[Gmod-help] GBrowse 2.0 (1.997) Error in installing.
Scott Cain
scott at scottcain.net
Wed Aug 19 14:38:30 EDT 2009
Hi Wan Ting,
I cc'ed this to the GBrowse mailing list; that is the best place to go
for questions about GBrowse, including installation issues.
The latest version of GBrowse2 that is in CPAN is in fact flawed and
won't install: Bio::Graphics::Browser::UserTracks was left out of the
package. While you can use "force" to make it install, the GBrowse
cgi will still crash because of the missing UserTracks module.
My best advice for the moment is to get a cvs checkout of GBrowse2:
cvs -d:pserver:anonymous at gmod.cvs.sourceforge.net:/cvsroot/gmod login
cvs -d:pserver:anonymous at gmod.cvs.sourceforge.net:/cvsroot/gmod co
Generic-Genome-Browser
and install from there.
Scott
On Aug 18, 2009, at 2:41 AM, POH Wan Ting wrote:
> 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/
> DataSource.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/
> Render.pm line 23, <DATA> line 192.
> BEGIN failed--compilation aborted at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.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/Render/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/Render.pm line 23, <DATA> line 192.
> BEGIN failed--compilation aborted at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.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/Render/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/
> Render.pm line 23, <DATA> line 192.
> BEGIN failed--compilation aborted at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.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/Render/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/
> Render.pm line 23, <DATA> line 192.
> BEGIN failed--compilation aborted at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.pm line 23,
> <DATA> line 192.
> Compilation failed in require at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/RenderPanels.pm line 9,
> <DATA> line 192.
> BEGIN failed--compilation aborted at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/RenderPanels.pm line 9,
> <DATA> line 192.
> Compilation failed in require at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render/Slave.pm line 16,
> <DATA> line 192.
> BEGIN failed--compilation aborted at /home/pohwat1/opensource/
> GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render/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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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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