installing GBrowse2 from SVN

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installing GBrowse2 from SVN

Cornel Ghiban
Hi,

I'd like to install GBrowse2 on a system that has GBrowse1.x installed.

When testing I get these errors:

t/01yeast.................ok
t/02.rearchitecture.......ok
t/03.render...............ok 108/138Subroutine
Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
/usr/lib/perl5/5.8.8/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined at
/usr/lib/perl5/5.8.8/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
/usr/lib/perl5/5.8.8/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE redefined at
/usr/lib/perl5/5.8.8/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW redefined at
/usr/lib/perl5/5.8.8/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
/usr/lib/perl5/5.8.8/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
t/03.render...............ok
t/04.remoteserver.........ok 1/43Storable binary image v26.48 more recent
than I am (v2.7) at ../../lib/Storable.pm (autosplit into
../../lib/auto/Storable/thaw.al) line 366, <> line 45, at
t/04.remoteserver.t line 126
t/04.remoteserver.........dubious
         Test returned status 4 (wstat 1024, 0x400)
DIED. FAILED tests 3, 5-43
         Failed 40/43 tests, 6.98% okay (less 1 skipped test: 2 okay, 4.65%)
t/05.deferredrendering....ok
t/06.featuresearch........ok
t/07.karyotype............ok
t/08.calign...............ok
Failed Test         Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/04.remoteserver.t    4  1024    43   79 183.72%  3 5-43
1 subtest skipped.
Failed 1/8 test scripts, 87.50% okay. 40/332 subtests failed, 87.95% okay.

I have all the dependencies installed and GBrowse 1.x works just fine.

Could you give me any hints on what I can try next?

Thanks,
Cornel

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Re: installing GBrowse2 from SVN

Cornel Ghiban
Running ./Build test verbose=1
gets me this output for test 4

(I also get similar outputs for GBrowse 2.09 and 2.10 from CPAN)

t/04.remoteserver.........1..43
ok 1
ok 2
Storable binary image v26.48 more recent than I am (v2.7) at
../../lib/Storable.pm (autosplit into ../../lib/auto/Storable/thaw.al) line
366, <> line 45, at t/04.remoteserver.t line 126
not ok 3
# Test 3 got: '' (t/04.remoteserver.t at line 121)
#   Expected: '1' (500 read timeout
Content-Type: text/plain
Client-Date: Wed, 16 Jun 2010 15:18:46 GMT
Client-Warning: Internal response

500 read timeout
)
ok 4 # skip
dubious
         Test returned status 4 (wstat 1024, 0x400)
DIED. FAILED tests 3, 5-43
         Failed 40/43 tests, 6.98% okay (less 1 skipped test: 2 okay, 4.65%)


Thanks,
Cornel

On 6/16/2010 10:55 AM, Cornel Ghiban wrote:

> Hi,
>
> I'd like to install GBrowse2 on a system that has GBrowse1.x installed.
>
> When testing I get these errors:
>
> t/01yeast.................ok
> t/02.rearchitecture.......ok
> t/03.render...............ok 108/138Subroutine
> Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
> /usr/lib/perl5/5.8.8/Exporter.pm line 65.
>    at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
> line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined at
> /usr/lib/perl5/5.8.8/Exporter.pm line 65.
>    at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
> line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
> /usr/lib/perl5/5.8.8/Exporter.pm line 65.
>    at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
> line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE redefined at
> /usr/lib/perl5/5.8.8/Exporter.pm line 65.
>    at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
> line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW redefined at
> /usr/lib/perl5/5.8.8/Exporter.pm line 65.
>    at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
> line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
> /usr/lib/perl5/5.8.8/Exporter.pm line 65.
>    at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm
> line 10
> t/03.render...............ok
> t/04.remoteserver.........ok 1/43Storable binary image v26.48 more recent
> than I am (v2.7) at ../../lib/Storable.pm (autosplit into
> ../../lib/auto/Storable/thaw.al) line 366,<>  line 45, at
> t/04.remoteserver.t line 126
> t/04.remoteserver.........dubious
>           Test returned status 4 (wstat 1024, 0x400)
> DIED. FAILED tests 3, 5-43
>           Failed 40/43 tests, 6.98% okay (less 1 skipped test: 2 okay, 4.65%)
> t/05.deferredrendering....ok
> t/06.featuresearch........ok
> t/07.karyotype............ok
> t/08.calign...............ok
> Failed Test         Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/04.remoteserver.t    4  1024    43   79 183.72%  3 5-43
> 1 subtest skipped.
> Failed 1/8 test scripts, 87.50% okay. 40/332 subtests failed, 87.95% okay.
>
> I have all the dependencies installed and GBrowse 1.x works just fine.
>
> Could you give me any hints on what I can try next?
>
> Thanks,
> Cornel
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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