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,  line 192.
BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Graphics/Glyph/
arrow.pm line 13,  line 192.
Compilation failed in require at /usr/share/perl/5.22/base.pm line 97,
 line 192.
...propagated at /usr/share/perl/5.22/base.pm line 106,  line 192.
BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Graphics/Glyph/
anchored_arrow.pm line 5,  line 192.
Compilation failed in require at /usr/share/perl/5.22/base.pm line 97,
 line 192.
...propagated at /usr/share/perl/5.22/base.pm line 106,  line 192.
BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Graphics/Glyph/
span.pm line 4,  line 192.
Compilation failed in require,  line 192.
BEGIN failed--compilation aborted,  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 
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 
> 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  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 p

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

[Lincoln Stein]

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 
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  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
>
> 
> *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 
> 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

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  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


*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 
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.

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

[Lincoln Stein]

That would have been my guess too, but Bio:: Graphics 2.40 is the right
version. When running build test on a virgin Mint 18.2 system with
Bio::Perl 1.7.1 and Bio::Graphics 2.40 I'm getting 100% test success.  This
is very puzzling.

I'll  take a closer look tonight.

Lincoln

On Tue, Jan 17, 2017 at 6:27 PM gregor herrmann  wrote:

> On Tue, 17 Jan 2017 18:06:02 -0500, Lincoln Stein wrote:
>
>
>
> > Not good! But I believe that Gregor found that all these were caused by
> the
>
> > testing suite not finding the proper data files due to an assumption
> about
>
> > the current working directory. When he fixed this, there were just a
>
> > handful of tests still failing.
>
>
>
> Right, that's when I built from a clone of the debian package git
>
> repo. With your github repo, this was not necessary for reasons I
>
> haven't yet understood.
>
>
>
> > Gregor, is there a patch file that I can
>
> > apply to get up to the same point you got to?
>
>
>
> Oh, scratch what I wrote above, now I get the same with the debian
>
> repo, so no more "Can't find foo in @INC". Good, at least the
>
> failures are consistent now (for whatever reason, maybe the 5.24.1
>
> upload to unstable changed something), and no patch for that part
>
> needed.
>
>
>
> So now we are still at:
>
>
>
>
>
> t/03.render.t .
>
> 1..150
>
> ok 1
>
> ok 2
>
> ok 3
>
> ok 4
>
> ok 5
>
> ok 6
>
> ok 7
>
> ok 8
>
> ok 9
>
> ok 10
>
> ok 11
>
> ok 12
>
> ok 13
>
> ok 14
>
> ok 15
>
> ok 16
>
> ok 17
>
> ok 18
>
> ok 19
>
> ok 20
>
> ok 21
>
> ok 22
>
> ok 23
>
> ok 24
>
> ok 25
>
> ok 26
>
> ok 27
>
> ok 28
>
> ok 29
>
> ok 30
>
> ok 31
>
> ok 32
>
> ok 33
>
> ok 34
>
> ok 35
>
> ok 36
>
> ok 37
>
> ok 38
>
> ok 39
>
> ok 40
>
> ok 41
>
> Dubious, test returned 255 (wstat 65280, 0xff00)
>
> Failed 109/150 subtests
>
> Sometimes this test gets 'stuck'. If this happens, kill the test and Build
> test again.
>
> RenderPanels error:
>
> - EXCEPTION -
>
> MSG: The requested glyph class, ``span'' is not available: Attempt to
> reload Bio/Graphics/Glyph/span.pm aborted.
>
> Compilation failed in require at (eval 138) line 2, <> line 132.
>
>
>
> STACK Bio::Graphics::Glyph::Factory::make_glyph
> /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
>
> STACK Bio::Graphics::Glyph::add_feature
> /usr/share/perl5/Bio/Graphics/Glyph.pm:424
>
> STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
>
> STACK (eval)
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
>
> STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
>
> STACK Bio::Graphics::Browser2::Render::Slave::render_tracks
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
>
> STACK Bio::Graphics::Browser2::Render::Slave::run_operation
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_request
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_connection
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
>
> STACK Bio::Graphics::Browser2::Render::Slave::request_loop
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
>
> STACK Bio::Graphics::Browser2::Render::Slave::run
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
>
> STACK toplevel t/04.remoteserver.t:81
>
> -
>
>
>
> Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line
> 136.
>
> RenderPanels error:
>
> - EXCEPTION -
>
> MSG: The requested glyph class, ``span'' is not available: Attempt to
> reload Bio/Graphics/Glyph/span.pm aborted.
>
> Compilation failed in require at (eval 138) line 2, <> line 132.
>
>
>
> STACK Bio::Graphics::Glyph::Factory::make_glyph
> /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
>
> STACK Bio::Graphics::Glyph::add_feature
> /usr/share/perl5/Bio/Graphics/Glyph.pm:424
>
> STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
>
> STACK (eval)
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
>
> STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
>
> STACK Bio::Graphics::Browser2::Render::Slave::render_tracks
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
>
> STACK Bio::Graphics::Browser2::Render::Slave::run_operation
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_request
> /build/gbrowse-2.56+dfsg/t/../li

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

[gregor herrmann]

On Tue, 17 Jan 2017 18:06:02 -0500, Lincoln Stein wrote:

> Not good! But I believe that Gregor found that all these were caused by the
> testing suite not finding the proper data files due to an assumption about
> the current working directory. When he fixed this, there were just a
> handful of tests still failing. 

Right, that's when I built from a clone of the debian package git
repo. With your github repo, this was not necessary for reasons I
haven't yet understood.

> Gregor, is there a patch file that I can
> apply to get up to the same point you got to?

Oh, scratch what I wrote above, now I get the same with the debian
repo, so no more "Can't find foo in @INC". Good, at least the
failures are consistent now (for whatever reason, maybe the 5.24.1
upload to unstable changed something), and no patch for that part
needed.

So now we are still at:
 

t/03.render.t . 
1..150
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 109/150 subtests 
Sometimes this test gets 'stuck'. If this happens, kill the test and Build test 
again.
RenderPanels error: 
- EXCEPTION -
MSG: The requested glyph class, ``span'' is not available: Attempt to reload 
Bio/Graphics/Glyph/span.pm aborted.
Compilation failed in require at (eval 138) line 2, <> line 132.

STACK Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK Bio::Graphics::Glyph::add_feature 
/usr/share/perl5/Bio/Graphics/Glyph.pm:424
STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
STACK (eval) 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
STACK Bio::Graphics::Browser2::Render::Slave::render_tracks 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
STACK Bio::Graphics::Browser2::Render::Slave::run_operation 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
STACK Bio::Graphics::Browser2::Render::Slave::process_request 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
STACK Bio::Graphics::Browser2::Render::Slave::process_connection 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
STACK Bio::Graphics::Browser2::Render::Slave::request_loop 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
STACK Bio::Graphics::Browser2::Render::Slave::run 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
STACK toplevel t/04.remoteserver.t:81
-

Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line 136.
RenderPanels error: 
- EXCEPTION -
MSG: The requested glyph class, ``span'' is not available: Attempt to reload 
Bio/Graphics/Glyph/span.pm aborted.
Compilation failed in require at (eval 138) line 2, <> line 132.

STACK Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK Bio::Graphics::Glyph::add_feature 
/usr/share/perl5/Bio/Graphics/Glyph.pm:424
STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
STACK (eval) 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
STACK Bio::Graphics::Browser2::Render::Slave::render_tracks 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
STACK Bio::Graphics::Browser2::Render::Slave::run_operation 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
STACK Bio::Graphics::Browser2::Render::Slave::process_request 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
STACK Bio::Graphics::Browser2::Render::Slave::process_connection 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
STACK Bio::Graphics::Browser2::Render::Slave::request_loop 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
STACK Bio::Graphics::Browser2::Render::Slave::run 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
STACK toplevel t/04.remoteserver.t:81
-

Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line 136.
RenderPanels error: 
- EXCEPTION -
MSG: The requested glyph class, ``span'' is not available: Attempt to reload 
Bio/Graphics

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

[Lincoln Stein]

Not good! But I believe that Gregor found that all these were caused by the
testing suite not finding the proper data files due to an assumption about
the current working directory. When he fixed this, there were just a
handful of tests still failing. Gregor, is there a patch file that I can
apply to get up to the same point you got to?

Lincoln

On Tue, Jan 17, 2017 at 2:07 AM, Andreas Tille  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


*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 
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.

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

[Andreas Tille]

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

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

[Lincoln Stein]

Hi,

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!



Lincoln

On Mon, Jan 16, 2017 at 3:01 PM, gregor herrmann  wrote:

> On Mon, 16 Jan 2017 16:45:52 +0100, Andreas Tille wrote:
>
> > > If you want to use the same list of tests to skip during build, you
> > > can do something like
> > > https://sources.debian.net/src/libipc-sharelite-perl/0.
> 17-4/debian/rules
> > Ahhh, OK.  I wrongly assumed that would be some magic since in the
> > bioperl case it worked without this extra means.
>
> The magic there worked because it was only needed for autopkgtest and
> not at build time :)
>
> > > I migt be able to try a build later today.
> >
> > After safely landing in Berlin (from Debian Med sprint in Bukarest) I
> > tried with your hints and the only remaining issue seems to be:
> >
> > 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
>
> Lucky you :)
> When I try to build the package from git, 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: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 90 tests but ran 0.
> t/03.render.t   (Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 150 tests but ran 0.
> t/04.remoteserver.t (Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 43 tests but ran 0.
> t/05.deferredrendering.t (Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 19 tests but ran 0.
> t/06.featuresearch.t(Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 26 tests but ran 0.
> t/07.karyotype.t(Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 3 tests but ran 0.
> Files=10, Tests=103,  5 wallclock secs ( 0.03 usr  0.03 sys +  4.19 cusr
> 0.36 csys =  4.61 CPU)
> Result: FAIL
> Failed 7/10 test programs. 15/103 subtests failed.
>
>
> Ah, found it:
>
> #   Failed test 'cgi-bin/das compiled ok'
> #   at t/00.compile.t line 47.
> # stdout:
> # stderr: Backslash found where operator expected at
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm
> line 963, near "$ENV\"
> #   (Missing operator before \?)
> # Backslash found where operator expected at /build/gbrowse-2.56+dfsg/blib/
> lib/Bio/Graphics/Browser2/DataSource.pm line 963, near "$1\"
> #   (Missing operator before \?)
> # Variable "$semantic_label" is not imported at
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm
> line 984,  line 192.
> #   (Did you mean &semantic_label instead?)
> # syntax error at 
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm
> line 963, near "$ENV\"
> # syntax error at 
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm
> line 963, near "''}"
>
> This seems to come from debian/patches/fix_perl_deprecation.
>
> *a bit later*
>
> Yes, this patch is wrong now and can be dropped, as the original
> issue was fixed in the 2.56 release. (Attached)
>
> This brings me to:
>
> Test Summary Report
> ---
> t/03.render.t   (Wstat: 65280 Tests: 41 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 150 tests but ran 41.
> t/04.remoteserver.t (Wstat: 0 Tests: 41 Failed: 4)
>   Failed tests:  11, 23, 35, 39
>   Parse errors: Bad plan.  You planned 43 tests but ran 41.
> t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 2)
>   Failed tests:  5, 14
>
> So t/00.compile.t just works. But I still have other issues.
>
> Seems they all fail with something like
> "Can't locate testdata/conf/../../../conf/plugins/Aligner.pm in @INC ..."
> which is quite weird path ... -- But it's fine, so we probably have a
> ". removed from @INC" problem here somewhere.
>
> I guess that's it:
>
> lib/Bio/Graphics/Browser2/PluginSet.pm
>
> my $class = "Bio\:\:Graphics\:\:Browser2\:\:Plugin\:\:$plugin";
> for my $search_path (@search_path) {
>   my $plugin_with_path = "$search_path/$plugin.pm";
>   if (eval {require $plugin_with_path}) {
>
> Ok, changing this to "./$plugin_with_path" gets rid of this error but
> later we still get something similar:
>
> # prove --blib --verbose t/05.deferredren

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

[gregor herrmann]

On Mon, 16 Jan 2017 21:38:14 +0100, Andreas Tille wrote:

> thanks a lot for you detailed analysis.  BTW, you should be able to `git
> push` into Debian Med repository - no need to do the attachment detour
> if this might be more convenient for you.

Ack, will do so next time.
 
> Hmmm, may be I misunderstand but the failed tests are preventing
> the build from succeeding and besides
> 
>   0001-Drop-patch-fix_perl_deprecation.patch
>   0002-debian-rules-update-name-of-a-config-file-in-chmod-c.patch
> 
> which I `git am`ed I did not found anything in your mail.

Right, the three tests are still failing, and I didn't provide a
patch because I haven't found a solution :)

(For the autopkgtest trial run, I first built the package with
DEB_BUILD_OPTIONS=nocheck.) 

Cheers,
gregor

-- 
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 : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D  85FA BB3A 6801 8649 AA06
 `. `'  Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe
   `-   NP: Bettina Wegner: Drei Schwester


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Description: Digital Signature

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

[gregor herrmann]

On Mon, 16 Jan 2017 20:23:37 +, Lincoln Stein wrote:

> Oh dear. What happens when you just "Build test" on the git checkout?

Voilà:

[..]
t/03.render.t . 1/150 
- EXCEPTION: Bio::Root::Exception -
MSG: The requested glyph class, ``arrow'' is not available: Attempt to reload 
Bio/Graphics/Glyph/arrow.pm aborted.
Compilation failed in require at (eval 178) line 2.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
STACK: Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK: Bio::Graphics::Glyph::make_subglyph 
/usr/share/perl5/Bio/Graphics/Glyph.pm:310
STACK: Bio::Graphics::Glyph::new /usr/share/perl5/Bio/Graphics/Glyph.pm:270
STACK: Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:346
STACK: Bio::Graphics::Panel::_add_track 
/usr/share/perl5/Bio/Graphics/Panel.pm:414
STACK: Bio::Graphics::Panel::_do_add_track 
/usr/share/perl5/Bio/Graphics/Panel.pm:386
STACK: Bio::Graphics::Panel::add_track 
/usr/share/perl5/Bio/Graphics/Panel.pm:312
STACK: Bio::Graphics::Browser2::RenderPanels::render_scale_bar 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1080
STACK: Bio::Graphics::Browser2::Render::asynchronous_update_overview_scale_bar 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:2547
STACK: Bio::Graphics::Browser2::Action::ACTION_navigate 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm:144
STACK: Bio::Graphics::Browser2::Render::asynchronous_event 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:432
STACK: t/03.render.t:178
---
RenderPanels error: can't create 
/tmp/gbrowse_testing/cache/volvox/c6/1a/93/c61a932ed29ba5ba0d5fb4cb62224dd1/data:
 No such file or directory at 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 158.
RenderPanels error: 
- EXCEPTION: Bio::Root::Exception -
MSG: The requested glyph class, ``span'' is not available: Attempt to reload 
Bio/Graphics/Glyph/span.pm aborted.
Compilation failed in require at (eval 178) line 2.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
STACK: Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK: Bio::Graphics::Glyph::add_feature 
/usr/share/perl5/Bio/Graphics/Glyph.pm:424
STACK: Bio::Graphics::Browser2::RenderPanels::add_features_to_track 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::RenderPanels::request_panels 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:192
STACK: Bio::Graphics::Browser2::Render::render_deferred 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:3602
STACK: Bio::Graphics::Browser2::Render::background_track_render 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:529
STACK: Bio::Graphics::Browser2::Action::ACTION_navigate 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm:141
STACK: Bio::Graphics::Browser2::Render::asynchronous_event 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:432
STACK: t/03.render.t:178
---
t/03.render.t . Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 109/150 subtests 
t/04.remoteserver.t ... Sometimes this test gets 'stuck'. If this happens, 
kill the test and Build test again.
t/04.remoteserver.t ... 1/43 RenderPanels error: 
- EXCEPTION: Bio::Root::Exception -
MSG: The requested glyph class, ``span'' is not available: Attempt to reload 
Bio/Graphics/Glyph/span.pm aborted.
Compilation failed in require at (eval 138) line 2, <> line 132.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
STACK: Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK: Bio::Graphics::Glyph::add_feature 
/usr/share/perl5/Bio/Graphics/Glyph.pm:424
STACK: Bio::Graphics::Browser2::RenderPanels::add_features_to_track 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::Render::Slave::render_tracks 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
STACK: Bio::Graphics::Browser2::Render::Slave::run_operation 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
STACK: Bio::Graphics::Browser2::Render::Slave::process_request 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
STACK: Bio::Graphics::Browser2::Render::Slave::process_connection 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
STACK: Bio::Graphics::Browser2::Render::Slave::req

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

[Andreas Tille]

Hi Gregor,

thanks a lot for you detailed analysis.  BTW, you should be able to `git
push` into Debian Med repository - no need to do the attachment detour
if this might be more convenient for you.

On Mon, Jan 16, 2017 at 09:01:11PM +0100, gregor herrmann wrote:
> On Mon, 16 Jan 2017 16:45:52 +0100, Andreas Tille wrote:
> > Ahhh, OK.  I wrongly assumed that would be some magic since in the
> > bioperl case it worked without this extra means.
> 
> The magic there worked because it was only needed for autopkgtest and
> not at build time :)

Ahhh ...
  
> > After safely landing in Berlin (from Debian Med sprint in Bukarest) I
> > tried with your hints and the only remaining issue seems to be:
> > 
> > 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
> 
> Lucky you :)

Hmmm, may be I was not looking properly - now I can reproduce all you
wrote.

> When I try to build the package from git, 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: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 90 tests but ran 0.
> t/03.render.t   (Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 150 tests but ran 0.
> t/04.remoteserver.t (Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 43 tests but ran 0.
> t/05.deferredrendering.t (Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 19 tests but ran 0.
> t/06.featuresearch.t(Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 26 tests but ran 0.
> t/07.karyotype.t(Wstat: 65280 Tests: 0 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 3 tests but ran 0.
> Files=10, Tests=103,  5 wallclock secs ( 0.03 usr  0.03 sys +  4.19 cusr  
> 0.36 csys =  4.61 CPU)
> Result: FAIL
> Failed 7/10 test programs. 15/103 subtests failed.
> 
> 
> Ah, found it:
> 
> #   Failed test 'cgi-bin/das compiled ok'
> #   at t/00.compile.t line 47.
> # stdout:
> # stderr: Backslash found where operator expected at 
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 
> 963, near "$ENV\"
> #   (Missing operator before \?)
> # Backslash found where operator expected at 
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 
> 963, near "$1\"
> #   (Missing operator before \?)
> # Variable "$semantic_label" is not imported at 
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 
> 984,  line 192.
> #   (Did you mean &semantic_label instead?)
> # syntax error at 
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 
> 963, near "$ENV\"
> # syntax error at 
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 
> 963, near "''}"
> 
> This seems to come from debian/patches/fix_perl_deprecation.
> 
> *a bit later*
> 
> Yes, this patch is wrong now and can be dropped, as the original
> issue was fixed in the 2.56 release. (Attached)
> 
> This brings me to:
> 
> Test Summary Report
> ---
> t/03.render.t   (Wstat: 65280 Tests: 41 Failed: 0)
>   Non-zero exit status: 255
>   Parse errors: Bad plan.  You planned 150 tests but ran 41.
> t/04.remoteserver.t (Wstat: 0 Tests: 41 Failed: 4)
>   Failed tests:  11, 23, 35, 39
>   Parse errors: Bad plan.  You planned 43 tests but ran 41.
> t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 2)
>   Failed tests:  5, 14
> 
> So t/00.compile.t just works. But I still have other issues.
> 
> Seems they all fail with something like 
> "Can't locate testdata/conf/../../../conf/plugins/Aligner.pm in @INC ..."
> which is quite weird path ... -- But it's fine, so we probably have a
> ". removed from @INC" problem here somewhere.
> 
> I guess that's it:
> 
> lib/Bio/Graphics/Browser2/PluginSet.pm
> 
> my $class = "Bio\:\:Graphics\:\:Browser2\:\:Plugin\:\:$plugin";
> for my $search_path (@search_path) {
>   my $plugin_with_path = "$search_path/$plugin.pm";
>   if (eval {require $plugin_with_path}) {
> 
> Ok, changing this to "./$plugin_with_path" gets rid of this error but
> later we still get something similar:
> 
> # prove --blib --verbose t/05.deferredrendering.t
> t/05.deferredrendering.t .. 
> 1..19
> ok 1
> ok 2
> ok 3
> RenderPanels error: 
> - EXCEPTION -
> MSG: The requested glyph class, ``span'' is not available: Attempt to reload 
> Bio/Graphics/Glyph/span.pm aborted.
> Compilation failed in require at (eval 181) line 2, <>

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

[Lincoln Stein]

Oh dear. What happens when you just "Build test" on the git checkout?
Sounds like path issues. I can try applying the Deb patches and try to
reproduce.  Unfortunately I am a Deb packaging newbie.

Lincoln




On Mon, Jan 16, 2017 at 3:01 PM gregor herrmann  wrote:

> On Mon, 16 Jan 2017 16:45:52 +0100, Andreas Tille wrote:
>
>
>
> > > If you want to use the same list of tests to skip during build, you
>
> > > can do something like
>
> > >
> https://sources.debian.net/src/libipc-sharelite-perl/0.17-4/debian/rules
>
> > Ahhh, OK.  I wrongly assumed that would be some magic since in the
>
> > bioperl case it worked without this extra means.
>
>
>
> The magic there worked because it was only needed for autopkgtest and
>
> not at build time :)
>
>
>
> > > I migt be able to try a build later today.
>
> >
>
> > After safely landing in Berlin (from Debian Med sprint in Bukarest) I
>
> > tried with your hints and the only remaining issue seems to be:
>
> >
>
> > 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
>
>
>
> Lucky you :)
>
> When I try to build the package from git, 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: 65280 Tests: 0 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 90 tests but ran 0.
>
> t/03.render.t   (Wstat: 65280 Tests: 0 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 150 tests but ran 0.
>
> t/04.remoteserver.t (Wstat: 65280 Tests: 0 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 43 tests but ran 0.
>
> t/05.deferredrendering.t (Wstat: 65280 Tests: 0 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 19 tests but ran 0.
>
> t/06.featuresearch.t(Wstat: 65280 Tests: 0 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 26 tests but ran 0.
>
> t/07.karyotype.t(Wstat: 65280 Tests: 0 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 3 tests but ran 0.
>
> Files=10, Tests=103,  5 wallclock secs ( 0.03 usr  0.03 sys +  4.19 cusr
> 0.36 csys =  4.61 CPU)
>
> Result: FAIL
>
> Failed 7/10 test programs. 15/103 subtests failed.
>
>
>
>
>
> Ah, found it:
>
>
>
> #   Failed test 'cgi-bin/das compiled ok'
>
> #   at t/00.compile.t line 47.
>
> # stdout:
>
> # stderr: Backslash found where operator expected at
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line
> 963, near "$ENV\"
>
> #   (Missing operator before \?)
>
> # Backslash found where operator expected at
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line
> 963, near "$1\"
>
> #   (Missing operator before \?)
>
> # Variable "$semantic_label" is not imported at
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line
> 984,  line 192.
>
> #   (Did you mean &semantic_label instead?)
>
> # syntax error at
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line
> 963, near "$ENV\"
>
> # syntax error at
> /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line
> 963, near "''}"
>
>
>
> This seems to come from debian/patches/fix_perl_deprecation.
>
>
>
> *a bit later*
>
>
>
> Yes, this patch is wrong now and can be dropped, as the original
>
> issue was fixed in the 2.56 release. (Attached)
>
>
>
> This brings me to:
>
>
>
> Test Summary Report
>
> ---
>
> t/03.render.t   (Wstat: 65280 Tests: 41 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 150 tests but ran 41.
>
> t/04.remoteserver.t (Wstat: 0 Tests: 41 Failed: 4)
>
>   Failed tests:  11, 23, 35, 39
>
>   Parse errors: Bad plan.  You planned 43 tests but ran 41.
>
> t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 2)
>
>   Failed tests:  5, 14
>
>
>
> So t/00.compile.t just works. But I still have other issues.
>
>
>
> Seems they all fail with something like
>
> "Can't locate testdata/conf/../../../conf/plugins/Aligner.pm in @INC ..."
>
> which is quite weird path ... -- But it's fine, so we probably have a
>
> ". removed from @INC" problem here somewhere.
>
>
>
> I guess that's it:
>
>
>
> lib/Bio/Graphics/Browser2/PluginSet.pm
>
>
>
> my $class = "Bio\:\:Graphics\:\:Browser2\:\:Plugin\:\:$plugin";
>
> for my $search_path (@search_path) {
>
>   my $plugin_with_path = "$search_path/$plugin.pm";
>
>   if (eval {require $plugin_with_path}) {
>
>
>
> Ok, changing this to "./$plugin_with_path" gets rid of this error but
>
> later we still get something similar:
>
>
>
> # prove --blib --

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

[gregor herrmann]

On Mon, 16 Jan 2017 16:45:52 +0100, Andreas Tille wrote:

> > If you want to use the same list of tests to skip during build, you
> > can do something like
> > https://sources.debian.net/src/libipc-sharelite-perl/0.17-4/debian/rules
> Ahhh, OK.  I wrongly assumed that would be some magic since in the
> bioperl case it worked without this extra means.

The magic there worked because it was only needed for autopkgtest and
not at build time :)
 
> > I migt be able to try a build later today.
> 
> After safely landing in Berlin (from Debian Med sprint in Bukarest) I
> tried with your hints and the only remaining issue seems to be:
> 
> 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

Lucky you :)
When I try to build the package from git, 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: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 90 tests but ran 0.
t/03.render.t   (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 150 tests but ran 0.
t/04.remoteserver.t (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 43 tests but ran 0.
t/05.deferredrendering.t (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 19 tests but ran 0.
t/06.featuresearch.t(Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 26 tests but ran 0.
t/07.karyotype.t(Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 3 tests but ran 0.
Files=10, Tests=103,  5 wallclock secs ( 0.03 usr  0.03 sys +  4.19 cusr  0.36 
csys =  4.61 CPU)
Result: FAIL
Failed 7/10 test programs. 15/103 subtests failed.


Ah, found it:

#   Failed test 'cgi-bin/das compiled ok'
#   at t/00.compile.t line 47.
# stdout:
# stderr: Backslash found where operator expected at 
/build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 963, 
near "$ENV\"
#   (Missing operator before \?)
# Backslash found where operator expected at 
/build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 963, 
near "$1\"
#   (Missing operator before \?)
# Variable "$semantic_label" is not imported at 
/build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 984, 
 line 192.
#   (Did you mean &semantic_label instead?)
# syntax error at 
/build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 963, 
near "$ENV\"
# syntax error at 
/build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line 963, 
near "''}"

This seems to come from debian/patches/fix_perl_deprecation.

*a bit later*

Yes, this patch is wrong now and can be dropped, as the original
issue was fixed in the 2.56 release. (Attached)

This brings me to:

Test Summary Report
---
t/03.render.t   (Wstat: 65280 Tests: 41 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 150 tests but ran 41.
t/04.remoteserver.t (Wstat: 0 Tests: 41 Failed: 4)
  Failed tests:  11, 23, 35, 39
  Parse errors: Bad plan.  You planned 43 tests but ran 41.
t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 2)
  Failed tests:  5, 14

So t/00.compile.t just works. But I still have other issues.

Seems they all fail with something like 
"Can't locate testdata/conf/../../../conf/plugins/Aligner.pm in @INC ..."
which is quite weird path ... -- But it's fine, so we probably have a
". removed from @INC" problem here somewhere.

I guess that's it:

lib/Bio/Graphics/Browser2/PluginSet.pm

my $class = "Bio\:\:Graphics\:\:Browser2\:\:Plugin\:\:$plugin";
for my $search_path (@search_path) {
  my $plugin_with_path = "$search_path/$plugin.pm";
  if (eval {require $plugin_with_path}) {

Ok, changing this to "./$plugin_with_path" gets rid of this error but
later we still get something similar:

# prove --blib --verbose t/05.deferredrendering.t
t/05.deferredrendering.t .. 
1..19
ok 1
ok 2
ok 3
RenderPanels error: 
- EXCEPTION -
MSG: The requested glyph class, ``span'' is not available: Attempt to reload 
Bio/Graphics/Glyph/span.pm aborted.
Compilation failed in require at (eval 181) line 2, <> line 45.

STACK Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK Bio::Graphics::Glyph::add_feature 
/usr/share/perl5/Bio/Graphics/Glyph.pm:424
STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track 
/build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
STACK (eval) 
/build/gbrowse-2

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

[Andreas Tille]

On Mon, Jan 16, 2017 at 12:04:31PM +0100, gregor herrmann wrote:
> That's not unexpected since debian/tests/pkg-perl/smoke-skip is an
> (optional) configuration file for the autopkgtest-pkg-perl framework
> and is not related to building the package.
> 
> If you want to use the same list of tests to skip during build, you
> can do something like
> 
> https://sources.debian.net/src/libipc-sharelite-perl/0.17-4/debian/rules

Ahhh, OK.  I wrongly assumed that would be some magic since in the
bioperl case it worked without this extra means.

> As for the
> https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/tests/pkg-perl/smoke-skip
>  
> file:
> It looks like you forgot the "t/" directory prefix for the test
> file names.

Yup, fixed.
 
> > Could anybody with better
> > Perl skills than me please have a look at the failed build time tests?
> 
> I migt be able to try a build later today.

After safely landing in Berlin (from Debian Med sprint in Bukarest) I
tried with your hints and the only remaining issue seems to be:

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

I wonder how these numbers relate to the tests inside the test file and
what might be the recommended procedure:  Patching single tests (those
1, 3, 5, ...) or the wimpy way to exclude the whole file.  May be there
is some hint how these tests might pass but I personally have no idea.

Kind regards

   Andreas.


-- 
http://fam-tille.de

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

[gregor herrmann]

On Mon, 16 Jan 2017 05:55:20 +0100, Andreas Tille wrote:

> Since I learned from Perl team (in CC) that I can exclude tests via
> 
>debian/tests/pkg-perl/smoke-skip
> 
> I tried to use this feature.  Unfortunately this does not work as
> expected - at least in the build process.  

That's not unexpected since debian/tests/pkg-perl/smoke-skip is an
(optional) configuration file for the autopkgtest-pkg-perl framework
and is not related to building the package.

If you want to use the same list of tests to skip during build, you
can do something like

https://sources.debian.net/src/libipc-sharelite-perl/0.17-4/debian/rules


As for the
https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/tests/pkg-perl/smoke-skip
 
file:
It looks like you forgot the "t/" directory prefix for the test
file names.


> Could anybody with better
> Perl skills than me please have a look at the failed build time tests?

I migt be able to try a build later today.
 

Cheers,
gregor

-- 
 .''`.  https://info.comodo.priv.at/ - Debian Developer https://www.debian.org
 : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D  85FA BB3A 6801 8649 AA06
 `. `'  Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe
   `-   BOFH excuse #238:  You did wha... oh _dear_ 

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

[Andreas Tille]

Hi Lincoln,

On Sun, Jan 15, 2017 at 04:25:46PM -0500, Lincoln Stein wrote:
> The bug in the memory adaptor that Scott found turns out to have been from
> using the old perl 1.6.9 installed by the Debian package. Updating to 1.7.1
> (1.007001) fixes the problem.
> 
> I have merged all GBrowse changes into git version 2.56 and have made a
> CPAN release. I think you can go ahead and package it.

thanks a lot for your work on this.

For the Debian packaging[1] I imported the new version and tried to
adapt the patches[2] (BTW, I have no idea whether any previous
maintainer of the package pointed to it but some of these might be
interesting to integrate into the upstream code).

Since I learned from Perl team (in CC) that I can exclude tests via

   debian/tests/pkg-perl/smoke-skip

I tried to use this feature.  Unfortunately this does not work as
expected - at least in the build process.  Could anybody with better
Perl skills than me please have a look at the failed build time tests?

Thanks to all who provided help so far to finally fix gbrowse for the
next Debian stable release

 Andreas.

[1] https://anonscm.debian.org/git/debian-med/gbrowse.git
[2] https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/patches

-- 
http://fam-tille.de

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

[Fields, Christopher J]

That’s great news Lincoln, fantastic!

chris

From: Lincoln Stein mailto:lincoln.st...@gmail.com>>
Date: Sunday, January 15, 2017 at 3:25 PM
To: Andreas Tille mailto:andr...@fam-tille.de>>
Cc: Scott Cain mailto:sc...@scottcain.net>>, 
"848...@bugs.debian.org" 
<848...@bugs.debian.org>, Chris Fields 
mailto:cjfie...@illinois.edu>>, Debian Med Project List 
mailto:debian-...@lists.debian.org>>, Charles 
Plessy mailto:char...@plessy.org>>, Olivier Sallou 
mailto:olivier.sal...@irisa.fr>>, Sascha Steinbiss 
mailto:sa...@debian.org>>, Carnë Draug 
mailto:carandraug+...@gmail.com>>
Subject: Re: Remaining issue with gbrowse - any help (Was: Urgent call to 
BioPerl users (Was: Bug#848236: src:gbrowse: ...)

Hi,

The bug in the memory adaptor that Scott found turns out to have been from 
using the old perl 1.6.9 installed by the Debian package. Updating to 1.7.1 
(1.007001) fixes the problem.

I have merged all GBrowse changes into git version 2.56 and have made a CPAN 
release. I think you can go ahead and package it.

Lincoln

On Thu, Jan 12, 2017 at 11:37 PM, Andreas Tille 
mailto:andr...@fam-tille.de>> wrote:
Thanks to you both.  I think the only question targeted directly at my
was the "how much time question":  On Februrar 5 is full freeze.  You
need to cut 10 days from this since a package has a 10 day migration
time until it makes it from unstable to the release candidates in
testing.  So this would make 2017-01-25 - but if there is a single (even
unrelated to gbrowse) issue that might prevent the migration gbrowse is
doomed.  So I'd recommend to get something out until beginning of next
week.

Kind regards

  Andreas.

On Thu, Jan 12, 2017 at 02:23:42PM -0500, Scott Cain wrote:
> I made a few changes in a branch off that security-bug-fixes branch that
> quieted several warning messages, though I still need to sort out at least
> one problem (the memory adaptor doesn't seem to be reading fasta files, but
> also doesn't emit a warning about a problem).  Lincoln, if you want to look
> at this pull request, you could pull those changes into the security bug
> fix branch:
>
> https://github.com/GMOD/GBrowse/pull/59
>
> Scott
>
>
> On Thu, Jan 12, 2017 at 1:57 PM, Lincoln Stein 
> mailto:lincoln.st...@gmail.com>>
> wrote:
>
> > Hi Andreas,
> >
> > I was able to remove the vast majority of the warnings and other
> > incompatibility issues, but need to do more testing to identify areas of
> > the code that were not covered. How much time do I have? If you want to go
> > with a fully functional version that may issue warnings when the user takes
> > certain rare actions, it is the "security-bug-fixes" branch at
> > https://github.com/GMOD/GBrowse
> >
> > Lincoln
> >
> > On Thu, Jan 12, 2017 at 1:39 PM, Andreas Tille 
> > mailto:andr...@an3as.eu>> wrote:
> >
> >> Hi Lincoln,
> >>
> >> On Wed, Dec 21, 2016 at 06:25:46PM -0500, Lincoln Stein wrote:
> >> > I am devoting several days over the Christmas holidays to fixing the
> >> > various outstanding bugs in gbrowse. Stay tuned!
> >>
> >> Did you managed to managed to work on this?  If not we probably can not
> >> include gbrowse in the next Debian stable release which would be a
> >> shame.
> >>
> >> 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
> >
> > >
> > *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)%

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

[Lincoln Stein]

Hi,

The bug in the memory adaptor that Scott found turns out to have been from
using the old perl 1.6.9 installed by the Debian package. Updating to 1.7.1
(1.007001) fixes the problem.

I have merged all GBrowse changes into git version 2.56 and have made a
CPAN release. I think you can go ahead and package it.

Lincoln

On Thu, Jan 12, 2017 at 11:37 PM, Andreas Tille 
wrote:

> Thanks to you both.  I think the only question targeted directly at my
> was the "how much time question":  On Februrar 5 is full freeze.  You
> need to cut 10 days from this since a package has a 10 day migration
> time until it makes it from unstable to the release candidates in
> testing.  So this would make 2017-01-25 - but if there is a single (even
> unrelated to gbrowse) issue that might prevent the migration gbrowse is
> doomed.  So I'd recommend to get something out until beginning of next
> week.
>
> Kind regards
>
>   Andreas.
>
> On Thu, Jan 12, 2017 at 02:23:42PM -0500, Scott Cain wrote:
> > I made a few changes in a branch off that security-bug-fixes branch that
> > quieted several warning messages, though I still need to sort out at
> least
> > one problem (the memory adaptor doesn't seem to be reading fasta files,
> but
> > also doesn't emit a warning about a problem).  Lincoln, if you want to
> look
> > at this pull request, you could pull those changes into the security bug
> > fix branch:
> >
> > https://github.com/GMOD/GBrowse/pull/59
> >
> > Scott
> >
> >
> > On Thu, Jan 12, 2017 at 1:57 PM, Lincoln Stein 
> > wrote:
> >
> > > Hi Andreas,
> > >
> > > I was able to remove the vast majority of the warnings and other
> > > incompatibility issues, but need to do more testing to identify areas
> of
> > > the code that were not covered. How much time do I have? If you want
> to go
> > > with a fully functional version that may issue warnings when the user
> takes
> > > certain rare actions, it is the "security-bug-fixes" branch at
> > > https://github.com/GMOD/GBrowse
> > >
> > > Lincoln
> > >
> > > On Thu, Jan 12, 2017 at 1:39 PM, Andreas Tille 
> wrote:
> > >
> > >> Hi Lincoln,
> > >>
> > >> On Wed, Dec 21, 2016 at 06:25:46PM -0500, Lincoln Stein wrote:
> > >> > I am devoting several days over the Christmas holidays to fixing the
> > >> > various outstanding bugs in gbrowse. Stay tuned!
> > >>
> > >> Did you managed to managed to work on this?  If not we probably can
> not
> > >> include gbrowse in the next Debian stable release which would be a
> > >> shame.
> > >>
> > >> 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
> > >
> > > 
> > > *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*
> > > *Frances Dirnbeck*
> > > Tel: 647-259-4253 <(647)%20259-4253>
> > > Email:frances.dirnb...@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.
> > >
> >
> >
> >
> > --
> > 
> > Scott Cain, Ph. D.   scott at scottcain
> dot
> > net
> > GMOD Coordinator (http://gmod.org/) 216-392-3087
> > Ontario Institute for Cancer Research
>
> --
> 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


*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 
www.oicr.on.ca

This message and any attachments may contain confidentia

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

[Andreas Tille]

Thanks to you both.  I think the only question targeted directly at my
was the "how much time question":  On Februrar 5 is full freeze.  You
need to cut 10 days from this since a package has a 10 day migration
time until it makes it from unstable to the release candidates in
testing.  So this would make 2017-01-25 - but if there is a single (even
unrelated to gbrowse) issue that might prevent the migration gbrowse is
doomed.  So I'd recommend to get something out until beginning of next
week.

Kind regards

  Andreas.

On Thu, Jan 12, 2017 at 02:23:42PM -0500, Scott Cain wrote:
> I made a few changes in a branch off that security-bug-fixes branch that
> quieted several warning messages, though I still need to sort out at least
> one problem (the memory adaptor doesn't seem to be reading fasta files, but
> also doesn't emit a warning about a problem).  Lincoln, if you want to look
> at this pull request, you could pull those changes into the security bug
> fix branch:
> 
> https://github.com/GMOD/GBrowse/pull/59
> 
> Scott
> 
> 
> On Thu, Jan 12, 2017 at 1:57 PM, Lincoln Stein 
> wrote:
> 
> > Hi Andreas,
> >
> > I was able to remove the vast majority of the warnings and other
> > incompatibility issues, but need to do more testing to identify areas of
> > the code that were not covered. How much time do I have? If you want to go
> > with a fully functional version that may issue warnings when the user takes
> > certain rare actions, it is the "security-bug-fixes" branch at
> > https://github.com/GMOD/GBrowse
> >
> > Lincoln
> >
> > On Thu, Jan 12, 2017 at 1:39 PM, Andreas Tille  wrote:
> >
> >> Hi Lincoln,
> >>
> >> On Wed, Dec 21, 2016 at 06:25:46PM -0500, Lincoln Stein wrote:
> >> > I am devoting several days over the Christmas holidays to fixing the
> >> > various outstanding bugs in gbrowse. Stay tuned!
> >>
> >> Did you managed to managed to work on this?  If not we probably can not
> >> include gbrowse in the next Debian stable release which would be a
> >> shame.
> >>
> >> 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
> >
> > 
> > *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*
> > *Frances Dirnbeck*
> > Tel: 647-259-4253 <(647)%20259-4253>
> > Email:frances.dirnb...@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.
> >
> 
> 
> 
> -- 
> 
> Scott Cain, Ph. D.   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research

-- 
http://fam-tille.de

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

[Scott Cain]

I made a few changes in a branch off that security-bug-fixes branch that
quieted several warning messages, though I still need to sort out at least
one problem (the memory adaptor doesn't seem to be reading fasta files, but
also doesn't emit a warning about a problem).  Lincoln, if you want to look
at this pull request, you could pull those changes into the security bug
fix branch:

https://github.com/GMOD/GBrowse/pull/59

Scott


On Thu, Jan 12, 2017 at 1:57 PM, Lincoln Stein 
wrote:

> Hi Andreas,
>
> I was able to remove the vast majority of the warnings and other
> incompatibility issues, but need to do more testing to identify areas of
> the code that were not covered. How much time do I have? If you want to go
> with a fully functional version that may issue warnings when the user takes
> certain rare actions, it is the "security-bug-fixes" branch at
> https://github.com/GMOD/GBrowse
>
> Lincoln
>
> On Thu, Jan 12, 2017 at 1:39 PM, Andreas Tille  wrote:
>
>> Hi Lincoln,
>>
>> On Wed, Dec 21, 2016 at 06:25:46PM -0500, Lincoln Stein wrote:
>> > I am devoting several days over the Christmas holidays to fixing the
>> > various outstanding bugs in gbrowse. Stay tuned!
>>
>> Did you managed to managed to work on this?  If not we probably can not
>> include gbrowse in the next Debian stable release which would be a
>> shame.
>>
>> 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
>
> 
> *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*
> *Frances Dirnbeck*
> Tel: 647-259-4253 <(647)%20259-4253>
> Email:frances.dirnb...@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.
>



-- 

Scott Cain, Ph. D.   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

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

[Andreas Tille]

Hi Lincoln,

On Wed, Dec 21, 2016 at 06:25:46PM -0500, Lincoln Stein wrote:
> I am devoting several days over the Christmas holidays to fixing the
> various outstanding bugs in gbrowse. Stay tuned!

Did you managed to managed to work on this?  If not we probably can not
include gbrowse in the next Debian stable release which would be a
shame.

Kind regards

   Andreas.

-- 
http://fam-tille.de

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

[Lincoln Stein]

I am devoting several days over the Christmas holidays to fixing the
various outstanding bugs in gbrowse. Stay tuned!

Lincoln

On Wed, Dec 21, 2016 at 5:23 PM, Fields, Christopher J <
cjfie...@illinois.edu> wrote:

> This may be something to pass by Lincoln or Scott Cain(CC'd).  Lincoln I
> did manage to get a new Bio-Graphics out (as well as BioPerl-Run), which
> seems to have addressed the latest, but I'm unable to look at gbrowse until
> well into the new year.
>
> Chris
>
> Chris
>
> Sent from my iPhone
>
> > On Dec 21, 2016, at 3:42 PM, Andreas Tille  wrote:
> >
> > Hi,
> >
> > here is an update and a cal for help with gbrowse since I'm not an
> > experienced Perl programmer.  My guess is that its not really hard to
> > solve for somebody familiar with Perl and specifically with Bioperl.
> >
> > On Sat, Dec 17, 2016 at 11:15:30PM +0100, Andreas Tille wrote:
> >>>  bioperl-run
> >>
> >> Works with patch, Test suite runs at Build time
> >
> > Just uploaded 1.7.1 after activating as much as possible unittest
> > at package build time.  Hope that this will not fire back ...
> >
> >>>  gbrowse
> >>
> >> Fails - help is urgently needed:
> >>
> >> ...
> >> syntax error at /home/andreas/debian-maintain/
> alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/../
> lib/Bio/Graphics/Browser2/DataSource.pm line 963, near "$ENV\"
> >> syntax error at /home/andreas/debian-maintain/
> alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/../
> lib/Bio/Graphics/Browser2/DataSource.pm line 963, near "''}"
> >> Global symbol "$self" requires explicit package name (did you forget to
> declare "my $self"?) at /home/andreas/debian-maintain/
> alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/../
> lib/Bio/Graphics/Browser2/DataSource.pm line 971,  line 192.
> >> Global symbol "$symbolic_db_name" requires explicit package name (did
> you forget to declare "my $symbolic_db_name"?) at
> /home/andreas/debian-maintain/alioth/debian-med_git/build-
> area/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/DataSource.pm line
> 971,  line 192.
> >> Global symbol "$length" requires explicit package name (did you forget
> to declare "my $length"?) at /home/andreas/debian-maintain/
> alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/..
> >> ...
> >
> > Any help?
> >
> >> So as far as I can see if we can solve the gbrowse issue the migration
> >> to 1.7.1 seems possible.
> >>
> >> What do you think?
> >
> > I decided to go with version 1.7.1 for Stretch since all rdepends except
> > gbrowse are working and regarding popcon the other packages seem to be
> > more important.  Fixing gbrowse would be wanted for sure.
> >
> > 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


*Ontario Institute for Cancer Research*
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*Frances Dirnbeck*
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