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<p class=MsoNormal>Hi,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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!<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>NOTE: Run ./Build reconfig to change existing configuration.<o:p></o:p></p>
<p class=MsoNormal>/etc/httpd/conf.d/gbrowse2.conf is already installed. Please
run ./Build apache_conf to see this file's recommended contents.<o:p></o:p></p>
<p class=MsoNormal>t/01yeast...................ok <o:p></o:p></p>
<p class=MsoNormal>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.<o:p></o:p></p>
<p class=MsoNormal>t/02.rearchitecture......... Dubious, test returned 255
(wstat 65280, 0xff00)<o:p></o:p></p>
<p class=MsoNormal> Failed 4/90 subtests <o:p></o:p></p>
<p class=MsoNormal>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.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.pm
line 23, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at (eval 56) line 3,
<DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal> ...propagated at
/usr/local/perl/5.8.8/lib/5.8.8/base.pm line 85, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render/HTML.pm
line 5, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at t/03.render.t line 48,
<DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at t/03.render.t line 48,
<DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>t/03.render................. Dubious, test returned 2 (wstat
512, 0x200)<o:p></o:p></p>
<p class=MsoNormal> Failed 148/148 subtests <o:p></o:p></p>
<p class=MsoNormal>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.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at /home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.pm
line 23, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at (eval 56) line 3,
<DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal> ...propagated at
/usr/local/perl/5.8.8/lib/5.8.8/base.pm line 85, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render/HTML.pm
line 5, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at t/04.remoteserver.t line
45, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at t/04.remoteserver.t
line 45, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>t/04.remoteserver........... Dubious, test returned 2 (wstat
512, 0x200)<o:p></o:p></p>
<p class=MsoNormal> Failed 43/43 subtests <o:p></o:p></p>
<p class=MsoNormal>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.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.pm
line 23, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at (eval 56) line 3,
<DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal> ...propagated at
/usr/local/perl/5.8.8/lib/5.8.8/base.pm line 85, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render/HTML.pm
line 5, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at t/05.deferredrendering.t
line 44, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
t/05.deferredrendering.t line 44, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>t/05.deferredrendering...... Dubious, test returned 2 (wstat
512, 0x200)<o:p></o:p></p>
<p class=MsoNormal> Failed 19/19 subtests <o:p></o:p></p>
<p class=MsoNormal>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.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at /home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render.pm
line 23, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/RenderPanels.pm
line 9, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/RenderPanels.pm
line 9, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render/Slave.pm
line 16, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at
/home/pohwat1/opensource/GBrowse-1.997/t/../lib/Bio/Graphics/Browser/Render/Slave.pm
line 16, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>Compilation failed in require at t/06.featuresearch.t line
42, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>BEGIN failed--compilation aborted at t/06.featuresearch.t
line 42, <DATA> line 192.<o:p></o:p></p>
<p class=MsoNormal>t/06.featuresearch.......... Dubious, test returned 2 (wstat
512, 0x200)<o:p></o:p></p>
<p class=MsoNormal> Failed 25/25 subtests <o:p></o:p></p>
<p class=MsoNormal>t/07.karyotype.............. Failed 2/3 subtests <o:p></o:p></p>
<p class=MsoNormal>t/08.calign.................ok <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Test Summary Report<o:p></o:p></p>
<p class=MsoNormal>-------------------<o:p></o:p></p>
<p class=MsoNormal>t/02.rearchitecture.t (Wstat: 65280 Tests: 86
Failed: 0)<o:p></o:p></p>
<p class=MsoNormal> Non-zero exit status: 255<o:p></o:p></p>
<p class=MsoNormal> Parse errors: Bad plan. You planned 90 tests
but ran 86.<o:p></o:p></p>
<p class=MsoNormal>t/03.render.t
(Wstat: 512 Tests: 0 Failed: 0)<o:p></o:p></p>
<p class=MsoNormal> Non-zero exit status: 2<o:p></o:p></p>
<p class=MsoNormal> Parse errors: Bad plan. You planned 148 tests
but ran 0.<o:p></o:p></p>
<p class=MsoNormal>t/04.remoteserver.t (Wstat: 512
Tests: 0 Failed: 0)<o:p></o:p></p>
<p class=MsoNormal> Non-zero exit status: 2<o:p></o:p></p>
<p class=MsoNormal> Parse errors: Bad plan. You planned 43 tests
but ran 0.<o:p></o:p></p>
<p class=MsoNormal>t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)<o:p></o:p></p>
<p class=MsoNormal> Non-zero exit status: 2<o:p></o:p></p>
<p class=MsoNormal> Parse errors: Bad plan. You planned 19 tests
but ran 0.<o:p></o:p></p>
<p class=MsoNormal>t/06.featuresearch.t (Wstat: 512 Tests: 0
Failed: 0)<o:p></o:p></p>
<p class=MsoNormal> Non-zero exit status: 2<o:p></o:p></p>
<p class=MsoNormal> Parse errors: Bad plan. You planned 25 tests
but ran 0.<o:p></o:p></p>
<p class=MsoNormal>t/07.karyotype.t
(Wstat: 11 Tests: 1 Failed: 0)<o:p></o:p></p>
<p class=MsoNormal> Parse errors: Bad plan. You planned 3 tests but
ran 1.<o:p></o:p></p>
<p class=MsoNormal>Files=8, Tests=100, 8 wallclock secs ( 0.01 usr
0.12 sys + 3.37 cusr 1.49 csys = 4.99 CPU)<o:p></o:p></p>
<p class=MsoNormal>Result: FAIL<o:p></o:p></p>
<p class=MsoNormal>Failed 6/8 test programs. 0/100 subtests failed.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Best
Regards,</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Wan
Ting</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'> <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:7.5pt;font-family:"Arial","sans-serif";
color:maroon'>---------------------------------</span><span style='font-size:
12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:7.5pt;font-family:"Arial","sans-serif";
color:maroon'>This email is confidential and may be privileged. If you are not
the intended recipient, please delete it and notify us immediately. </span><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:7.5pt;font-family:"Arial","sans-serif";
color:maroon'>Please do not copy or use it for any purpose, or disclose its
content to any other person. Thank you.</span><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:7.5pt;font-family:"Arial","sans-serif";
color:maroon'>---------------------------------</span><o:p></o:p></p>
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