[Gmod-help] GBrowse 2.0 (1.997) Error in installing.

Tue Aug 18 02:41:40 EDT 2009

Hi,

I am experience some problems in installing GBrowse 2.0. It seems that
Bio::Graphics::Browser::UserTracks.pm cannot be found. I tried locating
it manually through the gbrowse site but can seem to find it anywhere.
Any help would be much appreciated. Thank you!

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

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

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

t/02.rearchitecture.........1/90 Can't locate object method "parse_fh"
via package "Bio::Graphics::Browser::DataSource" at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Dat
aSource.pm line 929.

t/02.rearchitecture......... Dubious, test returned 255 (wstat 65280,
0xff00)

 Failed 4/90 subtests 

t/03.render.................Can't locate
Bio/Graphics/Browser/UserTracks.pm in @INC (@INC contains:
/home/pohwat1/opensource/GBrowse-1.997/t/../lib t
/home/pohwat1/opensource/GBrowse-1.997/t/testdata
/home/pohwat1/opensource/GBrowse-1.997/blib/lib
/home/pohwat1/opensource/GBrowse-1.997/blib/arch
/home/pohwat1/opensource/GBrowse-1.997/install_util
/usr/local/perl/5.8.8/lib/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/5.8.8
/usr/local/perl/5.8.8/lib/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/site_perl/5.8.8
/usr/local/perl/5.8.8/lib/site_perl .) at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

Compilation failed in require at (eval 56) line 3, <DATA> line 192.

        ...propagated at /usr/local/perl/5.8.8/lib/5.8.8/base.pm line
85, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der/HTML.pm line 5, <DATA> line 192.

Compilation failed in require at t/03.render.t line 48, <DATA> line 192.

BEGIN failed--compilation aborted at t/03.render.t line 48, <DATA> line
192.

t/03.render................. Dubious, test returned 2 (wstat 512, 0x200)

 Failed 148/148 subtests 

t/04.remoteserver...........Can't locate
Bio/Graphics/Browser/UserTracks.pm in @INC (@INC contains:
/home/pohwat1/opensource/GBrowse-1.997/t/../lib t
/home/pohwat1/opensource/GBrowse-1.997/blib/lib
/home/pohwat1/opensource/GBrowse-1.997/blib/arch
/home/pohwat1/opensource/GBrowse-1.997/install_util
/usr/local/perl/5.8.8/lib/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/5.8.8
/usr/local/perl/5.8.8/lib/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/site_perl/5.8.8
/usr/local/perl/5.8.8/lib/site_perl .) at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

Compilation failed in require at (eval 56) line 3, <DATA> line 192.

        ...propagated at /usr/local/perl/5.8.8/lib/5.8.8/base.pm line
85, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der/HTML.pm line 5, <DATA> line 192.

Compilation failed in require at t/04.remoteserver.t line 45, <DATA>
line 192.

BEGIN failed--compilation aborted at t/04.remoteserver.t line 45, <DATA>
line 192.

t/04.remoteserver........... Dubious, test returned 2 (wstat 512, 0x200)

 Failed 43/43 subtests 

t/05.deferredrendering......Can't locate
Bio/Graphics/Browser/UserTracks.pm in @INC (@INC contains:
/home/pohwat1/opensource/GBrowse-1.997/t/../lib t
/home/lstein/projects/bioperl-live
/home/pohwat1/opensource/GBrowse-1.997/blib/lib
/home/pohwat1/opensource/GBrowse-1.997/blib/arch
/home/pohwat1/opensource/GBrowse-1.997/install_util
/usr/local/perl/5.8.8/lib/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/5.8.8
/usr/local/perl/5.8.8/lib/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/site_perl/5.8.8
/usr/local/perl/5.8.8/lib/site_perl .) at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

Compilation failed in require at (eval 56) line 3, <DATA> line 192.

        ...propagated at /usr/local/perl/5.8.8/lib/5.8.8/base.pm line
85, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der/HTML.pm line 5, <DATA> line 192.

Compilation failed in require at t/05.deferredrendering.t line 44,
<DATA> line 192.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 44,
<DATA> line 192.

t/05.deferredrendering...... Dubious, test returned 2 (wstat 512, 0x200)

 Failed 19/19 subtests 

t/06.featuresearch..........Can't locate
Bio/Graphics/Browser/UserTracks.pm in @INC (@INC contains:
/home/pohwat1/opensource/GBrowse-1.997/t/../lib t
/home/lstein/projects/bioperl-live
/home/pohwat1/opensource/GBrowse-1.997/blib/lib
/home/pohwat1/opensource/GBrowse-1.997/blib/arch
/home/pohwat1/opensource/GBrowse-1.997/install_util
/usr/local/perl/5.8.8/lib/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/5.8.8
/usr/local/perl/5.8.8/lib/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/local/perl/5.8.8/lib/site_perl/5.8.8
/usr/local/perl/5.8.8/lib/site_perl .) at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der.pm line 23, <DATA> line 192.

Compilation failed in require at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
derPanels.pm line 9, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
derPanels.pm line 9, <DATA> line 192.

Compilation failed in require at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der/Slave.pm line 16, <DATA> line 192.

BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Ren
der/Slave.pm line 16, <DATA> line 192.

Compilation failed in require at t/06.featuresearch.t line 42, <DATA>
line 192.

BEGIN failed--compilation aborted at t/06.featuresearch.t line 42,
<DATA> line 192.

t/06.featuresearch.......... Dubious, test returned 2 (wstat 512, 0x200)

 Failed 25/25 subtests 

t/07.karyotype.............. Failed 2/3 subtests 

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

Test Summary Report

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

t/02.rearchitecture.t   (Wstat: 65280 Tests: 86 Failed: 0)

  Non-zero exit status: 255

  Parse errors: Bad plan.  You planned 90 tests but ran 86.

t/03.render.t           (Wstat: 512 Tests: 0 Failed: 0)

  Non-zero exit status: 2

  Parse errors: Bad plan.  You planned 148 tests but ran 0.

t/04.remoteserver.t     (Wstat: 512 Tests: 0 Failed: 0)

  Non-zero exit status: 2

  Parse errors: Bad plan.  You planned 43 tests but ran 0.

t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)

  Non-zero exit status: 2

  Parse errors: Bad plan.  You planned 19 tests but ran 0.

t/06.featuresearch.t    (Wstat: 512 Tests: 0 Failed: 0)

  Non-zero exit status: 2

  Parse errors: Bad plan.  You planned 25 tests but ran 0.

t/07.karyotype.t        (Wstat: 11 Tests: 1 Failed: 0)

  Parse errors: Bad plan.  You planned 3 tests but ran 1.

Files=8, Tests=100,  8 wallclock secs ( 0.01 usr  0.12 sys +  3.37 cusr
1.49 csys =  4.99 CPU)

Result: FAIL

Failed 6/8 test programs. 0/100 subtests failed.

Best Regards,

Wan Ting

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