Getting Gbrowse up

[Jeang, David - ARS]

I’ve tried to rebuild Gbrowse when the tutorial stopped working for me, and when I built test I got this.

Does anyone know what’s wrong?

 

David Jeang

 

NOTE: Run ./Build reconfig to change existing configuration.

Performing variable substitutions in blib/conf/GBrowse.conf

n/GBrowse.conf is already installed. New version will be installed as n/GBrowse.conf.new

Performing variable substitutions in blib/conf/pop_demo.conf

n/pop_demo.conf is already installed. New version will be installed as n/pop_demo.conf.new

Performing variable substitutions in blib/conf/slave_preload.conf

n/slave_preload.conf is already installed. New version will be installed as n/slave_preload.conf.new

Performing variable substitutions in blib/conf/volvox.conf

n/volvox.conf is already installed. New version will be installed as n/volvox.conf.new

Performing variable substitutions in blib/conf/yeast_chr1+2.conf

n/yeast_chr1+2.conf is already installed. New version will be installed as n/yeast_chr1+2.conf.new

Performing variable substitutions in blib/conf/yeast_renderfarm.conf

n/yeast_renderfarm.conf is already installed. New version will be installed as n/yeast_renderfarm.conf.new

Performing variable substitutions in blib/conf/yeast_simple.conf

n/yeast_simple.conf is already installed. New version will be installed as n/yeast_simple.conf.new

Performing variable substitutions in blib/etc/default/gbrowse-slave

/etc/default/gbrowse-slave is already installed. New version will be installed as /etc/default/gbrowse-slave.new

Performing variable substitutions in blib/etc/init.d/gbrowse-slave

/etc/init.d/gbrowse-slave is already installed. New version will be installed as /etc/init.d/gbrowse-slave.new

/etc/httpd/conf.d/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.

Use of uninitialized value in length at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 2764.

t/00.compile.t ............ ok

t/01.yeast.t .............. ok

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

t/03.render.t ............. 1/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 87/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 102/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 110/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 121/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. ok

t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.

t/04.remoteserver.t ....... 1/47 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:44043; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:33660; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Object #5636 should have been retrieved already at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279.

t/04.remoteserver.t ....... 3/47 Storable binary image v41.101 more recent than I am (v2.8) at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at t/04.remoteserver.t line 129.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 44/47 subtests

        (less 1 skipped subtest: 2 okay)

t/05.deferredrendering.t .. 1/19 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40862; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:37416; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/05.deferredrendering.t .. ok

t/06.featuresearch.t ...... 4/26 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

t/06.featuresearch.t ...... Failed 3/26 subtests

t/07.karyotype.t .......... ok

t/08.calign.t ............. ok

 

Test Summary Report

-------------------

t/04.remoteserver.t     (Wstat: 65280 Tests: 4 Failed: 1)

  Failed test:  3

  Non-zero exit status: 255

  Parse errors: Bad plan.  You planned 47 tests but ran 4.

t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)

  Failed tests:  24-26

Files=9, Tests=399, 24 wallclock secs ( 0.14 usr  0.03 sys + 19.55 cusr  2.94 csys = 22.66 CPU)

Result: FAIL

Failed 2/9 test programs. 4/399 subtests failed.

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[Olivier Sallou]

Le 7/16/12 10:11 PM, Jeang, David - ARS a écrit :

I’ve tried to rebuild Gbrowse when the tutorial stopped working for me, and when I built test I got this.

Does anyone know what’s wrong?

This is a known issue. It seems it is related to a problem with an other library, but I don't know which one. I created a bug for this.
You can simply skip the "make test".
It seems however this bug affects plugins.

Olivier

 

David Jeang

 

NOTE: Run ./Build reconfig to change existing configuration.

Performing variable substitutions in blib/conf/GBrowse.conf

n/GBrowse.conf is already installed. New version will be installed as n/GBrowse.conf.new

Performing variable substitutions in blib/conf/pop_demo.conf

n/pop_demo.conf is already installed. New version will be installed as n/pop_demo.conf.new

Performing variable substitutions in blib/conf/slave_preload.conf

n/slave_preload.conf is already installed. New version will be installed as n/slave_preload.conf.new

Performing variable substitutions in blib/conf/volvox.conf

n/volvox.conf is already installed. New version will be installed as n/volvox.conf.new

Performing variable substitutions in blib/conf/yeast_chr1+2.conf

n/yeast_chr1+2.conf is already installed. New version will be installed as n/yeast_chr1+2.conf.new

Performing variable substitutions in blib/conf/yeast_renderfarm.conf

n/yeast_renderfarm.conf is already installed. New version will be installed as n/yeast_renderfarm.conf.new

Performing variable substitutions in blib/conf/yeast_simple.conf

n/yeast_simple.conf is already installed. New version will be installed as n/yeast_simple.conf.new

Performing variable substitutions in blib/etc/default/gbrowse-slave

/etc/default/gbrowse-slave is already installed. New version will be installed as /etc/default/gbrowse-slave.new

Performing variable substitutions in blib/etc/init.d/gbrowse-slave

/etc/init.d/gbrowse-slave is already installed. New version will be installed as /etc/init.d/gbrowse-slave.new

/etc/httpd/conf.d/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.

Use of uninitialized value in length at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 2764.

t/00.compile.t ............ ok

t/01.yeast.t .............. ok

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

t/03.render.t ............. 1/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 87/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 102/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 110/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 121/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. ok

t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.

t/04.remoteserver.t ....... 1/47 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:44043; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:33660; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Object #5636 should have been retrieved already at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279.

t/04.remoteserver.t ....... 3/47 Storable binary image v41.101 more recent than I am (v2.8) at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at t/04.remoteserver.t line 129.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 44/47 subtests

        (less 1 skipped subtest: 2 okay)

t/05.deferredrendering.t .. 1/19 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40862; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:37416; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/05.deferredrendering.t .. ok

t/06.featuresearch.t ...... 4/26 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

t/06.featuresearch.t ...... Failed 3/26 subtests

t/07.karyotype.t .......... ok

t/08.calign.t ............. ok

 

Test Summary Report

-------------------

t/04.remoteserver.t     (Wstat: 65280 Tests: 4 Failed: 1)

  Failed test:  3

  Non-zero exit status: 255

  Parse errors: Bad plan.  You planned 47 tests but ran 4.

t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)

  Failed tests:  24-26

Files=9, Tests=399, 24 wallclock secs ( 0.14 usr  0.03 sys + 19.55 cusr  2.94 csys = 22.66 CPU)

Result: FAIL

Failed 2/9 test programs. 4/399 subtests failed.

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[Jeang, David - ARS]

The library that was modified before this started was the DBD::Pg source. There was a path problem in the perl directories that was adjusted since we had two versions of perl, and there was a missing GSS_C_NT_HOSTBASED_SERVICE symbol error that kept popping up as part of a C library problem that we managed to stop with this:

The root cause of the problem is that Makefile.PL is not including the needed postgres libraries in its LIBS variable.    Study Makefile.PL, specifically, this comment:

 

By default Makefile.PL uses App::Info to find the location of the

PostgreSQL library and include directories.  However, if you want to

control it yourself, define the environment variables POSTGRES_INCLUDE

and POSTGRESLIB, or define just POSTGRES_HOME. Note that if you have

compiled PostgreSQL with SSL support, you must define the POSTGRES_LIB

environment variable and add "-lssl" to it, like this:

 

Essentially, this is telling you to define additional Postgres libraries in the POSTGRES_LIB variable if your postgres version is using SSL, which ours is.   (You can find this out by running pg_config.)   Now, here are the additional libraries you need for the version of postgres installed on the server:   -lgssapi_krb5 -lkrb5 -lcrypto -lssl –lldap.  So, the solution is that before you build the  Makefile, you need to set a POSTGRES_LIB variable: 

 

[gmoore@metagenomics DBD-Pg-2.19.2]$ export POSTGRES_LIB=”-lgssapi_krb5 -lkrb5 -lcrypto -lssl –lldap”

[gmoore@metagenomics DBD-Pg-2.19.2]$ perl Makefile.PL

[gmoore@metagenomics DBD-Pg-2.19.2]$make

[gmoore@metagenomics DBD-Pg-2.19.2]$make test

[gmoore@metagenomics DBD-Pg-2.19.2]$make install

 

We’re getting internal server errors, even with the demos…

 

David Jeang

 

From: Olivier Sallou [mailto:[hidden email]]
Sent: Tuesday, July 17, 2012 1:45 AM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Getting Gbrowse up

 

 

Le 7/16/12 10:11 PM, Jeang, David - ARS a écrit :

I’ve tried to rebuild Gbrowse when the tutorial stopped working for me, and when I built test I got this.

Does anyone know what’s wrong?

This is a known issue. It seems it is related to a problem with an other library, but I don't know which one. I created a bug for this.
You can simply skip the "make test".
It seems however this bug affects plugins.

Olivier

 

David Jeang

 

NOTE: Run ./Build reconfig to change existing configuration.

Performing variable substitutions in blib/conf/GBrowse.conf

n/GBrowse.conf is already installed. New version will be installed as n/GBrowse.conf.new

Performing variable substitutions in blib/conf/pop_demo.conf

n/pop_demo.conf is already installed. New version will be installed as n/pop_demo.conf.new

Performing variable substitutions in blib/conf/slave_preload.conf

n/slave_preload.conf is already installed. New version will be installed as n/slave_preload.conf.new

Performing variable substitutions in blib/conf/volvox.conf

n/volvox.conf is already installed. New version will be installed as n/volvox.conf.new

Performing variable substitutions in blib/conf/yeast_chr1+2.conf

n/yeast_chr1+2.conf is already installed. New version will be installed as n/yeast_chr1+2.conf.new

Performing variable substitutions in blib/conf/yeast_renderfarm.conf

n/yeast_renderfarm.conf is already installed. New version will be installed as n/yeast_renderfarm.conf.new

Performing variable substitutions in blib/conf/yeast_simple.conf

n/yeast_simple.conf is already installed. New version will be installed as n/yeast_simple.conf.new

Performing variable substitutions in blib/etc/default/gbrowse-slave

/etc/default/gbrowse-slave is already installed. New version will be installed as /etc/default/gbrowse-slave.new

Performing variable substitutions in blib/etc/init.d/gbrowse-slave

/etc/init.d/gbrowse-slave is already installed. New version will be installed as /etc/init.d/gbrowse-slave.new

/etc/httpd/conf.d/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.

Use of uninitialized value in length at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 2764.

t/00.compile.t ............ ok

t/01.yeast.t .............. ok

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

t/03.render.t ............. 1/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 87/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 102/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 110/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 121/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. ok

t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.

t/04.remoteserver.t ....... 1/47 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:44043; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:33660; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Object #5636 should have been retrieved already at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279.

t/04.remoteserver.t ....... 3/47 Storable binary image v41.101 more recent than I am (v2.8) at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at t/04.remoteserver.t line 129.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 44/47 subtests

        (less 1 skipped subtest: 2 okay)

t/05.deferredrendering.t .. 1/19 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40862; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:37416; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/05.deferredrendering.t .. ok

t/06.featuresearch.t ...... 4/26 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

t/06.featuresearch.t ...... Failed 3/26 subtests

t/07.karyotype.t .......... ok

t/08.calign.t ............. ok

 

Test Summary Report

-------------------

t/04.remoteserver.t     (Wstat: 65280 Tests: 4 Failed: 1)

  Failed test:  3

  Non-zero exit status: 255

  Parse errors: Bad plan.  You planned 47 tests but ran 4.

t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)

  Failed tests:  24-26

Files=9, Tests=399, 24 wallclock secs ( 0.14 usr  0.03 sys + 19.55 cusr  2.94 csys = 22.66 CPU)

Result: FAIL

Failed 2/9 test programs. 4/399 subtests failed.

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[Jeang, David - ARS]

 

 

From: Jeang, David - ARS
Sent: Monday, July 16, 2012 4:12 PM
To: [hidden email]
Subject: Getting Gbrowse up

 

I’ve tried to rebuild Gbrowse when the tutorial stopped working for me, and when I built test I got this.

Does anyone know what’s wrong?

 

David Jeang

 

NOTE: Run ./Build reconfig to change existing configuration.

Performing variable substitutions in blib/conf/GBrowse.conf

n/GBrowse.conf is already installed. New version will be installed as n/GBrowse.conf.new

Performing variable substitutions in blib/conf/pop_demo.conf

n/pop_demo.conf is already installed. New version will be installed as n/pop_demo.conf.new

Performing variable substitutions in blib/conf/slave_preload.conf

n/slave_preload.conf is already installed. New version will be installed as n/slave_preload.conf.new

Performing variable substitutions in blib/conf/volvox.conf

n/volvox.conf is already installed. New version will be installed as n/volvox.conf.new

Performing variable substitutions in blib/conf/yeast_chr1+2.conf

n/yeast_chr1+2.conf is already installed. New version will be installed as n/yeast_chr1+2.conf.new

Performing variable substitutions in blib/conf/yeast_renderfarm.conf

n/yeast_renderfarm.conf is already installed. New version will be installed as n/yeast_renderfarm.conf.new

Performing variable substitutions in blib/conf/yeast_simple.conf

n/yeast_simple.conf is already installed. New version will be installed as n/yeast_simple.conf.new

Performing variable substitutions in blib/etc/default/gbrowse-slave

/etc/default/gbrowse-slave is already installed. New version will be installed as /etc/default/gbrowse-slave.new

Performing variable substitutions in blib/etc/init.d/gbrowse-slave

/etc/init.d/gbrowse-slave is already installed. New version will be installed as /etc/init.d/gbrowse-slave.new

/etc/httpd/conf.d/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.

Use of uninitialized value in length at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 2764.

t/00.compile.t ............ ok

t/01.yeast.t .............. ok

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

t/03.render.t ............. 1/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 87/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 102/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 110/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 121/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. ok

t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.

t/04.remoteserver.t ....... 1/47 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:44043; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:33660; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Object #5636 should have been retrieved already at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279.

t/04.remoteserver.t ....... 3/47 Storable binary image v41.101 more recent than I am (v2.8) at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at t/04.remoteserver.t line 129.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 44/47 subtests

        (less 1 skipped subtest: 2 okay)

t/05.deferredrendering.t .. 1/19 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40862; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:37416; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/05.deferredrendering.t .. ok

t/06.featuresearch.t ...... 4/26 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

t/06.featuresearch.t ...... Failed 3/26 subtests

t/07.karyotype.t .......... ok

t/08.calign.t ............. ok

 

Test Summary Report

-------------------

t/04.remoteserver.t     (Wstat: 65280 Tests: 4 Failed: 1)

  Failed test:  3

  Non-zero exit status: 255

  Parse errors: Bad plan.  You planned 47 tests but ran 4.

t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)

  Failed tests:  24-26

Files=9, Tests=399, 24 wallclock secs ( 0.14 usr  0.03 sys + 19.55 cusr  2.94 csys = 22.66 CPU)

Result: FAIL

Failed 2/9 test programs. 4/399 subtests failed.

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[Fields, Christopher J]

Olivier,

I have seen similar hard-to-diagnose bugs pop up when using indirect object syntax when creating objects (now considered bad form):

# indirect
my $foo = new Bar;

# direct
my $foo = Bar->new();

It's rare, but it's happened to me twice in BioPerl code.

chris

On Jul 17, 2012, at 12:45 AM, Olivier Sallou wrote:

>
> Le 7/16/12 10:11 PM, Jeang, David - ARS a écrit :
>> I’ve tried to rebuild Gbrowse when the tutorial stopped working for me, and when I built test I got this.
>> Does anyone know what’s wrong?
> This is a known issue. It seems it is related to a problem with an other library, but I don't know which one. I created a bug for this.
> You can simply skip the "make test".
> It seems however this bug affects plugins.
>
> Olivier
>>  
>> David Jeang
>>  
>> NOTE: Run ./Build reconfig to change existing configuration.
>> Performing variable substitutions in blib/conf/GBrowse.conf
>> n/GBrowse.conf is already installed. New version will be installed as n/GBrowse.conf.new
>> Performing variable substitutions in blib/conf/pop_demo.conf
>> n/pop_demo.conf is already installed. New version will be installed as n/pop_demo.conf.new
>> Performing variable substitutions in blib/conf/slave_preload.conf
>> n/slave_preload.conf is already installed. New version will be installed as n/slave_preload.conf.new
>> Performing variable substitutions in blib/conf/volvox.conf
>> n/volvox.conf is already installed. New version will be installed as n/volvox.conf.new
>> Performing variable substitutions in blib/conf/yeast_chr1+2.conf
>> n/yeast_chr1+2.conf is already installed. New version will be installed as n/yeast_chr1+2.conf.new
>> Performing variable substitutions in blib/conf/yeast_renderfarm.conf
>> n/yeast_renderfarm.conf is already installed. New version will be installed as n/yeast_renderfarm.conf.new
>> Performing variable substitutions in blib/conf/yeast_simple.conf
>> n/yeast_simple.conf is already installed. New version will be installed as n/yeast_simple.conf.new
>> Performing variable substitutions in blib/etc/default/gbrowse-slave
>> /etc/default/gbrowse-slave is already installed. New version will be installed as /etc/default/gbrowse-slave.new
>> Performing variable substitutions in blib/etc/init.d/gbrowse-slave
>> /etc/init.d/gbrowse-slave is already installed. New version will be installed as /etc/init.d/gbrowse-slave.new
>> /etc/httpd/conf.d/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.
>> Use of uninitialized value in length at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 2764.
>> t/00.compile.t ............ ok
>> t/01.yeast.t .............. ok
>> t/02.rearchitecture.t ..... ok
>> t/03.render.t ............. 1/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> t/03.render.t ............. 87/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> t/03.render.t ............. 102/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> t/03.render.t ............. 110/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> t/03.render.t ............. 121/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40255;">http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:54546;">http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> t/03.render.t ............. ok
>> t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
>> t/04.remoteserver.t ....... 1/47 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:44043;">http://localhost:44043; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> <a href="http://localhost:33660;">http://localhost:33660; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> Object #5636 should have been retrieved already at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279.
>> t/04.remoteserver.t ....... 3/47 Storable binary image v41.101 more recent than I am (v2.8) at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at t/04.remoteserver.t line 129.
>> t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)
>> Failed 44/47 subtests
>>         (less 1 skipped subtest: 2 okay)
>> t/05.deferredrendering.t .. 1/19 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:40862;">http://localhost:40862; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> <a href="http://localhost:37416;">http://localhost:37416; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.
>> t/05.deferredrendering.t .. ok
>> t/06.featuresearch.t ...... 4/26 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:56256;">http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:58455;">http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:56256;">http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:58455;">http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:56256;">http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.
>> Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.
>> <a href="http://localhost:58455;">http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.
>> t/06.featuresearch.t ...... Failed 3/26 subtests
>> t/07.karyotype.t .......... ok
>> t/08.calign.t ............. ok
>>  
>> Test Summary Report
>> -------------------
>> t/04.remoteserver.t     (Wstat: 65280 Tests: 4 Failed: 1)
>>   Failed test:  3
>>   Non-zero exit status: 255
>>   Parse errors: Bad plan.  You planned 47 tests but ran 4.
>> t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)
>>   Failed tests:  24-26
>> Files=9, Tests=399, 24 wallclock secs ( 0.14 usr  0.03 sys + 19.55 cusr  2.94 csys = 22.66 CPU)
>> Result: FAIL
>> Failed 2/9 test programs. 4/399 subtests failed.
>>
>>
>>
>>
>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
>>
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>> will include endpoint security, mobile security and the latest in malware
>> threats.
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>
>>
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>>
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>
> --
> Olivier Sallou
> IRISA / University of Rennes 1
> Campus de Beaulieu, 35000 RENNES - FRANCE
> Tel: [phone]
>
> gpg key id: 4096R/326D8438  (keyring.debian.org)
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
>
>
>
>
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> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
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Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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[Lincoln Stein]

The location of the bug points to a problem with Storable. I have not yet been able to reproduce the problem on any of my test systems. If you are able to reproduce this, please send the output of "cat /etc/issue" and "perl -V" to me.

Lincoln 

On Mon, Jul 16, 2012 at 4:11 PM, Jeang, David - ARS <[hidden email]> wrote:

I’ve tried to rebuild Gbrowse when the tutorial stopped working for me, and when I built test I got this.

Does anyone know what’s wrong?

 

David Jeang

 

NOTE: Run ./Build reconfig to change existing configuration.

Performing variable substitutions in blib/conf/GBrowse.conf

n/GBrowse.conf is already installed. New version will be installed as n/GBrowse.conf.new

Performing variable substitutions in blib/conf/pop_demo.conf

n/pop_demo.conf is already installed. New version will be installed as n/pop_demo.conf.new

Performing variable substitutions in blib/conf/slave_preload.conf

n/slave_preload.conf is already installed. New version will be installed as n/slave_preload.conf.new

Performing variable substitutions in blib/conf/volvox.conf

n/volvox.conf is already installed. New version will be installed as n/volvox.conf.new

Performing variable substitutions in blib/conf/yeast_chr1+2.conf

n/yeast_chr1+2.conf is already installed. New version will be installed as n/yeast_chr1+2.conf.new

Performing variable substitutions in blib/conf/yeast_renderfarm.conf

n/yeast_renderfarm.conf is already installed. New version will be installed as n/yeast_renderfarm.conf.new

Performing variable substitutions in blib/conf/yeast_simple.conf

n/yeast_simple.conf is already installed. New version will be installed as n/yeast_simple.conf.new

Performing variable substitutions in blib/etc/default/gbrowse-slave

/etc/default/gbrowse-slave is already installed. New version will be installed as /etc/default/gbrowse-slave.new

Performing variable substitutions in blib/etc/init.d/gbrowse-slave

/etc/init.d/gbrowse-slave is already installed. New version will be installed as /etc/init.d/gbrowse-slave.new

/etc/httpd/conf.d/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.

Use of uninitialized value in length at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 2764.

t/00.compile.t ............ ok

t/01.yeast.t .............. ok

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

t/03.render.t ............. 1/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 87/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 102/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 110/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. 121/150 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40255; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:54546; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/03.render.t ............. ok

t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.

t/04.remoteserver.t ....... 1/47 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:44043; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:33660; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Object #5636 should have been retrieved already at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 279.

t/04.remoteserver.t ....... 3/47 Storable binary image v41.101 more recent than I am (v2.8) at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 416, at t/04.remoteserver.t line 129.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 44/47 subtests

        (less 1 skipped subtest: 2 okay)

t/05.deferredrendering.t .. 1/19 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:40862; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

http://localhost:37416; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

t/05.deferredrendering.t .. ok

t/06.featuresearch.t ...... 4/26 Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:56256; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

Can't call method "FETCH" without a package or object reference at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 551.

http://localhost:58455; search failed: 500 Server closed connection without sending any data back at /home/djeang/GBrowse-2.49/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563, <> line 45.

t/06.featuresearch.t ...... Failed 3/26 subtests

t/07.karyotype.t .......... ok

t/08.calign.t ............. ok

 

Test Summary Report

-------------------

t/04.remoteserver.t     (Wstat: 65280 Tests: 4 Failed: 1)

  Failed test:  3

  Non-zero exit status: 255

  Parse errors: Bad plan.  You planned 47 tests but ran 4.

t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)

  Failed tests:  24-26

Files=9, Tests=399, 24 wallclock secs ( 0.14 usr  0.03 sys + 19.55 cusr  2.94 csys = 22.66 CPU)

Result: FAIL

Failed 2/9 test programs. 4/399 subtests failed.

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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]>

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse