GBrowse2: test hanging at t/03.render.t

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GBrowse2: test hanging at t/03.render.t

Prem Anand
Hi All

I am trying to install GBrowse2 and get struck at t/03.render.t.   It
hangs at roughly around the tests 108-110/138, on installing both via
the CPAN shell and manually.
I am installing it on ubuntu.

A similar error was reported in
http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
and Lincoln has suggested to reinstall libgd.  I did try that, but
didn't succeed. Test hung at same place.

Any pointers will be highly appreciated.

./Build test
NOTE: Run ./Build reconfig to change existing configuration.
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... ok
t/03.render.t ............. 106/138 Subroutine
Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
/usr/local/share/perl/5.8.8/Exporter.pm line 67.
 at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
 at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
/usr/local/share/perl/5.8.8/Exporter.pm line 67.
 at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
 at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
 at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
/usr/local/share/perl/5.8.8/Exporter.pm line 67.
 at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
t/03.render.t ............. 110/138


Many Thanks
Prem

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Re: GBrowse2: test hanging at t/03.render.t

Scott Cain
Hi Prem,

In the past when I've had hangs at this point, updating Bio::Graphics
has fixed the problem.  Make sure that the most recent version is
installed.  Also, while I'm not thrilled to be suggesting this, you
could install it anyway and see if it appears to work.

Scott


On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]> wrote:

> Hi All
>
> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
> hangs at roughly around the tests 108-110/138, on installing both via
> the CPAN shell and manually.
> I am installing it on ubuntu.
>
> A similar error was reported in
> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
> and Lincoln has suggested to reinstall libgd.  I did try that, but
> didn't succeed. Test hung at same place.
>
> Any pointers will be highly appreciated.
>
> ./Build test
> NOTE: Run ./Build reconfig to change existing configuration.
> t/01yeast.t ............... ok
> t/02.rearchitecture.t ..... ok
> t/03.render.t ............. 106/138 Subroutine
> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> t/03.render.t ............. 110/138
>
>
> Many Thanks
> Prem
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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

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Re: GBrowse2: test hanging at t/03.render.t

Prem Anand
Thanks for the tip Scott.

I updated Bio::Graphics to 2.10 and tried again, but still the same.

perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
2.10

Could be related to this issue?? not sure!!!
http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291

Thanks
Prem


On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain <[hidden email]> wrote:

> Hi Prem,
>
> In the past when I've had hangs at this point, updating Bio::Graphics
> has fixed the problem.  Make sure that the most recent version is
> installed.  Also, while I'm not thrilled to be suggesting this, you
> could install it anyway and see if it appears to work.
>
> Scott
>
>
> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]> wrote:
>> Hi All
>>
>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>> hangs at roughly around the tests 108-110/138, on installing both via
>> the CPAN shell and manually.
>> I am installing it on ubuntu.
>>
>> A similar error was reported in
>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>> didn't succeed. Test hung at same place.
>>
>> Any pointers will be highly appreciated.
>>
>> ./Build test
>> NOTE: Run ./Build reconfig to change existing configuration.
>> t/01yeast.t ............... ok
>> t/02.rearchitecture.t ..... ok
>> t/03.render.t ............. 106/138 Subroutine
>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> t/03.render.t ............. 110/138
>>
>>
>> Many Thanks
>> Prem
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

------------------------------------------------------------------------------
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Re: GBrowse2: test hanging at t/03.render.t

Scott Cain
Hi Prem,

I don't think that bug is related.  That bug was due to a missing
file, and gave a pretty clear message to that effect.

What happens if you just install it?  If there is still a problem, we
might at least get more information from a the apache error_log.

One other thing that might give us more information is if execute the
test directly, like this:

  perl t/03.render.t

Scott




On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]> wrote:

> Thanks for the tip Scott.
>
> I updated Bio::Graphics to 2.10 and tried again, but still the same.
>
> perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
> 2.10
>
> Could be related to this issue?? not sure!!!
> http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>
> Thanks
> Prem
>
>
> On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain <[hidden email]> wrote:
>> Hi Prem,
>>
>> In the past when I've had hangs at this point, updating Bio::Graphics
>> has fixed the problem.  Make sure that the most recent version is
>> installed.  Also, while I'm not thrilled to be suggesting this, you
>> could install it anyway and see if it appears to work.
>>
>> Scott
>>
>>
>> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]> wrote:
>>> Hi All
>>>
>>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>>> hangs at roughly around the tests 108-110/138, on installing both via
>>> the CPAN shell and manually.
>>> I am installing it on ubuntu.
>>>
>>> A similar error was reported in
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>>> didn't succeed. Test hung at same place.
>>>
>>> Any pointers will be highly appreciated.
>>>
>>> ./Build test
>>> NOTE: Run ./Build reconfig to change existing configuration.
>>> t/01yeast.t ............... ok
>>> t/02.rearchitecture.t ..... ok
>>> t/03.render.t ............. 106/138 Subroutine
>>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> t/03.render.t ............. 110/138
>>>
>>>
>>> Many Thanks
>>> Prem
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>



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

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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: GBrowse2: test hanging at t/03.render.t

J.M.P. Alves
In reply to this post by Scott Cain
Hi,

I sent an email earlier reporting a similar problem, although in my case
the test does not hang, it just fails (see below), at 03.render and
07.karyotype. And in my case force installing works, but not all
functionality of GBrowse2 works. (the "karyotype" display that shoud
come up when there is more than one result for a search does not work,
and there's no error message in Apache logs)

So I tried updating Bio::Graphics (to 2.10) as Scott suggested, and
update was fine. Still, installing GBrowse2 (2.10) gives exactly the
same test errors as before (I've tried with 2.08 and 2.09).

This is in a machine that already has GBrowse 1.x installed (which works
fine).

The errors, again, after building:

==================================================================
   ./Build -- OK
Running Build test
NOTE: Run ./Build reconfig to change existing configuration.
/etc/apache2/conf.d/gbrowse2.conf is already installed. Please run
./Build apache_conf to see this file's recommended contents.
t/01yeast.................ok

t/02.rearchitecture.......ok

t/03.render...............dubious

        Test returned status 0 (wstat 11, 0xb)
DIED. FAILED tests 116-138
        Failed 23/138 tests, 83.33% okay
t/04.remoteserver.........ok

t/05.deferredrendering....ok

t/06.featuresearch........ok

t/07.karyotype............dubious

        Test returned status 0 (wstat 11, 0xb)
DIED. FAILED tests 2-3
        Failed 2/3 tests, 33.33% okay
t/08.calign...............ok

Failed Test      Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/03.render.t       0    11   138   46  116-138
t/07.karyotype.t    0    11     3    4  2-3
Failed 2/8 test scripts. 25/332 subtests failed.
Files=8, Tests=332, 32 wallclock secs (21.06 cusr +  2.88 csys = 23.94 CPU)
Failed 2/8 test programs. 25/332 subtests failed.
   LDS/GBrowse-2.10.tar.gz
   ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
   reports LDS/GBrowse-2.10.tar.gz
Running Build install
   make test had returned bad status, won't install without force
Failed during this command:
  LDS/GBrowse-2.10.tar.gz                      : make_test NO
==================================================================

Regards
J

Scott Cain wrote:

> Hi Prem,
>
> In the past when I've had hangs at this point, updating Bio::Graphics
> has fixed the problem.  Make sure that the most recent version is
> installed.  Also, while I'm not thrilled to be suggesting this, you
> could install it anyway and see if it appears to work.
>
> Scott
>
>
> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]> wrote:
>> Hi All
>>
>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>> hangs at roughly around the tests 108-110/138, on installing both via
>> the CPAN shell and manually.
>> I am installing it on ubuntu.
>>
>> A similar error was reported in
>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>> didn't succeed. Test hung at same place.
>>
>> Any pointers will be highly appreciated.
>>
>> ./Build test
>> NOTE: Run ./Build reconfig to change existing configuration.
>> t/01yeast.t ............... ok
>> t/02.rearchitecture.t ..... ok
>> t/03.render.t ............. 106/138 Subroutine
>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>> t/03.render.t ............. 110/138
>>
>>
>> Many Thanks
>> Prem
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


------------------------------------------------------------------------------
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Re: GBrowse2: test hanging at t/03.render.t

Jayaraman, Pushkala
In reply to this post by Scott Cain
I had a problem with the render.t test.. I simple stopped the process..and started from scratch .. it seems to work fine now..

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Wednesday, June 16, 2010 10:51 AM
To: Prem Anand
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t

Hi Prem,

I don't think that bug is related.  That bug was due to a missing
file, and gave a pretty clear message to that effect.

What happens if you just install it?  If there is still a problem, we
might at least get more information from a the apache error_log.

One other thing that might give us more information is if execute the
test directly, like this:

  perl t/03.render.t

Scott




On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]> wrote:

> Thanks for the tip Scott.
>
> I updated Bio::Graphics to 2.10 and tried again, but still the same.
>
> perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
> 2.10
>
> Could be related to this issue?? not sure!!!
> http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>
> Thanks
> Prem
>
>
> On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain <[hidden email]> wrote:
>> Hi Prem,
>>
>> In the past when I've had hangs at this point, updating Bio::Graphics
>> has fixed the problem.  Make sure that the most recent version is
>> installed.  Also, while I'm not thrilled to be suggesting this, you
>> could install it anyway and see if it appears to work.
>>
>> Scott
>>
>>
>> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]> wrote:
>>> Hi All
>>>
>>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>>> hangs at roughly around the tests 108-110/138, on installing both via
>>> the CPAN shell and manually.
>>> I am installing it on ubuntu.
>>>
>>> A similar error was reported in
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>>> didn't succeed. Test hung at same place.
>>>
>>> Any pointers will be highly appreciated.
>>>
>>> ./Build test
>>> NOTE: Run ./Build reconfig to change existing configuration.
>>> t/01yeast.t ............... ok
>>> t/02.rearchitecture.t ..... ok
>>> t/03.render.t ............. 106/138 Subroutine
>>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> t/03.render.t ............. 110/138
>>>
>>>
>>> Many Thanks
>>> Prem
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>



--
------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GBrowse2: test hanging at t/03.render.t

Lincoln Stein
There is an intermittent problem when running the regression tests involving a race condition between the slave (renderfarm) servers and the master server. This causes the tests to hang. Typically they run correctly if you just restart them. Sorry I haven't fixed the issue for good (it seems to be dependent on system load) but the hanging does not seem to affect the server in operation.

Lincoln

On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala <[hidden email]> wrote:
I had a problem with the render.t test.. I simple stopped the process..and started from scratch .. it seems to work fine now..

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Wednesday, June 16, 2010 10:51 AM
To: Prem Anand
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t

Hi Prem,

I don't think that bug is related.  That bug was due to a missing
file, and gave a pretty clear message to that effect.

What happens if you just install it?  If there is still a problem, we
might at least get more information from a the apache error_log.

One other thing that might give us more information is if execute the
test directly, like this:

 perl t/03.render.t

Scott




On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]> wrote:
> Thanks for the tip Scott.
>
> I updated Bio::Graphics to 2.10 and tried again, but still the same.
>
> perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
> 2.10
>
> Could be related to this issue?? not sure!!!
> http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>
> Thanks
> Prem
>
>
> On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain <[hidden email]> wrote:
>> Hi Prem,
>>
>> In the past when I've had hangs at this point, updating Bio::Graphics
>> has fixed the problem.  Make sure that the most recent version is
>> installed.  Also, while I'm not thrilled to be suggesting this, you
>> could install it anyway and see if it appears to work.
>>
>> Scott
>>
>>
>> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]> wrote:
>>> Hi All
>>>
>>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>>> hangs at roughly around the tests 108-110/138, on installing both via
>>> the CPAN shell and manually.
>>> I am installing it on ubuntu.
>>>
>>> A similar error was reported in
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>>> didn't succeed. Test hung at same place.
>>>
>>> Any pointers will be highly appreciated.
>>>
>>> ./Build test
>>> NOTE: Run ./Build reconfig to change existing configuration.
>>> t/01yeast.t ............... ok
>>> t/02.rearchitecture.t ..... ok
>>> t/03.render.t ............. 106/138 Subroutine
>>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>> t/03.render.t ............. 110/138
>>>
>>>
>>> Many Thanks
>>> Prem
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
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_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse2: test hanging at t/03.render.t

Prem Anand
Thanks to all.

I tried to run the test individually as Scott suggested.

perl 03.render.t
1..138
# Running under perl version 5.008008 for linux
# Current time local: Wed Jun 16 17:33:37 2010

ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
Killed


For some reason, it gets killed.  But I still could see two process running.

ps -ef | grep perl
prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl

I didn't get how to restart the master/slave servers. Do you mean
restarting the tests/servers?!

I did try killing the process as Pushkala suggested and started again,
but it doesn't help either.

Thanks for your time
Prem




On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein <[hidden email]> wrote:

> There is an intermittent problem when running the regression tests involving
> a race condition between the slave (renderfarm) servers and the master
> server. This causes the tests to hang. Typically they run correctly if you
> just restart them. Sorry I haven't fixed the issue for good (it seems to be
> dependent on system load) but the hanging does not seem to affect the server
> in operation.
> Lincoln
>
> On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>>
>> I had a problem with the render.t test.. I simple stopped the process..and
>> started from scratch .. it seems to work fine now..
>>
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Wednesday, June 16, 2010 10:51 AM
>> To: Prem Anand
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>
>> Hi Prem,
>>
>> I don't think that bug is related.  That bug was due to a missing
>> file, and gave a pretty clear message to that effect.
>>
>> What happens if you just install it?  If there is still a problem, we
>> might at least get more information from a the apache error_log.
>>
>> One other thing that might give us more information is if execute the
>> test directly, like this:
>>
>>  perl t/03.render.t
>>
>> Scott
>>
>>
>>
>>
>> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]> wrote:
>> > Thanks for the tip Scott.
>> >
>> > I updated Bio::Graphics to 2.10 and tried again, but still the same.
>> >
>> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>> > 2.10
>> >
>> > Could be related to this issue?? not sure!!!
>> >
>> > http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>> >
>> > Thanks
>> > Prem
>> >
>> >
>> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain <[hidden email]> wrote:
>> >> Hi Prem,
>> >>
>> >> In the past when I've had hangs at this point, updating Bio::Graphics
>> >> has fixed the problem.  Make sure that the most recent version is
>> >> installed.  Also, while I'm not thrilled to be suggesting this, you
>> >> could install it anyway and see if it appears to work.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]>
>> >> wrote:
>> >>> Hi All
>> >>>
>> >>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>> >>> hangs at roughly around the tests 108-110/138, on installing both via
>> >>> the CPAN shell and manually.
>> >>> I am installing it on ubuntu.
>> >>>
>> >>> A similar error was reported in
>> >>>
>> >>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>> >>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>> >>> didn't succeed. Test hung at same place.
>> >>>
>> >>> Any pointers will be highly appreciated.
>> >>>
>> >>> ./Build test
>> >>> NOTE: Run ./Build reconfig to change existing configuration.
>> >>> t/01yeast.t ............... ok
>> >>> t/02.rearchitecture.t ..... ok
>> >>> t/03.render.t ............. 106/138 Subroutine
>> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> t/03.render.t ............. 110/138
>> >>>
>> >>>
>> >>> Many Thanks
>> >>> Prem
>> >>>
>> >>>
>> >>> ------------------------------------------------------------------------------
>> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> >>> lucky parental unit.  See the prize list and enter to win:
>> >>> http://p.sf.net/sfu/thinkgeek-promo
>> >>> _______________________________________________
>> >>> Gmod-gbrowse mailing list
>> >>> [hidden email]
>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >>
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>

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Re: GBrowse2: test hanging at t/03.render.t

J.M.P. Alves
In reply to this post by Scott Cain
Hi, Scott

Doing that gives me:

...
ok 114
ok 115
Segmentation fault

Using the verbose=1 option that was mentioned earlier by Cornel did not
give any better idea. I looked at the code but could not figure out
which tests are 116 to 138, so I don't know which part is giving the seg
fault.

J

Scott Cain wrote:

> Hi Prem,
>
> I don't think that bug is related.  That bug was due to a missing
> file, and gave a pretty clear message to that effect.
>
> What happens if you just install it?  If there is still a problem, we
> might at least get more information from a the apache error_log.
>
> One other thing that might give us more information is if execute the
> test directly, like this:
>
>   perl t/03.render.t
>
> Scott
>
>
>
>
> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]> wrote:
>> Thanks for the tip Scott.
>>
>> I updated Bio::Graphics to 2.10 and tried again, but still the same.
>>
>> perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>> 2.10
>>
>> Could be related to this issue?? not sure!!!
>> http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>>
>> Thanks
>> Prem
>>
>>
>> On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain <[hidden email]> wrote:
>>> Hi Prem,
>>>
>>> In the past when I've had hangs at this point, updating Bio::Graphics
>>> has fixed the problem.  Make sure that the most recent version is
>>> installed.  Also, while I'm not thrilled to be suggesting this, you
>>> could install it anyway and see if it appears to work.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]> wrote:
>>>> Hi All
>>>>
>>>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>>>> hangs at roughly around the tests 108-110/138, on installing both via
>>>> the CPAN shell and manually.
>>>> I am installing it on ubuntu.
>>>>
>>>> A similar error was reported in
>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>>>> didn't succeed. Test hung at same place.
>>>>
>>>> Any pointers will be highly appreciated.
>>>>
>>>> ./Build test
>>>> NOTE: Run ./Build reconfig to change existing configuration.
>>>> t/01yeast.t ............... ok
>>>> t/02.rearchitecture.t ..... ok
>>>> t/03.render.t ............. 106/138 Subroutine
>>>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>>>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>>>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>>>> t/03.render.t ............. 110/138
>>>>
>>>>
>>>> Many Thanks
>>>> Prem
>>>>
>>>> ------------------------------------------------------------------------------
>>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>> lucky parental unit.  See the prize list and enter to win:
>>>> http://p.sf.net/sfu/thinkgeek-promo
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>
>
>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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Re: GBrowse2: test hanging at t/03.render.t

Lincoln Stein
In reply to this post by Prem Anand
The two left-over processes are slave servers. Kill them from the command line and try again. This problem may be related to the way that signaling handling has changed between perl versions 5.08 and 5.10. Would you be adverse to upgrading to perl 5.10 to see if it fixes the problem?

Lincoln

On Wed, Jun 16, 2010 at 12:45 PM, Prem Anand <[hidden email]> wrote:
Thanks to all.

I tried to run the test individually as Scott suggested.

perl 03.render.t
1..138
# Running under perl version 5.008008 for linux
# Current time local: Wed Jun 16 17:33:37 2010

ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
Killed


For some reason, it gets killed.  But I still could see two process running.

ps -ef | grep perl
prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl

I didn't get how to restart the master/slave servers. Do you mean
restarting the tests/servers?!

I did try killing the process as Pushkala suggested and started again,
but it doesn't help either.

Thanks for your time
Prem




On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein <[hidden email]> wrote:
> There is an intermittent problem when running the regression tests involving
> a race condition between the slave (renderfarm) servers and the master
> server. This causes the tests to hang. Typically they run correctly if you
> just restart them. Sorry I haven't fixed the issue for good (it seems to be
> dependent on system load) but the hanging does not seem to affect the server
> in operation.
> Lincoln
>
> On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>>
>> I had a problem with the render.t test.. I simple stopped the process..and
>> started from scratch .. it seems to work fine now..
>>
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Wednesday, June 16, 2010 10:51 AM
>> To: Prem Anand
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>
>> Hi Prem,
>>
>> I don't think that bug is related.  That bug was due to a missing
>> file, and gave a pretty clear message to that effect.
>>
>> What happens if you just install it?  If there is still a problem, we
>> might at least get more information from a the apache error_log.
>>
>> One other thing that might give us more information is if execute the
>> test directly, like this:
>>
>>  perl t/03.render.t
>>
>> Scott
>>
>>
>>
>>
>> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]> wrote:
>> > Thanks for the tip Scott.
>> >
>> > I updated Bio::Graphics to 2.10 and tried again, but still the same.
>> >
>> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>> > 2.10
>> >
>> > Could be related to this issue?? not sure!!!
>> >
>> > http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>> >
>> > Thanks
>> > Prem
>> >
>> >
>> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain <[hidden email]> wrote:
>> >> Hi Prem,
>> >>
>> >> In the past when I've had hangs at this point, updating Bio::Graphics
>> >> has fixed the problem.  Make sure that the most recent version is
>> >> installed.  Also, while I'm not thrilled to be suggesting this, you
>> >> could install it anyway and see if it appears to work.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand <[hidden email]>
>> >> wrote:
>> >>> Hi All
>> >>>
>> >>> I am trying to install GBrowse2 and get struck at t/03.render.t.   It
>> >>> hangs at roughly around the tests 108-110/138, on installing both via
>> >>> the CPAN shell and manually.
>> >>> I am installing it on ubuntu.
>> >>>
>> >>> A similar error was reported in
>> >>>
>> >>> http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>> >>> and Lincoln has suggested to reinstall libgd.  I did try that, but
>> >>> didn't succeed. Test hung at same place.
>> >>>
>> >>> Any pointers will be highly appreciated.
>> >>>
>> >>> ./Build test
>> >>> NOTE: Run ./Build reconfig to change existing configuration.
>> >>> t/01yeast.t ............... ok
>> >>> t/02.rearchitecture.t ..... ok
>> >>> t/03.render.t ............. 106/138 Subroutine
>> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined
>> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
>> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
>> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>> >>>  at /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>> >>> line 10
>> >>> t/03.render.t ............. 110/138
>> >>>
>> >>>
>> >>> Many Thanks
>> >>> Prem
>> >>>
>> >>>
>> >>> ------------------------------------------------------------------------------
>> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> >>> lucky parental unit.  See the prize list and enter to win:
>> >>> http://p.sf.net/sfu/thinkgeek-promo
>> >>> _______________________________________________
>> >>> Gmod-gbrowse mailing list
>> >>> [hidden email]
>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >>
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse2: test hanging at t/03.render.t

J.M.P. Alves
Hi,

I have Perl 5.10.0, and had the same issue (actually I had about 30 of
those processes there, from all my tries of getting this to work). I
killed all of them, but that did not solve the problem when I tried again.

Prem, I don't remember if you have mentioned this before or not, but
does the computer where you are trying to install GBrowse 2.x already
have GBrowse 1.x? In two cases here (mine and someone else's), it had.
In another computer of mine that had never seen GBrowse or any of its
dependencies, install of 2.08 was quite smooth and everything works.

Therefore I have the hunch that something used by older BioPerl/GBrowse
(some maybe it was installed manually at the time) is conflicting with
the new ones, and it's not getting upgraded when I upgrade all the
prerequisites for GBrowse2.

J

Lincoln Stein wrote:

> The two left-over processes are slave servers. Kill them from the
> command line and try again. This problem may be related to the way that
> signaling handling has changed between perl versions 5.08 and 5.10.
> Would you be adverse to upgrading to perl 5.10 to see if it fixes the
> problem?
>
> Lincoln
>
> On Wed, Jun 16, 2010 at 12:45 PM, Prem Anand <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Thanks to all.
>
>     I tried to run the test individually as Scott suggested.
>
>     perl 03.render.t
>     1..138
>     # Running under perl version 5.008008 for linux
>     # Current time local: Wed Jun 16 17:33:37 2010
>
>     ok 110
>     ok 111
>     ok 112
>     ok 113
>     ok 114
>     ok 115
>     Killed
>
>
>     For some reason, it gets killed.  But I still could see two process
>     running.
>
>     ps -ef | grep perl
>     prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
>     prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
>     prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl
>
>     I didn't get how to restart the master/slave servers. Do you mean
>     restarting the tests/servers?!
>
>     I did try killing the process as Pushkala suggested and started again,
>     but it doesn't help either.
>
>     Thanks for your time
>     Prem
>
>
>
>
>     On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein
>     <[hidden email] <mailto:[hidden email]>> wrote:
>      > There is an intermittent problem when running the regression
>     tests involving
>      > a race condition between the slave (renderfarm) servers and the
>     master
>      > server. This causes the tests to hang. Typically they run
>     correctly if you
>      > just restart them. Sorry I haven't fixed the issue for good (it
>     seems to be
>      > dependent on system load) but the hanging does not seem to affect
>     the server
>      > in operation.
>      > Lincoln
>      >
>      > On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala
>     <[hidden email] <mailto:[hidden email]>>
>      > wrote:
>      >>
>      >> I had a problem with the render.t test.. I simple stopped the
>     process..and
>      >> started from scratch .. it seems to work fine now..
>      >>
>      >> Pushkala Jayaraman
>      >> Programmer/Analyst
>      >> Rat Genome Database
>      >> Human and Molecular Genetics Center
>      >> Medical College of Wisconsin
>      >> Email: [hidden email] <mailto:[hidden email]>
>      >> Work: 414-955-2229
>      >> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>      >>
>      >>
>      >> -----Original Message-----
>      >> From: Scott Cain [mailto:[hidden email]
>     <mailto:[hidden email]>]
>      >> Sent: Wednesday, June 16, 2010 10:51 AM
>      >> To: Prem Anand
>      >> Cc: [hidden email]
>     <mailto:[hidden email]>
>      >> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>      >>
>      >> Hi Prem,
>      >>
>      >> I don't think that bug is related.  That bug was due to a missing
>      >> file, and gave a pretty clear message to that effect.
>      >>
>      >> What happens if you just install it?  If there is still a
>     problem, we
>      >> might at least get more information from a the apache error_log.
>      >>
>      >> One other thing that might give us more information is if
>     execute the
>      >> test directly, like this:
>      >>
>      >>  perl t/03.render.t
>      >>
>      >> Scott
>      >>
>      >>
>      >>
>      >>
>      >> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]
>     <mailto:[hidden email]>> wrote:
>      >> > Thanks for the tip Scott.
>      >> >
>      >> > I updated Bio::Graphics to 2.10 and tried again, but still the
>     same.
>      >> >
>      >> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>      >> > 2.10
>      >> >
>      >> > Could be related to this issue?? not sure!!!
>      >> >
>      >> >
>     http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>     <http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291>
>      >> >
>      >> > Thanks
>      >> > Prem
>      >> >
>      >> >
>      >> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain
>     <[hidden email] <mailto:[hidden email]>> wrote:
>      >> >> Hi Prem,
>      >> >>
>      >> >> In the past when I've had hangs at this point, updating
>     Bio::Graphics
>      >> >> has fixed the problem.  Make sure that the most recent version is
>      >> >> installed.  Also, while I'm not thrilled to be suggesting
>     this, you
>      >> >> could install it anyway and see if it appears to work.
>      >> >>
>      >> >> Scott
>      >> >>
>      >> >>
>      >> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand
>     <[hidden email] <mailto:[hidden email]>>
>      >> >> wrote:
>      >> >>> Hi All
>      >> >>>
>      >> >>> I am trying to install GBrowse2 and get struck at
>     t/03.render.t.   It
>      >> >>> hangs at roughly around the tests 108-110/138, on installing
>     both via
>      >> >>> the CPAN shell and manually.
>      >> >>> I am installing it on ubuntu.
>      >> >>>
>      >> >>> A similar error was reported in
>      >> >>>
>      >> >>>
>     http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>      >> >>> and Lincoln has suggested to reinstall libgd.  I did try
>     that, but
>      >> >>> didn't succeed. Test hung at same place.
>      >> >>>
>      >> >>> Any pointers will be highly appreciated.
>      >> >>>
>      >> >>> ./Build test
>      >> >>> NOTE: Run ./Build reconfig to change existing configuration.
>      >> >>> t/01yeast.t ............... ok
>      >> >>> t/02.rearchitecture.t ..... ok
>      >> >>> t/03.render.t ............. 106/138 Subroutine
>      >> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT
>     redefined
>      >> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL
>     redefined at
>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR
>     redefined at
>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> t/03.render.t ............. 110/138
>      >> >>>
>      >> >>>
>      >> >>> Many Thanks
>      >> >>> Prem
>      >> >>>
>      >> >>>
>      >> >>>
>     ------------------------------------------------------------------------------
>      >> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>      >> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>      >> >>> lucky parental unit.  See the prize list and enter to win:
>      >> >>> http://p.sf.net/sfu/thinkgeek-promo
>      >> >>> _______________________________________________
>      >> >>> Gmod-gbrowse mailing list
>      >> >>> [hidden email]
>     <mailto:[hidden email]>
>      >> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>      >> >>>
>      >> >>
>      >> >>
>      >> >>
>      >> >> --
>      >> >>
>      >> >>
>     ------------------------------------------------------------------------
>      >> >> Scott Cain, Ph. D.                                   scott at
>     scottcain
>      >> >> dot net
>      >> >> GMOD Coordinator (http://gmod.org/)                    
>     216-392-3087
>      >> >> Ontario Institute for Cancer Research
>      >> >>
>      >> >
>      >>
>      >>
>      >>
>      >> --
>      >>
>     ------------------------------------------------------------------------
>      >> Scott Cain, Ph. D.                                   scott at
>     scottcain
>      >> dot net
>      >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>      >> Ontario Institute for Cancer Research
>      >>
>      >>
>      >>
>     ------------------------------------------------------------------------------
>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>      >> lucky parental unit.  See the prize list and enter to win:
>      >> http://p.sf.net/sfu/thinkgeek-promo
>      >> _______________________________________________
>      >> Gmod-gbrowse mailing list
>      >> [hidden email]
>     <mailto:[hidden email]>
>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>      >>
>      >>
>      >>
>     ------------------------------------------------------------------------------
>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>      >> lucky parental unit.  See the prize list and enter to win:
>      >> http://p.sf.net/sfu/thinkgeek-promo
>      >> _______________________________________________
>      >> Gmod-gbrowse mailing list
>      >> [hidden email]
>     <mailto:[hidden email]>
>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>      >
>      >
>      >
>      > --
>      > Lincoln D. Stein
>      > Director, Informatics and Biocomputing Platform
>      > Ontario Institute for Cancer Research
>      > 101 College St., Suite 800
>      > Toronto, ON, Canada M5G0A3
>      > 416 673-8514
>      > Assistant: Renata Musa <[hidden email]
>     <mailto:[hidden email]>>
>      >
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]
> <mailto:[hidden email]>>
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
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Re: GBrowse2: test hanging at t/03.render.t

Jayaraman, Pushkala
Yes,
We had the same problem that James mentioned. There were different versions of BioPerl installed on the same system and I guess some of the modules use the older BioPerl instead..

Our system admin had to work around the problem. He mentioned that there were hardcoded references to old bioperl-live directories for (.profile, .bashrc)- manually setting PERL5LIB overrides.....
as well as multiple copies of Bio::Graphics in the standard perl @INC tree. He also said that he had to "manually wipe them all out and start fresh"

Dunno if that is the problem..
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: J.M.P. Alves [mailto:[hidden email]]
Sent: Wednesday, June 16, 2010 1:17 PM
To: Lincoln Stein
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t

Hi,

I have Perl 5.10.0, and had the same issue (actually I had about 30 of
those processes there, from all my tries of getting this to work). I
killed all of them, but that did not solve the problem when I tried again.

Prem, I don't remember if you have mentioned this before or not, but
does the computer where you are trying to install GBrowse 2.x already
have GBrowse 1.x? In two cases here (mine and someone else's), it had.
In another computer of mine that had never seen GBrowse or any of its
dependencies, install of 2.08 was quite smooth and everything works.

Therefore I have the hunch that something used by older BioPerl/GBrowse
(some maybe it was installed manually at the time) is conflicting with
the new ones, and it's not getting upgraded when I upgrade all the
prerequisites for GBrowse2.

J

Lincoln Stein wrote:

> The two left-over processes are slave servers. Kill them from the
> command line and try again. This problem may be related to the way that
> signaling handling has changed between perl versions 5.08 and 5.10.
> Would you be adverse to upgrading to perl 5.10 to see if it fixes the
> problem?
>
> Lincoln
>
> On Wed, Jun 16, 2010 at 12:45 PM, Prem Anand <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Thanks to all.
>
>     I tried to run the test individually as Scott suggested.
>
>     perl 03.render.t
>     1..138
>     # Running under perl version 5.008008 for linux
>     # Current time local: Wed Jun 16 17:33:37 2010
>
>     ok 110
>     ok 111
>     ok 112
>     ok 113
>     ok 114
>     ok 115
>     Killed
>
>
>     For some reason, it gets killed.  But I still could see two process
>     running.
>
>     ps -ef | grep perl
>     prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
>     prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
>     prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl
>
>     I didn't get how to restart the master/slave servers. Do you mean
>     restarting the tests/servers?!
>
>     I did try killing the process as Pushkala suggested and started again,
>     but it doesn't help either.
>
>     Thanks for your time
>     Prem
>
>
>
>
>     On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein
>     <[hidden email] <mailto:[hidden email]>> wrote:
>      > There is an intermittent problem when running the regression
>     tests involving
>      > a race condition between the slave (renderfarm) servers and the
>     master
>      > server. This causes the tests to hang. Typically they run
>     correctly if you
>      > just restart them. Sorry I haven't fixed the issue for good (it
>     seems to be
>      > dependent on system load) but the hanging does not seem to affect
>     the server
>      > in operation.
>      > Lincoln
>      >
>      > On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala
>     <[hidden email] <mailto:[hidden email]>>
>      > wrote:
>      >>
>      >> I had a problem with the render.t test.. I simple stopped the
>     process..and
>      >> started from scratch .. it seems to work fine now..
>      >>
>      >> Pushkala Jayaraman
>      >> Programmer/Analyst
>      >> Rat Genome Database
>      >> Human and Molecular Genetics Center
>      >> Medical College of Wisconsin
>      >> Email: [hidden email] <mailto:[hidden email]>
>      >> Work: 414-955-2229
>      >> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>      >>
>      >>
>      >> -----Original Message-----
>      >> From: Scott Cain [mailto:[hidden email]
>     <mailto:[hidden email]>]
>      >> Sent: Wednesday, June 16, 2010 10:51 AM
>      >> To: Prem Anand
>      >> Cc: [hidden email]
>     <mailto:[hidden email]>
>      >> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>      >>
>      >> Hi Prem,
>      >>
>      >> I don't think that bug is related.  That bug was due to a missing
>      >> file, and gave a pretty clear message to that effect.
>      >>
>      >> What happens if you just install it?  If there is still a
>     problem, we
>      >> might at least get more information from a the apache error_log.
>      >>
>      >> One other thing that might give us more information is if
>     execute the
>      >> test directly, like this:
>      >>
>      >>  perl t/03.render.t
>      >>
>      >> Scott
>      >>
>      >>
>      >>
>      >>
>      >> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]
>     <mailto:[hidden email]>> wrote:
>      >> > Thanks for the tip Scott.
>      >> >
>      >> > I updated Bio::Graphics to 2.10 and tried again, but still the
>     same.
>      >> >
>      >> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>      >> > 2.10
>      >> >
>      >> > Could be related to this issue?? not sure!!!
>      >> >
>      >> >
>     http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>     <http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291>
>      >> >
>      >> > Thanks
>      >> > Prem
>      >> >
>      >> >
>      >> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain
>     <[hidden email] <mailto:[hidden email]>> wrote:
>      >> >> Hi Prem,
>      >> >>
>      >> >> In the past when I've had hangs at this point, updating
>     Bio::Graphics
>      >> >> has fixed the problem.  Make sure that the most recent version is
>      >> >> installed.  Also, while I'm not thrilled to be suggesting
>     this, you
>      >> >> could install it anyway and see if it appears to work.
>      >> >>
>      >> >> Scott
>      >> >>
>      >> >>
>      >> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand
>     <[hidden email] <mailto:[hidden email]>>
>      >> >> wrote:
>      >> >>> Hi All
>      >> >>>
>      >> >>> I am trying to install GBrowse2 and get struck at
>     t/03.render.t.   It
>      >> >>> hangs at roughly around the tests 108-110/138, on installing
>     both via
>      >> >>> the CPAN shell and manually.
>      >> >>> I am installing it on ubuntu.
>      >> >>>
>      >> >>> A similar error was reported in
>      >> >>>
>      >> >>>
>     http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>      >> >>> and Lincoln has suggested to reinstall libgd.  I did try
>     that, but
>      >> >>> didn't succeed. Test hung at same place.
>      >> >>>
>      >> >>> Any pointers will be highly appreciated.
>      >> >>>
>      >> >>> ./Build test
>      >> >>> NOTE: Run ./Build reconfig to change existing configuration.
>      >> >>> t/01yeast.t ............... ok
>      >> >>> t/02.rearchitecture.t ..... ok
>      >> >>> t/03.render.t ............. 106/138 Subroutine
>      >> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT
>     redefined
>      >> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL
>     redefined at
>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR
>     redefined at
>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>      >> >>>  at
>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>     <http://berkeleydb.pm>
>      >> >>> line 10
>      >> >>> t/03.render.t ............. 110/138
>      >> >>>
>      >> >>>
>      >> >>> Many Thanks
>      >> >>> Prem
>      >> >>>
>      >> >>>
>      >> >>>
>     ------------------------------------------------------------------------------
>      >> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>      >> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>      >> >>> lucky parental unit.  See the prize list and enter to win:
>      >> >>> http://p.sf.net/sfu/thinkgeek-promo
>      >> >>> _______________________________________________
>      >> >>> Gmod-gbrowse mailing list
>      >> >>> [hidden email]
>     <mailto:[hidden email]>
>      >> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>      >> >>>
>      >> >>
>      >> >>
>      >> >>
>      >> >> --
>      >> >>
>      >> >>
>     ------------------------------------------------------------------------
>      >> >> Scott Cain, Ph. D.                                   scott at
>     scottcain
>      >> >> dot net
>      >> >> GMOD Coordinator (http://gmod.org/)                    
>     216-392-3087
>      >> >> Ontario Institute for Cancer Research
>      >> >>
>      >> >
>      >>
>      >>
>      >>
>      >> --
>      >>
>     ------------------------------------------------------------------------
>      >> Scott Cain, Ph. D.                                   scott at
>     scottcain
>      >> dot net
>      >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>      >> Ontario Institute for Cancer Research
>      >>
>      >>
>      >>
>     ------------------------------------------------------------------------------
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>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>      >> lucky parental unit.  See the prize list and enter to win:
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>      >> _______________________________________________
>      >> Gmod-gbrowse mailing list
>      >> [hidden email]
>     <mailto:[hidden email]>
>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>      >>
>      >>
>      >>
>     ------------------------------------------------------------------------------
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>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>      >> lucky parental unit.  See the prize list and enter to win:
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>      >> _______________________________________________
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>     <mailto:[hidden email]>
>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>      >
>      >
>      >
>      > --
>      > Lincoln D. Stein
>      > Director, Informatics and Biocomputing Platform
>      > Ontario Institute for Cancer Research
>      > 101 College St., Suite 800
>      > Toronto, ON, Canada M5G0A3
>      > 416 673-8514
>      > Assistant: Renata Musa <[hidden email]
>     <mailto:[hidden email]>>
>      >
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]
> <mailto:[hidden email]>>
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
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> lucky parental unit.  See the prize list and enter to win:
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>
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--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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Re: GBrowse2: test hanging at t/03.render.t

Prem Anand
Yes James

I have GBrowse 1.70 already installed. Also I am installing it in a
virtual machine.
As Pushkala suggested, will try to do a clean up and start again.

Thanks
Prem


On Wed, Jun 16, 2010 at 7:33 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Yes,
> We had the same problem that James mentioned. There were different versions of BioPerl installed on the same system and I guess some of the modules use the older BioPerl instead..
>
> Our system admin had to work around the problem. He mentioned that there were hardcoded references to old bioperl-live directories for (.profile, .bashrc)- manually setting PERL5LIB overrides.....
> as well as multiple copies of Bio::Graphics in the standard perl @INC tree. He also said that he had to "manually wipe them all out and start fresh"
>
> Dunno if that is the problem..
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: J.M.P. Alves [mailto:[hidden email]]
> Sent: Wednesday, June 16, 2010 1:17 PM
> To: Lincoln Stein
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>
> Hi,
>
> I have Perl 5.10.0, and had the same issue (actually I had about 30 of
> those processes there, from all my tries of getting this to work). I
> killed all of them, but that did not solve the problem when I tried again.
>
> Prem, I don't remember if you have mentioned this before or not, but
> does the computer where you are trying to install GBrowse 2.x already
> have GBrowse 1.x? In two cases here (mine and someone else's), it had.
> In another computer of mine that had never seen GBrowse or any of its
> dependencies, install of 2.08 was quite smooth and everything works.
>
> Therefore I have the hunch that something used by older BioPerl/GBrowse
> (some maybe it was installed manually at the time) is conflicting with
> the new ones, and it's not getting upgraded when I upgrade all the
> prerequisites for GBrowse2.
>
> J
>
> Lincoln Stein wrote:
>> The two left-over processes are slave servers. Kill them from the
>> command line and try again. This problem may be related to the way that
>> signaling handling has changed between perl versions 5.08 and 5.10.
>> Would you be adverse to upgrading to perl 5.10 to see if it fixes the
>> problem?
>>
>> Lincoln
>>
>> On Wed, Jun 16, 2010 at 12:45 PM, Prem Anand <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Thanks to all.
>>
>>     I tried to run the test individually as Scott suggested.
>>
>>     perl 03.render.t
>>     1..138
>>     # Running under perl version 5.008008 for linux
>>     # Current time local: Wed Jun 16 17:33:37 2010
>>
>>     ok 110
>>     ok 111
>>     ok 112
>>     ok 113
>>     ok 114
>>     ok 115
>>     Killed
>>
>>
>>     For some reason, it gets killed.  But I still could see two process
>>     running.
>>
>>     ps -ef | grep perl
>>     prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
>>     prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
>>     prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl
>>
>>     I didn't get how to restart the master/slave servers. Do you mean
>>     restarting the tests/servers?!
>>
>>     I did try killing the process as Pushkala suggested and started again,
>>     but it doesn't help either.
>>
>>     Thanks for your time
>>     Prem
>>
>>
>>
>>
>>     On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein
>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>      > There is an intermittent problem when running the regression
>>     tests involving
>>      > a race condition between the slave (renderfarm) servers and the
>>     master
>>      > server. This causes the tests to hang. Typically they run
>>     correctly if you
>>      > just restart them. Sorry I haven't fixed the issue for good (it
>>     seems to be
>>      > dependent on system load) but the hanging does not seem to affect
>>     the server
>>      > in operation.
>>      > Lincoln
>>      >
>>      > On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala
>>     <[hidden email] <mailto:[hidden email]>>
>>      > wrote:
>>      >>
>>      >> I had a problem with the render.t test.. I simple stopped the
>>     process..and
>>      >> started from scratch .. it seems to work fine now..
>>      >>
>>      >> Pushkala Jayaraman
>>      >> Programmer/Analyst
>>      >> Rat Genome Database
>>      >> Human and Molecular Genetics Center
>>      >> Medical College of Wisconsin
>>      >> Email: [hidden email] <mailto:[hidden email]>
>>      >> Work: 414-955-2229
>>      >> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>>      >>
>>      >>
>>      >> -----Original Message-----
>>      >> From: Scott Cain [mailto:[hidden email]
>>     <mailto:[hidden email]>]
>>      >> Sent: Wednesday, June 16, 2010 10:51 AM
>>      >> To: Prem Anand
>>      >> Cc: [hidden email]
>>     <mailto:[hidden email]>
>>      >> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>      >>
>>      >> Hi Prem,
>>      >>
>>      >> I don't think that bug is related.  That bug was due to a missing
>>      >> file, and gave a pretty clear message to that effect.
>>      >>
>>      >> What happens if you just install it?  If there is still a
>>     problem, we
>>      >> might at least get more information from a the apache error_log.
>>      >>
>>      >> One other thing that might give us more information is if
>>     execute the
>>      >> test directly, like this:
>>      >>
>>      >>  perl t/03.render.t
>>      >>
>>      >> Scott
>>      >>
>>      >>
>>      >>
>>      >>
>>      >> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]
>>     <mailto:[hidden email]>> wrote:
>>      >> > Thanks for the tip Scott.
>>      >> >
>>      >> > I updated Bio::Graphics to 2.10 and tried again, but still the
>>     same.
>>      >> >
>>      >> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>>      >> > 2.10
>>      >> >
>>      >> > Could be related to this issue?? not sure!!!
>>      >> >
>>      >> >
>>     http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>>     <http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291>
>>      >> >
>>      >> > Thanks
>>      >> > Prem
>>      >> >
>>      >> >
>>      >> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain
>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>      >> >> Hi Prem,
>>      >> >>
>>      >> >> In the past when I've had hangs at this point, updating
>>     Bio::Graphics
>>      >> >> has fixed the problem.  Make sure that the most recent version is
>>      >> >> installed.  Also, while I'm not thrilled to be suggesting
>>     this, you
>>      >> >> could install it anyway and see if it appears to work.
>>      >> >>
>>      >> >> Scott
>>      >> >>
>>      >> >>
>>      >> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand
>>     <[hidden email] <mailto:[hidden email]>>
>>      >> >> wrote:
>>      >> >>> Hi All
>>      >> >>>
>>      >> >>> I am trying to install GBrowse2 and get struck at
>>     t/03.render.t.   It
>>      >> >>> hangs at roughly around the tests 108-110/138, on installing
>>     both via
>>      >> >>> the CPAN shell and manually.
>>      >> >>> I am installing it on ubuntu.
>>      >> >>>
>>      >> >>> A similar error was reported in
>>      >> >>>
>>      >> >>>
>>     http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>      >> >>> and Lincoln has suggested to reinstall libgd.  I did try
>>     that, but
>>      >> >>> didn't succeed. Test hung at same place.
>>      >> >>>
>>      >> >>> Any pointers will be highly appreciated.
>>      >> >>>
>>      >> >>> ./Build test
>>      >> >>> NOTE: Run ./Build reconfig to change existing configuration.
>>      >> >>> t/01yeast.t ............... ok
>>      >> >>> t/02.rearchitecture.t ..... ok
>>      >> >>> t/03.render.t ............. 106/138 Subroutine
>>      >> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>      >> >>>  at
>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>     <http://berkeleydb.pm>
>>      >> >>> line 10
>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT
>>     redefined
>>      >> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>      >> >>>  at
>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>     <http://berkeleydb.pm>
>>      >> >>> line 10
>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL
>>     redefined at
>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>      >> >>>  at
>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>     <http://berkeleydb.pm>
>>      >> >>> line 10
>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>      >> >>>  at
>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>     <http://berkeleydb.pm>
>>      >> >>> line 10
>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>      >> >>>  at
>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>     <http://berkeleydb.pm>
>>      >> >>> line 10
>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR
>>     redefined at
>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>      >> >>>  at
>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>     <http://berkeleydb.pm>
>>      >> >>> line 10
>>      >> >>> t/03.render.t ............. 110/138
>>      >> >>>
>>      >> >>>
>>      >> >>> Many Thanks
>>      >> >>> Prem
>>      >> >>>
>>      >> >>>
>>      >> >>>
>>     ------------------------------------------------------------------------------
>>      >> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>      >> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>      >> >>> lucky parental unit.  See the prize list and enter to win:
>>      >> >>> http://p.sf.net/sfu/thinkgeek-promo
>>      >> >>> _______________________________________________
>>      >> >>> Gmod-gbrowse mailing list
>>      >> >>> [hidden email]
>>     <mailto:[hidden email]>
>>      >> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>      >> >>>
>>      >> >>
>>      >> >>
>>      >> >>
>>      >> >> --
>>      >> >>
>>      >> >>
>>     ------------------------------------------------------------------------
>>      >> >> Scott Cain, Ph. D.                                   scott at
>>     scottcain
>>      >> >> dot net
>>      >> >> GMOD Coordinator (http://gmod.org/)
>>     216-392-3087
>>      >> >> Ontario Institute for Cancer Research
>>      >> >>
>>      >> >
>>      >>
>>      >>
>>      >>
>>      >> --
>>      >>
>>     ------------------------------------------------------------------------
>>      >> Scott Cain, Ph. D.                                   scott at
>>     scottcain
>>      >> dot net
>>      >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>      >> Ontario Institute for Cancer Research
>>      >>
>>      >>
>>      >>
>>     ------------------------------------------------------------------------------
>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>      >> lucky parental unit.  See the prize list and enter to win:
>>      >> http://p.sf.net/sfu/thinkgeek-promo
>>      >> _______________________________________________
>>      >> Gmod-gbrowse mailing list
>>      >> [hidden email]
>>     <mailto:[hidden email]>
>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>      >>
>>      >>
>>      >>
>>     ------------------------------------------------------------------------------
>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>      >> lucky parental unit.  See the prize list and enter to win:
>>      >> http://p.sf.net/sfu/thinkgeek-promo
>>      >> _______________________________________________
>>      >> Gmod-gbrowse mailing list
>>      >> [hidden email]
>>     <mailto:[hidden email]>
>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>      >
>>      >
>>      >
>>      > --
>>      > Lincoln D. Stein
>>      > Director, Informatics and Biocomputing Platform
>>      > Ontario Institute for Cancer Research
>>      > 101 College St., Suite 800
>>      > Toronto, ON, Canada M5G0A3
>>      > 416 673-8514
>>      > Assistant: Renata Musa <[hidden email]
>>     <mailto:[hidden email]>>
>>      >
>>
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]
>> <mailto:[hidden email]>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> --
> -------------------------------
> João Marcelo Pereira Alves (J)
> Post-doctoral fellow
> MCV / VCU - Richmond, VA
> http://bioinfo.lpb.mic.vcu.edu
> f. 1-804-828-3897
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> ------------------------------------------------------------------------------
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> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
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>

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Re: GBrowse2: test hanging at t/03.render.t

Prem Anand
Managed to install GBrowse2 :)
The issue was, I had multiple versions of Bio::Graphics.   Did some
cleanup and started fresh. It worked smooth.

Thanks a lot for all the tips and your time.

Cheers
Prem

=====================
Achuthan Premanand
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
University of Cambridge
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
[hidden email]



On Wed, Jun 16, 2010 at 9:39 PM, Prem Anand <[hidden email]> wrote:

> Yes James
>
> I have GBrowse 1.70 already installed. Also I am installing it in a
> virtual machine.
> As Pushkala suggested, will try to do a clean up and start again.
>
> Thanks
> Prem
>
>
> On Wed, Jun 16, 2010 at 7:33 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Yes,
>> We had the same problem that James mentioned. There were different versions of BioPerl installed on the same system and I guess some of the modules use the older BioPerl instead..
>>
>> Our system admin had to work around the problem. He mentioned that there were hardcoded references to old bioperl-live directories for (.profile, .bashrc)- manually setting PERL5LIB overrides.....
>> as well as multiple copies of Bio::Graphics in the standard perl @INC tree. He also said that he had to "manually wipe them all out and start fresh"
>>
>> Dunno if that is the problem..
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: J.M.P. Alves [mailto:[hidden email]]
>> Sent: Wednesday, June 16, 2010 1:17 PM
>> To: Lincoln Stein
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>
>> Hi,
>>
>> I have Perl 5.10.0, and had the same issue (actually I had about 30 of
>> those processes there, from all my tries of getting this to work). I
>> killed all of them, but that did not solve the problem when I tried again.
>>
>> Prem, I don't remember if you have mentioned this before or not, but
>> does the computer where you are trying to install GBrowse 2.x already
>> have GBrowse 1.x? In two cases here (mine and someone else's), it had.
>> In another computer of mine that had never seen GBrowse or any of its
>> dependencies, install of 2.08 was quite smooth and everything works.
>>
>> Therefore I have the hunch that something used by older BioPerl/GBrowse
>> (some maybe it was installed manually at the time) is conflicting with
>> the new ones, and it's not getting upgraded when I upgrade all the
>> prerequisites for GBrowse2.
>>
>> J
>>
>> Lincoln Stein wrote:
>>> The two left-over processes are slave servers. Kill them from the
>>> command line and try again. This problem may be related to the way that
>>> signaling handling has changed between perl versions 5.08 and 5.10.
>>> Would you be adverse to upgrading to perl 5.10 to see if it fixes the
>>> problem?
>>>
>>> Lincoln
>>>
>>> On Wed, Jun 16, 2010 at 12:45 PM, Prem Anand <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>>     Thanks to all.
>>>
>>>     I tried to run the test individually as Scott suggested.
>>>
>>>     perl 03.render.t
>>>     1..138
>>>     # Running under perl version 5.008008 for linux
>>>     # Current time local: Wed Jun 16 17:33:37 2010
>>>
>>>     ok 110
>>>     ok 111
>>>     ok 112
>>>     ok 113
>>>     ok 114
>>>     ok 115
>>>     Killed
>>>
>>>
>>>     For some reason, it gets killed.  But I still could see two process
>>>     running.
>>>
>>>     ps -ef | grep perl
>>>     prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
>>>     prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
>>>     prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl
>>>
>>>     I didn't get how to restart the master/slave servers. Do you mean
>>>     restarting the tests/servers?!
>>>
>>>     I did try killing the process as Pushkala suggested and started again,
>>>     but it doesn't help either.
>>>
>>>     Thanks for your time
>>>     Prem
>>>
>>>
>>>
>>>
>>>     On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein
>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>      > There is an intermittent problem when running the regression
>>>     tests involving
>>>      > a race condition between the slave (renderfarm) servers and the
>>>     master
>>>      > server. This causes the tests to hang. Typically they run
>>>     correctly if you
>>>      > just restart them. Sorry I haven't fixed the issue for good (it
>>>     seems to be
>>>      > dependent on system load) but the hanging does not seem to affect
>>>     the server
>>>      > in operation.
>>>      > Lincoln
>>>      >
>>>      > On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala
>>>     <[hidden email] <mailto:[hidden email]>>
>>>      > wrote:
>>>      >>
>>>      >> I had a problem with the render.t test.. I simple stopped the
>>>     process..and
>>>      >> started from scratch .. it seems to work fine now..
>>>      >>
>>>      >> Pushkala Jayaraman
>>>      >> Programmer/Analyst
>>>      >> Rat Genome Database
>>>      >> Human and Molecular Genetics Center
>>>      >> Medical College of Wisconsin
>>>      >> Email: [hidden email] <mailto:[hidden email]>
>>>      >> Work: 414-955-2229
>>>      >> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>>>      >>
>>>      >>
>>>      >> -----Original Message-----
>>>      >> From: Scott Cain [mailto:[hidden email]
>>>     <mailto:[hidden email]>]
>>>      >> Sent: Wednesday, June 16, 2010 10:51 AM
>>>      >> To: Prem Anand
>>>      >> Cc: [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>>      >>
>>>      >> Hi Prem,
>>>      >>
>>>      >> I don't think that bug is related.  That bug was due to a missing
>>>      >> file, and gave a pretty clear message to that effect.
>>>      >>
>>>      >> What happens if you just install it?  If there is still a
>>>     problem, we
>>>      >> might at least get more information from a the apache error_log.
>>>      >>
>>>      >> One other thing that might give us more information is if
>>>     execute the
>>>      >> test directly, like this:
>>>      >>
>>>      >>  perl t/03.render.t
>>>      >>
>>>      >> Scott
>>>      >>
>>>      >>
>>>      >>
>>>      >>
>>>      >> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]
>>>     <mailto:[hidden email]>> wrote:
>>>      >> > Thanks for the tip Scott.
>>>      >> >
>>>      >> > I updated Bio::Graphics to 2.10 and tried again, but still the
>>>     same.
>>>      >> >
>>>      >> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>>>      >> > 2.10
>>>      >> >
>>>      >> > Could be related to this issue?? not sure!!!
>>>      >> >
>>>      >> >
>>>     http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>>>     <http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291>
>>>      >> >
>>>      >> > Thanks
>>>      >> > Prem
>>>      >> >
>>>      >> >
>>>      >> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain
>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>      >> >> Hi Prem,
>>>      >> >>
>>>      >> >> In the past when I've had hangs at this point, updating
>>>     Bio::Graphics
>>>      >> >> has fixed the problem.  Make sure that the most recent version is
>>>      >> >> installed.  Also, while I'm not thrilled to be suggesting
>>>     this, you
>>>      >> >> could install it anyway and see if it appears to work.
>>>      >> >>
>>>      >> >> Scott
>>>      >> >>
>>>      >> >>
>>>      >> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand
>>>     <[hidden email] <mailto:[hidden email]>>
>>>      >> >> wrote:
>>>      >> >>> Hi All
>>>      >> >>>
>>>      >> >>> I am trying to install GBrowse2 and get struck at
>>>     t/03.render.t.   It
>>>      >> >>> hangs at roughly around the tests 108-110/138, on installing
>>>     both via
>>>      >> >>> the CPAN shell and manually.
>>>      >> >>> I am installing it on ubuntu.
>>>      >> >>>
>>>      >> >>> A similar error was reported in
>>>      >> >>>
>>>      >> >>>
>>>     http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>>      >> >>> and Lincoln has suggested to reinstall libgd.  I did try
>>>     that, but
>>>      >> >>> didn't succeed. Test hung at same place.
>>>      >> >>>
>>>      >> >>> Any pointers will be highly appreciated.
>>>      >> >>>
>>>      >> >>> ./Build test
>>>      >> >>> NOTE: Run ./Build reconfig to change existing configuration.
>>>      >> >>> t/01yeast.t ............... ok
>>>      >> >>> t/02.rearchitecture.t ..... ok
>>>      >> >>> t/03.render.t ............. 106/138 Subroutine
>>>      >> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT
>>>     redefined
>>>      >> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL
>>>     redefined at
>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR
>>>     redefined at
>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> t/03.render.t ............. 110/138
>>>      >> >>>
>>>      >> >>>
>>>      >> >>> Many Thanks
>>>      >> >>> Prem
>>>      >> >>>
>>>      >> >>>
>>>      >> >>>
>>>     ------------------------------------------------------------------------------
>>>      >> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>      >> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>      >> >>> lucky parental unit.  See the prize list and enter to win:
>>>      >> >>> http://p.sf.net/sfu/thinkgeek-promo
>>>      >> >>> _______________________________________________
>>>      >> >>> Gmod-gbrowse mailing list
>>>      >> >>> [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>      >> >>>
>>>      >> >>
>>>      >> >>
>>>      >> >>
>>>      >> >> --
>>>      >> >>
>>>      >> >>
>>>     ------------------------------------------------------------------------
>>>      >> >> Scott Cain, Ph. D.                                   scott at
>>>     scottcain
>>>      >> >> dot net
>>>      >> >> GMOD Coordinator (http://gmod.org/)
>>>     216-392-3087
>>>      >> >> Ontario Institute for Cancer Research
>>>      >> >>
>>>      >> >
>>>      >>
>>>      >>
>>>      >>
>>>      >> --
>>>      >>
>>>     ------------------------------------------------------------------------
>>>      >> Scott Cain, Ph. D.                                   scott at
>>>     scottcain
>>>      >> dot net
>>>      >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>      >> Ontario Institute for Cancer Research
>>>      >>
>>>      >>
>>>      >>
>>>     ------------------------------------------------------------------------------
>>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>      >> lucky parental unit.  See the prize list and enter to win:
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>>>      >> _______________________________________________
>>>      >> Gmod-gbrowse mailing list
>>>      >> [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>      >>
>>>      >>
>>>      >>
>>>     ------------------------------------------------------------------------------
>>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>      >> lucky parental unit.  See the prize list and enter to win:
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>>>      >> _______________________________________________
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>>>      >> [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>      >
>>>      >
>>>      >
>>>      > --
>>>      > Lincoln D. Stein
>>>      > Director, Informatics and Biocomputing Platform
>>>      > Ontario Institute for Cancer Research
>>>      > 101 College St., Suite 800
>>>      > Toronto, ON, Canada M5G0A3
>>>      > 416 673-8514
>>>      > Assistant: Renata Musa <[hidden email]
>>>     <mailto:[hidden email]>>
>>>      >
>>>
>>>
>>>
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]
>>> <mailto:[hidden email]>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
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>> lucky parental unit.  See the prize list and enter to win:
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>

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Re: GBrowse2: test hanging at t/03.render.t

Lincoln Stein
I'm glad it got sorted out.

Lincoln

On Thu, Jun 17, 2010 at 1:13 PM, Prem Anand <[hidden email]> wrote:
Managed to install GBrowse2 :)
The issue was, I had multiple versions of Bio::Graphics.   Did some
cleanup and started fresh. It worked smooth.

Thanks a lot for all the tips and your time.

Cheers
Prem

=====================
Achuthan Premanand
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
Cambridge Institute for Medical Research (CIMR)
University of Cambridge
Wellcome Trust/MRC Building
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
[hidden email]



On Wed, Jun 16, 2010 at 9:39 PM, Prem Anand <[hidden email]> wrote:
> Yes James
>
> I have GBrowse 1.70 already installed. Also I am installing it in a
> virtual machine.
> As Pushkala suggested, will try to do a clean up and start again.
>
> Thanks
> Prem
>
>
> On Wed, Jun 16, 2010 at 7:33 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Yes,
>> We had the same problem that James mentioned. There were different versions of BioPerl installed on the same system and I guess some of the modules use the older BioPerl instead..
>>
>> Our system admin had to work around the problem. He mentioned that there were hardcoded references to old bioperl-live directories for (.profile, .bashrc)- manually setting PERL5LIB overrides.....
>> as well as multiple copies of Bio::Graphics in the standard perl @INC tree. He also said that he had to "manually wipe them all out and start fresh"
>>
>> Dunno if that is the problem..
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: J.M.P. Alves [mailto:[hidden email]]
>> Sent: Wednesday, June 16, 2010 1:17 PM
>> To: Lincoln Stein
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>
>> Hi,
>>
>> I have Perl 5.10.0, and had the same issue (actually I had about 30 of
>> those processes there, from all my tries of getting this to work). I
>> killed all of them, but that did not solve the problem when I tried again.
>>
>> Prem, I don't remember if you have mentioned this before or not, but
>> does the computer where you are trying to install GBrowse 2.x already
>> have GBrowse 1.x? In two cases here (mine and someone else's), it had.
>> In another computer of mine that had never seen GBrowse or any of its
>> dependencies, install of 2.08 was quite smooth and everything works.
>>
>> Therefore I have the hunch that something used by older BioPerl/GBrowse
>> (some maybe it was installed manually at the time) is conflicting with
>> the new ones, and it's not getting upgraded when I upgrade all the
>> prerequisites for GBrowse2.
>>
>> J
>>
>> Lincoln Stein wrote:
>>> The two left-over processes are slave servers. Kill them from the
>>> command line and try again. This problem may be related to the way that
>>> signaling handling has changed between perl versions 5.08 and 5.10.
>>> Would you be adverse to upgrading to perl 5.10 to see if it fixes the
>>> problem?
>>>
>>> Lincoln
>>>
>>> On Wed, Jun 16, 2010 at 12:45 PM, Prem Anand <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>>     Thanks to all.
>>>
>>>     I tried to run the test individually as Scott suggested.
>>>
>>>     perl 03.render.t
>>>     1..138
>>>     # Running under perl version 5.008008 for linux
>>>     # Current time local: Wed Jun 16 17:33:37 2010
>>>
>>>     ok 110
>>>     ok 111
>>>     ok 112
>>>     ok 113
>>>     ok 114
>>>     ok 115
>>>     Killed
>>>
>>>
>>>     For some reason, it gets killed.  But I still could see two process
>>>     running.
>>>
>>>     ps -ef | grep perl
>>>     prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
>>>     prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
>>>     prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl
>>>
>>>     I didn't get how to restart the master/slave servers. Do you mean
>>>     restarting the tests/servers?!
>>>
>>>     I did try killing the process as Pushkala suggested and started again,
>>>     but it doesn't help either.
>>>
>>>     Thanks for your time
>>>     Prem
>>>
>>>
>>>
>>>
>>>     On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein
>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>      > There is an intermittent problem when running the regression
>>>     tests involving
>>>      > a race condition between the slave (renderfarm) servers and the
>>>     master
>>>      > server. This causes the tests to hang. Typically they run
>>>     correctly if you
>>>      > just restart them. Sorry I haven't fixed the issue for good (it
>>>     seems to be
>>>      > dependent on system load) but the hanging does not seem to affect
>>>     the server
>>>      > in operation.
>>>      > Lincoln
>>>      >
>>>      > On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala
>>>     <[hidden email] <mailto:[hidden email]>>
>>>      > wrote:
>>>      >>
>>>      >> I had a problem with the render.t test.. I simple stopped the
>>>     process..and
>>>      >> started from scratch .. it seems to work fine now..
>>>      >>
>>>      >> Pushkala Jayaraman
>>>      >> Programmer/Analyst
>>>      >> Rat Genome Database
>>>      >> Human and Molecular Genetics Center
>>>      >> Medical College of Wisconsin
>>>      >> Email: [hidden email] <mailto:[hidden email]>
>>>      >> Work: 414-955-2229
>>>      >> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>>>      >>
>>>      >>
>>>      >> -----Original Message-----
>>>      >> From: Scott Cain [mailto:[hidden email]
>>>     <mailto:[hidden email]>]
>>>      >> Sent: Wednesday, June 16, 2010 10:51 AM
>>>      >> To: Prem Anand
>>>      >> Cc: [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>>      >>
>>>      >> Hi Prem,
>>>      >>
>>>      >> I don't think that bug is related.  That bug was due to a missing
>>>      >> file, and gave a pretty clear message to that effect.
>>>      >>
>>>      >> What happens if you just install it?  If there is still a
>>>     problem, we
>>>      >> might at least get more information from a the apache error_log.
>>>      >>
>>>      >> One other thing that might give us more information is if
>>>     execute the
>>>      >> test directly, like this:
>>>      >>
>>>      >>  perl t/03.render.t
>>>      >>
>>>      >> Scott
>>>      >>
>>>      >>
>>>      >>
>>>      >>
>>>      >> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]
>>>     <mailto:[hidden email]>> wrote:
>>>      >> > Thanks for the tip Scott.
>>>      >> >
>>>      >> > I updated Bio::Graphics to 2.10 and tried again, but still the
>>>     same.
>>>      >> >
>>>      >> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>>>      >> > 2.10
>>>      >> >
>>>      >> > Could be related to this issue?? not sure!!!
>>>      >> >
>>>      >> >
>>>     http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>>>     <http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291>
>>>      >> >
>>>      >> > Thanks
>>>      >> > Prem
>>>      >> >
>>>      >> >
>>>      >> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain
>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>      >> >> Hi Prem,
>>>      >> >>
>>>      >> >> In the past when I've had hangs at this point, updating
>>>     Bio::Graphics
>>>      >> >> has fixed the problem.  Make sure that the most recent version is
>>>      >> >> installed.  Also, while I'm not thrilled to be suggesting
>>>     this, you
>>>      >> >> could install it anyway and see if it appears to work.
>>>      >> >>
>>>      >> >> Scott
>>>      >> >>
>>>      >> >>
>>>      >> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand
>>>     <[hidden email] <mailto:[hidden email]>>
>>>      >> >> wrote:
>>>      >> >>> Hi All
>>>      >> >>>
>>>      >> >>> I am trying to install GBrowse2 and get struck at
>>>     t/03.render.t.   It
>>>      >> >>> hangs at roughly around the tests 108-110/138, on installing
>>>     both via
>>>      >> >>> the CPAN shell and manually.
>>>      >> >>> I am installing it on ubuntu.
>>>      >> >>>
>>>      >> >>> A similar error was reported in
>>>      >> >>>
>>>      >> >>>
>>>     http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>>      >> >>> and Lincoln has suggested to reinstall libgd.  I did try
>>>     that, but
>>>      >> >>> didn't succeed. Test hung at same place.
>>>      >> >>>
>>>      >> >>> Any pointers will be highly appreciated.
>>>      >> >>>
>>>      >> >>> ./Build test
>>>      >> >>> NOTE: Run ./Build reconfig to change existing configuration.
>>>      >> >>> t/01yeast.t ............... ok
>>>      >> >>> t/02.rearchitecture.t ..... ok
>>>      >> >>> t/03.render.t ............. 106/138 Subroutine
>>>      >> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT
>>>     redefined
>>>      >> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL
>>>     redefined at
>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR
>>>     redefined at
>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>      >> >>>  at
>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>     <http://berkeleydb.pm>
>>>      >> >>> line 10
>>>      >> >>> t/03.render.t ............. 110/138
>>>      >> >>>
>>>      >> >>>
>>>      >> >>> Many Thanks
>>>      >> >>> Prem
>>>      >> >>>
>>>      >> >>>
>>>      >> >>>
>>>     ------------------------------------------------------------------------------
>>>      >> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>      >> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>      >> >>> lucky parental unit.  See the prize list and enter to win:
>>>      >> >>> http://p.sf.net/sfu/thinkgeek-promo
>>>      >> >>> _______________________________________________
>>>      >> >>> Gmod-gbrowse mailing list
>>>      >> >>> [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>      >> >>>
>>>      >> >>
>>>      >> >>
>>>      >> >>
>>>      >> >> --
>>>      >> >>
>>>      >> >>
>>>     ------------------------------------------------------------------------
>>>      >> >> Scott Cain, Ph. D.                                   scott at
>>>     scottcain
>>>      >> >> dot net
>>>      >> >> GMOD Coordinator (http://gmod.org/)
>>>     216-392-3087
>>>      >> >> Ontario Institute for Cancer Research
>>>      >> >>
>>>      >> >
>>>      >>
>>>      >>
>>>      >>
>>>      >> --
>>>      >>
>>>     ------------------------------------------------------------------------
>>>      >> Scott Cain, Ph. D.                                   scott at
>>>     scottcain
>>>      >> dot net
>>>      >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>      >> Ontario Institute for Cancer Research
>>>      >>
>>>      >>
>>>      >>
>>>     ------------------------------------------------------------------------------
>>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>      >> lucky parental unit.  See the prize list and enter to win:
>>>      >> http://p.sf.net/sfu/thinkgeek-promo
>>>      >> _______________________________________________
>>>      >> Gmod-gbrowse mailing list
>>>      >> [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>      >>
>>>      >>
>>>      >>
>>>     ------------------------------------------------------------------------------
>>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>      >> lucky parental unit.  See the prize list and enter to win:
>>>      >> http://p.sf.net/sfu/thinkgeek-promo
>>>      >> _______________________________________________
>>>      >> Gmod-gbrowse mailing list
>>>      >> [hidden email]
>>>     <mailto:[hidden email]>
>>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>      >
>>>      >
>>>      >
>>>      > --
>>>      > Lincoln D. Stein
>>>      > Director, Informatics and Biocomputing Platform
>>>      > Ontario Institute for Cancer Research
>>>      > 101 College St., Suite 800
>>>      > Toronto, ON, Canada M5G0A3
>>>      > 416 673-8514
>>>      > Assistant: Renata Musa <[hidden email]
>>>     <mailto:[hidden email]>>
>>>      >
>>>
>>>
>>>
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]
>>> <mailto:[hidden email]>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse2: test hanging at t/03.render.t

J.M.P. Alves
In reply to this post by Prem Anand
Thanks a lot for the pointer, Prem!

That was my problem too: too many Bio::Graphics versions (and maybe
BioPerl versions too) all over the place (old computer). After a lot of
tinkering and reinstalling it is working here too.

For the record, after I got GBrowse2 to work, GBrowse 1.7 still works on
the same machine.

Thanks
J

Prem Anand wrote:

> Managed to install GBrowse2 :)
> The issue was, I had multiple versions of Bio::Graphics.   Did some
> cleanup and started fresh. It worked smooth.
>
> Thanks a lot for all the tips and your time.
>
> Cheers
> Prem
>
> =====================
> Achuthan Premanand
> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
> Cambridge Institute for Medical Research (CIMR)
> University of Cambridge
> Wellcome Trust/MRC Building
> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
> [hidden email]
>
>
>
> On Wed, Jun 16, 2010 at 9:39 PM, Prem Anand <[hidden email]> wrote:
>> Yes James
>>
>> I have GBrowse 1.70 already installed. Also I am installing it in a
>> virtual machine.
>> As Pushkala suggested, will try to do a clean up and start again.
>>
>> Thanks
>> Prem
>>
>>
>> On Wed, Jun 16, 2010 at 7:33 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>>> Yes,
>>> We had the same problem that James mentioned. There were different versions of BioPerl installed on the same system and I guess some of the modules use the older BioPerl instead..
>>>
>>> Our system admin had to work around the problem. He mentioned that there were hardcoded references to old bioperl-live directories for (.profile, .bashrc)- manually setting PERL5LIB overrides.....
>>> as well as multiple copies of Bio::Graphics in the standard perl @INC tree. He also said that he had to "manually wipe them all out and start fresh"
>>>
>>> Dunno if that is the problem..
>>> Pushkala Jayaraman
>>> Programmer/Analyst
>>> Rat Genome Database
>>> Human and Molecular Genetics Center
>>> Medical College of Wisconsin
>>> Email: [hidden email]
>>> Work: 414-955-2229
>>> www.rgd.mcw.edu
>>>
>>>
>>> -----Original Message-----
>>> From: J.M.P. Alves [mailto:[hidden email]]
>>> Sent: Wednesday, June 16, 2010 1:17 PM
>>> To: Lincoln Stein
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>>
>>> Hi,
>>>
>>> I have Perl 5.10.0, and had the same issue (actually I had about 30 of
>>> those processes there, from all my tries of getting this to work). I
>>> killed all of them, but that did not solve the problem when I tried again.
>>>
>>> Prem, I don't remember if you have mentioned this before or not, but
>>> does the computer where you are trying to install GBrowse 2.x already
>>> have GBrowse 1.x? In two cases here (mine and someone else's), it had.
>>> In another computer of mine that had never seen GBrowse or any of its
>>> dependencies, install of 2.08 was quite smooth and everything works.
>>>
>>> Therefore I have the hunch that something used by older BioPerl/GBrowse
>>> (some maybe it was installed manually at the time) is conflicting with
>>> the new ones, and it's not getting upgraded when I upgrade all the
>>> prerequisites for GBrowse2.
>>>
>>> J
>>>
>>> Lincoln Stein wrote:
>>>> The two left-over processes are slave servers. Kill them from the
>>>> command line and try again. This problem may be related to the way that
>>>> signaling handling has changed between perl versions 5.08 and 5.10.
>>>> Would you be adverse to upgrading to perl 5.10 to see if it fixes the
>>>> problem?
>>>>
>>>> Lincoln
>>>>
>>>> On Wed, Jun 16, 2010 at 12:45 PM, Prem Anand <[hidden email]
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>>     Thanks to all.
>>>>
>>>>     I tried to run the test individually as Scott suggested.
>>>>
>>>>     perl 03.render.t
>>>>     1..138
>>>>     # Running under perl version 5.008008 for linux
>>>>     # Current time local: Wed Jun 16 17:33:37 2010
>>>>
>>>>     ok 110
>>>>     ok 111
>>>>     ok 112
>>>>     ok 113
>>>>     ok 114
>>>>     ok 115
>>>>     Killed
>>>>
>>>>
>>>>     For some reason, it gets killed.  But I still could see two process
>>>>     running.
>>>>
>>>>     ps -ef | grep perl
>>>>     prem     18612     1  0 17:33 ?        00:00:00 perl 03.render.t
>>>>     prem     18613     1  0 17:33 ?        00:00:00 perl 03.render.t
>>>>     prem     18770 18565  0 17:37 pts/10   00:00:00 grep perl
>>>>
>>>>     I didn't get how to restart the master/slave servers. Do you mean
>>>>     restarting the tests/servers?!
>>>>
>>>>     I did try killing the process as Pushkala suggested and started again,
>>>>     but it doesn't help either.
>>>>
>>>>     Thanks for your time
>>>>     Prem
>>>>
>>>>
>>>>
>>>>
>>>>     On Wed, Jun 16, 2010 at 4:56 PM, Lincoln Stein
>>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>>      > There is an intermittent problem when running the regression
>>>>     tests involving
>>>>      > a race condition between the slave (renderfarm) servers and the
>>>>     master
>>>>      > server. This causes the tests to hang. Typically they run
>>>>     correctly if you
>>>>      > just restart them. Sorry I haven't fixed the issue for good (it
>>>>     seems to be
>>>>      > dependent on system load) but the hanging does not seem to affect
>>>>     the server
>>>>      > in operation.
>>>>      > Lincoln
>>>>      >
>>>>      > On Wed, Jun 16, 2010 at 11:52 AM, Jayaraman, Pushkala
>>>>     <[hidden email] <mailto:[hidden email]>>
>>>>      > wrote:
>>>>      >>
>>>>      >> I had a problem with the render.t test.. I simple stopped the
>>>>     process..and
>>>>      >> started from scratch .. it seems to work fine now..
>>>>      >>
>>>>      >> Pushkala Jayaraman
>>>>      >> Programmer/Analyst
>>>>      >> Rat Genome Database
>>>>      >> Human and Molecular Genetics Center
>>>>      >> Medical College of Wisconsin
>>>>      >> Email: [hidden email] <mailto:[hidden email]>
>>>>      >> Work: 414-955-2229
>>>>      >> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>>>>      >>
>>>>      >>
>>>>      >> -----Original Message-----
>>>>      >> From: Scott Cain [mailto:[hidden email]
>>>>     <mailto:[hidden email]>]
>>>>      >> Sent: Wednesday, June 16, 2010 10:51 AM
>>>>      >> To: Prem Anand
>>>>      >> Cc: [hidden email]
>>>>     <mailto:[hidden email]>
>>>>      >> Subject: Re: [Gmod-gbrowse] GBrowse2: test hanging at t/03.render.t
>>>>      >>
>>>>      >> Hi Prem,
>>>>      >>
>>>>      >> I don't think that bug is related.  That bug was due to a missing
>>>>      >> file, and gave a pretty clear message to that effect.
>>>>      >>
>>>>      >> What happens if you just install it?  If there is still a
>>>>     problem, we
>>>>      >> might at least get more information from a the apache error_log.
>>>>      >>
>>>>      >> One other thing that might give us more information is if
>>>>     execute the
>>>>      >> test directly, like this:
>>>>      >>
>>>>      >>  perl t/03.render.t
>>>>      >>
>>>>      >> Scott
>>>>      >>
>>>>      >>
>>>>      >>
>>>>      >>
>>>>      >> On Wed, Jun 16, 2010 at 11:17 AM, Prem Anand <[hidden email]
>>>>     <mailto:[hidden email]>> wrote:
>>>>      >> > Thanks for the tip Scott.
>>>>      >> >
>>>>      >> > I updated Bio::Graphics to 2.10 and tried again, but still the
>>>>     same.
>>>>      >> >
>>>>      >> > perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '
>>>>      >> > 2.10
>>>>      >> >
>>>>      >> > Could be related to this issue?? not sure!!!
>>>>      >> >
>>>>      >> >
>>>>     http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291
>>>>     <http://sourceforge.net/tracker/index.php?func=detail&aid=2432707&group_id=27707&atid=391291>
>>>>      >> >
>>>>      >> > Thanks
>>>>      >> > Prem
>>>>      >> >
>>>>      >> >
>>>>      >> > On Wed, Jun 16, 2010 at 3:48 PM, Scott Cain
>>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>>      >> >> Hi Prem,
>>>>      >> >>
>>>>      >> >> In the past when I've had hangs at this point, updating
>>>>     Bio::Graphics
>>>>      >> >> has fixed the problem.  Make sure that the most recent version is
>>>>      >> >> installed.  Also, while I'm not thrilled to be suggesting
>>>>     this, you
>>>>      >> >> could install it anyway and see if it appears to work.
>>>>      >> >>
>>>>      >> >> Scott
>>>>      >> >>
>>>>      >> >>
>>>>      >> >> On Wed, Jun 16, 2010 at 10:38 AM, Prem Anand
>>>>     <[hidden email] <mailto:[hidden email]>>
>>>>      >> >> wrote:
>>>>      >> >>> Hi All
>>>>      >> >>>
>>>>      >> >>> I am trying to install GBrowse2 and get struck at
>>>>     t/03.render.t.   It
>>>>      >> >>> hangs at roughly around the tests 108-110/138, on installing
>>>>     both via
>>>>      >> >>> the CPAN shell and manually.
>>>>      >> >>> I am installing it on ubuntu.
>>>>      >> >>>
>>>>      >> >>> A similar error was reported in
>>>>      >> >>>
>>>>      >> >>>
>>>>     http://generic-model-organism-system-database.450254.n5.nabble.com/Build-test-fails-for-gbrowse2-td451064.html#a451064
>>>>      >> >>> and Lincoln has suggested to reinstall libgd.  I did try
>>>>     that, but
>>>>      >> >>> didn't succeed. Test hung at same place.
>>>>      >> >>>
>>>>      >> >>> Any pointers will be highly appreciated.
>>>>      >> >>>
>>>>      >> >>> ./Build test
>>>>      >> >>> NOTE: Run ./Build reconfig to change existing configuration.
>>>>      >> >>> t/01yeast.t ............... ok
>>>>      >> >>> t/02.rearchitecture.t ..... ok
>>>>      >> >>> t/03.render.t ............. 106/138 Subroutine
>>>>      >> >>> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>      >> >>>  at
>>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>>     <http://berkeleydb.pm>
>>>>      >> >>> line 10
>>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT
>>>>     redefined
>>>>      >> >>> at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>      >> >>>  at
>>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>>     <http://berkeleydb.pm>
>>>>      >> >>> line 10
>>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL
>>>>     redefined at
>>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>      >> >>>  at
>>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>>     <http://berkeleydb.pm>
>>>>      >> >>> line 10
>>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE
>>>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>      >> >>>  at
>>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>>     <http://berkeleydb.pm>
>>>>      >> >>> line 10
>>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW
>>>>      >> >>> redefined at /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>      >> >>>  at
>>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>>     <http://berkeleydb.pm>
>>>>      >> >>> line 10
>>>>      >> >>> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR
>>>>     redefined at
>>>>      >> >>> /usr/local/share/perl/5.8.8/Exporter.pm line 67.
>>>>      >> >>>  at
>>>>     /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
>>>>     <http://berkeleydb.pm>
>>>>      >> >>> line 10
>>>>      >> >>> t/03.render.t ............. 110/138
>>>>      >> >>>
>>>>      >> >>>
>>>>      >> >>> Many Thanks
>>>>      >> >>> Prem
>>>>      >> >>>
>>>>      >> >>>
>>>>      >> >>>
>>>>     ------------------------------------------------------------------------------
>>>>      >> >>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>>      >> >>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>>      >> >>> lucky parental unit.  See the prize list and enter to win:
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>>>>      >> >>> _______________________________________________
>>>>      >> >>> Gmod-gbrowse mailing list
>>>>      >> >>> [hidden email]
>>>>     <mailto:[hidden email]>
>>>>      >> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>      >> >>>
>>>>      >> >>
>>>>      >> >>
>>>>      >> >>
>>>>      >> >> --
>>>>      >> >>
>>>>      >> >>
>>>>     ------------------------------------------------------------------------
>>>>      >> >> Scott Cain, Ph. D.                                   scott at
>>>>     scottcain
>>>>      >> >> dot net
>>>>      >> >> GMOD Coordinator (http://gmod.org/)
>>>>     216-392-3087
>>>>      >> >> Ontario Institute for Cancer Research
>>>>      >> >>
>>>>      >> >
>>>>      >>
>>>>      >>
>>>>      >>
>>>>      >> --
>>>>      >>
>>>>     ------------------------------------------------------------------------
>>>>      >> Scott Cain, Ph. D.                                   scott at
>>>>     scottcain
>>>>      >> dot net
>>>>      >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>      >> Ontario Institute for Cancer Research
>>>>      >>
>>>>      >>
>>>>      >>
>>>>     ------------------------------------------------------------------------------
>>>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>>      >> lucky parental unit.  See the prize list and enter to win:
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>>>>      >> _______________________________________________
>>>>      >> Gmod-gbrowse mailing list
>>>>      >> [hidden email]
>>>>     <mailto:[hidden email]>
>>>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>      >>
>>>>      >>
>>>>      >>
>>>>     ------------------------------------------------------------------------------
>>>>      >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>>      >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>>      >> lucky parental unit.  See the prize list and enter to win:
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>>>>      >> _______________________________________________
>>>>      >> Gmod-gbrowse mailing list
>>>>      >> [hidden email]
>>>>     <mailto:[hidden email]>
>>>>      >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>      >
>>>>      >
>>>>      >
>>>>      > --
>>>>      > Lincoln D. Stein
>>>>      > Director, Informatics and Biocomputing Platform
>>>>      > Ontario Institute for Cancer Research
>>>>      > 101 College St., Suite 800
>>>>      > Toronto, ON, Canada M5G0A3
>>>>      > 416 673-8514
>>>>      > Assistant: Renata Musa <[hidden email]
>>>>     <mailto:[hidden email]>>
>>>>      >
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <[hidden email]
>>>> <mailto:[hidden email]>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> ------------------------------------------------------------------------------
>>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>> lucky parental unit.  See the prize list and enter to win:
>>>> http://p.sf.net/sfu/thinkgeek-promo
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>> --
>>> -------------------------------
>>> João Marcelo Pereira Alves (J)
>>> Post-doctoral fellow
>>> MCV / VCU - Richmond, VA
>>> http://bioinfo.lpb.mic.vcu.edu
>>> f. 1-804-828-3897
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
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>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
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>>> _______________________________________________
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>>>

--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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