GBrowse and Bio::Root::Version

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GBrowse and Bio::Root::Version

lthiberiol
Hi you all!


I've already installed GBrowse about five times, never had any great problem
doing it, but now it's not working at all!!

When I perform the "perl Buil.PL" it shows that the Bio::Root::Version is
not installed
"""

Checking prerequisites...
  requires:
    !  Bio::Root::Version is not installed
  recommends:
    *  Bio::DB::BigFile is not installed
    *  Bio::DB::Sam is not installed
    *  DBD::Pg is not installed
    *  DBD::SQLite is not installed
    *  DB_File::Lock is not installed
    *  File::NFSLock is not installed
    *  GD::SVG is not installed
    *  Net::OpenID::Consumer is not installed
    *  Template is not installed
  * Do not worry if some "recommended" prerequisites are missing. You can
install *
  * them later if you need the features they provide. Do not proceed with
the     *
  * install if any of "REQUIRED" prerequisites are missing.                      
*
  *                                                                              
*
  * The optional Safe::World module does not currently run on Perl 5.10 or      
*
  * higher, and so cannot be installed.                                          
*


ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
versions
of the modules indicated above before proceeding with this installation

Run 'Build installdeps' to install missing prerequisites.

**** WARNING
*****************************************************************************************
If you are upgrading from an earlier version of GBrowse and wish to use
named user accounts, please
set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run
bin/gbrowse_metadb_config.pl to
create/update your user account database.

See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
******************************************************************************************************
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'GBrowse' version '2.39'
Now run:
  ./Build test
  ./Build demo          (optional)
  ./Build install       (as superuser/administrator)
        -or-
  ./Build install_slave (optional, for slave installations)

Other useful targets:
  ./Build register      (to register your copy of GBrowse)
  ./Build reconfig      (to reconfigure install locations)
  ./Build demostop      (to stop the demo)
"""

but when I try to "cpan Bio::Root::Version" it appears:

"""
Removing previously used /root/.cpan/build/BioPerl-1.6.901
Package seems to come without Makefile.PL.
  (The test -f "/root/.cpan/build/BioPerl-1.6.901/Makefile.PL" returned
false.)
  Writing one on our own (setting NAME to BioRootVersion)

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz

Checking if your kit is complete...
Looks good
Writing Makefile for BioRootVersion
cp BioPerl.pm blib/lib/BioPerl.pm
Manifying blib/man3/BioPerl.3pm
  /usr/bin/make  -- OK
Running make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Alphabet.t ...... ok      
t/nexml.t ......... 1/125 # WARNING: NeXML parsing for NeXML v0.9 is
currently very experimental support
t/nexml.t ......... ok      
t/Perl.t .......... 1/31 Can't find 'build_params' in _build at
/usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
# Looks like you planned 31 tests but ran 19.
# Looks like your test exited with 2 just after 19.
t/Perl.t .......... Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/31 subtests
t/PodSyntax.t ..... skipped: Test::Pod 1.00 required for testing POD
t/SearchDist.t .... skipped: The optional module Bio::Ext::Align (or
dependencies thereof) was not installed
t/SeqEvolution.t .. ok    
t/Species.t ....... 1/23 Can't find 'build_params' in _build at
/usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
# Looks like you planned 23 tests but ran 16.
# Looks like your test exited with 2 just after 16.
t/Species.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 7/23 subtests
t/Symbol.t ........ ok  
t/TaxonTree.t ..... skipped: All tests are being skipped, probably because
the module(s) being tested here are now deprecated

Test Summary Report
-------------------
t/Perl.t        (Wstat: 512 Tests: 19 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 31 tests but ran 19.
t/Species.t     (Wstat: 512 Tests: 16 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 23 tests but ran 16.
Files=9, Tests=308,  2 wallclock secs ( 0.11 usr  0.04 sys +  1.80 cusr
0.21 csys =  2.16 CPU)
Result: FAIL
Failed 2/9 test programs. 0/308 subtests failed.
make: *** [test_dynamic] Error 255
  /usr/bin/make test -- NOT OK
Running make install
  make test had returned bad status, won't install without force
"""


I've already tried to install different versions or whatever but nothing
works, what can I do?

(I'm using a Ubuntu Server 8.04)

--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-and-Bio-Root-Version-tp4846737p4846737.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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Re: GBrowse and Bio::Root::Version

simon rayner
do you mean you installed the missing perl modules as prerequisites prior to installing bioperl?

you have messages such as..

   *  Bio::DB::BigFile is not installed
   *  Bio::DB::Sam is not installed
   *  DBD::Pg is not installed
   *  DBD::SQLite is not installed
   *  DB_File::Lock is not installed
   *  File::NFSLock is not installed
   *  GD::SVG is not installed
   *  Net::OpenID::Consumer is not installed
   *  Template is not installed

But i always install these before i attempt to install bioperl.

On Wed, Sep 28, 2011 at 3:39 AM, lthiberiol <[hidden email]> wrote:
Hi you all!


I've already installed GBrowse about five times, never had any great problem
doing it, but now it's not working at all!!

When I perform the "perl Buil.PL" it shows that the Bio::Root::Version is
not installed
"""

Checking prerequisites...
 requires:
   !  Bio::Root::Version is not installed
 recommends:
   *  Bio::DB::BigFile is not installed
   *  Bio::DB::Sam is not installed
   *  DBD::Pg is not installed
   *  DBD::SQLite is not installed
   *  DB_File::Lock is not installed
   *  File::NFSLock is not installed
   *  GD::SVG is not installed
   *  Net::OpenID::Consumer is not installed
   *  Template is not installed
 * Do not worry if some "recommended" prerequisites are missing. You can
install *
 * them later if you need the features they provide. Do not proceed with
the     *
 * install if any of "REQUIRED" prerequisites are missing.
*
 *
*
 * The optional Safe::World module does not currently run on Perl 5.10 or
*
 * higher, and so cannot be installed.
*


ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
versions
of the modules indicated above before proceeding with this installation

Run 'Build installdeps' to install missing prerequisites.

**** WARNING
*****************************************************************************************
If you are upgrading from an earlier version of GBrowse and wish to use
named user accounts, please
set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run
bin/gbrowse_metadb_config.pl to
create/update your user account database.

See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
******************************************************************************************************
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'GBrowse' version '2.39'
Now run:
 ./Build test
 ./Build demo          (optional)
 ./Build install       (as superuser/administrator)
       -or-
 ./Build install_slave (optional, for slave installations)

Other useful targets:
 ./Build register      (to register your copy of GBrowse)
 ./Build reconfig      (to reconfigure install locations)
 ./Build demostop      (to stop the demo)
"""

but when I try to "cpan Bio::Root::Version" it appears:

"""
Removing previously used /root/.cpan/build/BioPerl-1.6.901
Package seems to come without Makefile.PL.
 (The test -f "/root/.cpan/build/BioPerl-1.6.901/Makefile.PL" returned
false.)
 Writing one on our own (setting NAME to BioRootVersion)

 CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz

Checking if your kit is complete...
Looks good
Writing Makefile for BioRootVersion
cp BioPerl.pm blib/lib/BioPerl.pm
Manifying blib/man3/BioPerl.3pm
 /usr/bin/make  -- OK
Running make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Alphabet.t ...... ok
t/nexml.t ......... 1/125 # WARNING: NeXML parsing for NeXML v0.9 is
currently very experimental support
t/nexml.t ......... ok
t/Perl.t .......... 1/31 Can't find 'build_params' in _build at
/usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
# Looks like you planned 31 tests but ran 19.
# Looks like your test exited with 2 just after 19.
t/Perl.t .......... Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/31 subtests
t/PodSyntax.t ..... skipped: Test::Pod 1.00 required for testing POD
t/SearchDist.t .... skipped: The optional module Bio::Ext::Align (or
dependencies thereof) was not installed
t/SeqEvolution.t .. ok
t/Species.t ....... 1/23 Can't find 'build_params' in _build at
/usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
# Looks like you planned 23 tests but ran 16.
# Looks like your test exited with 2 just after 16.
t/Species.t ....... Dubious, test returned 2 (wstat 512, 0x200)
Failed 7/23 subtests
t/Symbol.t ........ ok
t/TaxonTree.t ..... skipped: All tests are being skipped, probably because
the module(s) being tested here are now deprecated

Test Summary Report
-------------------
t/Perl.t        (Wstat: 512 Tests: 19 Failed: 0)
 Non-zero exit status: 2
 Parse errors: Bad plan.  You planned 31 tests but ran 19.
t/Species.t     (Wstat: 512 Tests: 16 Failed: 0)
 Non-zero exit status: 2
 Parse errors: Bad plan.  You planned 23 tests but ran 16.
Files=9, Tests=308,  2 wallclock secs ( 0.11 usr  0.04 sys +  1.80 cusr
0.21 csys =  2.16 CPU)
Result: FAIL
Failed 2/9 test programs. 0/308 subtests failed.
make: *** [test_dynamic] Error 255
 /usr/bin/make test -- NOT OK
Running make install
 make test had returned bad status, won't install without force
"""


I've already tried to install different versions or whatever but nothing
works, what can I do?

(I'm using a Ubuntu Server 8.04)

--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-and-Bio-Root-Version-tp4846737p4846737.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Simon Rayner

State Key Laboratory of Virology
Wuhan Institute of Virology
Chinese Academy of Sciences
Wuhan, Hubei 430071
P.R.China

+86 (27) 87199895 (office)
+86 18627113001 (cell)


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: GBrowse and Bio::Root::Version

Scott Cain
In reply to this post by lthiberiol
Hello,

So the immediate problem is that BioPerl tests are not passing, which
is odd, since I just installed BioPerl on a new system a few days ago
and all the tests passed.  I can tell you with certainty that the
Species tests don't matter for GBrowse.  The Perl tests are slightly
more disconcerting, since the point to a more fundamental problem, but
since the SeqIO and database tests pass, I'm not concerned about these
failures either.  So, if it doesn't bother you (and you don't need
BioPerl for anything else that might be impacted by these failures),
you can force the installation.

Scott


On Tue, Sep 27, 2011 at 3:39 PM, lthiberiol <[hidden email]> wrote:

> Hi you all!
>
>
> I've already installed GBrowse about five times, never had any great problem
> doing it, but now it's not working at all!!
>
> When I perform the "perl Buil.PL" it shows that the Bio::Root::Version is
> not installed
> """
>
> Checking prerequisites...
>  requires:
>    !  Bio::Root::Version is not installed
>  recommends:
>    *  Bio::DB::BigFile is not installed
>    *  Bio::DB::Sam is not installed
>    *  DBD::Pg is not installed
>    *  DBD::SQLite is not installed
>    *  DB_File::Lock is not installed
>    *  File::NFSLock is not installed
>    *  GD::SVG is not installed
>    *  Net::OpenID::Consumer is not installed
>    *  Template is not installed
>  * Do not worry if some "recommended" prerequisites are missing. You can
> install *
>  * them later if you need the features they provide. Do not proceed with
> the     *
>  * install if any of "REQUIRED" prerequisites are missing.
> *
>  *
> *
>  * The optional Safe::World module does not currently run on Perl 5.10 or
> *
>  * higher, and so cannot be installed.
> *
>
>
> ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
> versions
> of the modules indicated above before proceeding with this installation
>
> Run 'Build installdeps' to install missing prerequisites.
>
> **** WARNING
> *****************************************************************************************
> If you are upgrading from an earlier version of GBrowse and wish to use
> named user accounts, please
> set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run
> bin/gbrowse_metadb_config.pl to
> create/update your user account database.
>
> See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
> ******************************************************************************************************
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'GBrowse' version '2.39'
> Now run:
>  ./Build test
>  ./Build demo          (optional)
>  ./Build install       (as superuser/administrator)
>        -or-
>  ./Build install_slave (optional, for slave installations)
>
> Other useful targets:
>  ./Build register      (to register your copy of GBrowse)
>  ./Build reconfig      (to reconfigure install locations)
>  ./Build demostop      (to stop the demo)
> """
>
> but when I try to "cpan Bio::Root::Version" it appears:
>
> """
> Removing previously used /root/.cpan/build/BioPerl-1.6.901
> Package seems to come without Makefile.PL.
>  (The test -f "/root/.cpan/build/BioPerl-1.6.901/Makefile.PL" returned
> false.)
>  Writing one on our own (setting NAME to BioRootVersion)
>
>  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
>
> Checking if your kit is complete...
> Looks good
> Writing Makefile for BioRootVersion
> cp BioPerl.pm blib/lib/BioPerl.pm
> Manifying blib/man3/BioPerl.3pm
>  /usr/bin/make  -- OK
> Running make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/Alphabet.t ...... ok
> t/nexml.t ......... 1/125 # WARNING: NeXML parsing for NeXML v0.9 is
> currently very experimental support
> t/nexml.t ......... ok
> t/Perl.t .......... 1/31 Can't find 'build_params' in _build at
> /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
> # Looks like you planned 31 tests but ran 19.
> # Looks like your test exited with 2 just after 19.
> t/Perl.t .......... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 12/31 subtests
> t/PodSyntax.t ..... skipped: Test::Pod 1.00 required for testing POD
> t/SearchDist.t .... skipped: The optional module Bio::Ext::Align (or
> dependencies thereof) was not installed
> t/SeqEvolution.t .. ok
> t/Species.t ....... 1/23 Can't find 'build_params' in _build at
> /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
> # Looks like you planned 23 tests but ran 16.
> # Looks like your test exited with 2 just after 16.
> t/Species.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 7/23 subtests
> t/Symbol.t ........ ok
> t/TaxonTree.t ..... skipped: All tests are being skipped, probably because
> the module(s) being tested here are now deprecated
>
> Test Summary Report
> -------------------
> t/Perl.t        (Wstat: 512 Tests: 19 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 31 tests but ran 19.
> t/Species.t     (Wstat: 512 Tests: 16 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 23 tests but ran 16.
> Files=9, Tests=308,  2 wallclock secs ( 0.11 usr  0.04 sys +  1.80 cusr
> 0.21 csys =  2.16 CPU)
> Result: FAIL
> Failed 2/9 test programs. 0/308 subtests failed.
> make: *** [test_dynamic] Error 255
>  /usr/bin/make test -- NOT OK
> Running make install
>  make test had returned bad status, won't install without force
> """
>
>
> I've already tried to install different versions or whatever but nothing
> works, what can I do?
>
> (I'm using a Ubuntu Server 8.04)
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-and-Bio-Root-Version-tp4846737p4846737.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: GBrowse and Bio::Root::Version

Fields, Christopher J
Will check into the tests on the bioperl end.  If one is pulling from github we can't guarantee tests will pass (though we strive to make sure they do).  Also, make sure to disable remote database tests, they tend to be the most fragile.

chris

On Sep 27, 2011, at 10:24 PM, Scott Cain wrote:

> Hello,
>
> So the immediate problem is that BioPerl tests are not passing, which
> is odd, since I just installed BioPerl on a new system a few days ago
> and all the tests passed.  I can tell you with certainty that the
> Species tests don't matter for GBrowse.  The Perl tests are slightly
> more disconcerting, since the point to a more fundamental problem, but
> since the SeqIO and database tests pass, I'm not concerned about these
> failures either.  So, if it doesn't bother you (and you don't need
> BioPerl for anything else that might be impacted by these failures),
> you can force the installation.
>
> Scott
>
>
> On Tue, Sep 27, 2011 at 3:39 PM, lthiberiol <[hidden email]> wrote:
>> Hi you all!
>>
>>
>> I've already installed GBrowse about five times, never had any great problem
>> doing it, but now it's not working at all!!
>>
>> When I perform the "perl Buil.PL" it shows that the Bio::Root::Version is
>> not installed
>> """
>>
>> Checking prerequisites...
>>  requires:
>>    !  Bio::Root::Version is not installed
>>  recommends:
>>    *  Bio::DB::BigFile is not installed
>>    *  Bio::DB::Sam is not installed
>>    *  DBD::Pg is not installed
>>    *  DBD::SQLite is not installed
>>    *  DB_File::Lock is not installed
>>    *  File::NFSLock is not installed
>>    *  GD::SVG is not installed
>>    *  Net::OpenID::Consumer is not installed
>>    *  Template is not installed
>>  * Do not worry if some "recommended" prerequisites are missing. You can
>> install *
>>  * them later if you need the features they provide. Do not proceed with
>> the     *
>>  * install if any of "REQUIRED" prerequisites are missing.
>> *
>>  *
>> *
>>  * The optional Safe::World module does not currently run on Perl 5.10 or
>> *
>>  * higher, and so cannot be installed.
>> *
>>
>>
>> ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
>> versions
>> of the modules indicated above before proceeding with this installation
>>
>> Run 'Build installdeps' to install missing prerequisites.
>>
>> **** WARNING
>> *****************************************************************************************
>> If you are upgrading from an earlier version of GBrowse and wish to use
>> named user accounts, please
>> set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run
>> bin/gbrowse_metadb_config.pl to
>> create/update your user account database.
>>
>> See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
>> ******************************************************************************************************
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'GBrowse' version '2.39'
>> Now run:
>>  ./Build test
>>  ./Build demo          (optional)
>>  ./Build install       (as superuser/administrator)
>>        -or-
>>  ./Build install_slave (optional, for slave installations)
>>
>> Other useful targets:
>>  ./Build register      (to register your copy of GBrowse)
>>  ./Build reconfig      (to reconfigure install locations)
>>  ./Build demostop      (to stop the demo)
>> """
>>
>> but when I try to "cpan Bio::Root::Version" it appears:
>>
>> """
>> Removing previously used /root/.cpan/build/BioPerl-1.6.901
>> Package seems to come without Makefile.PL.
>>  (The test -f "/root/.cpan/build/BioPerl-1.6.901/Makefile.PL" returned
>> false.)
>>  Writing one on our own (setting NAME to BioRootVersion)
>>
>>  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
>>
>> Checking if your kit is complete...
>> Looks good
>> Writing Makefile for BioRootVersion
>> cp BioPerl.pm blib/lib/BioPerl.pm
>> Manifying blib/man3/BioPerl.3pm
>>  /usr/bin/make  -- OK
>> Running make test
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>> t/Alphabet.t ...... ok
>> t/nexml.t ......... 1/125 # WARNING: NeXML parsing for NeXML v0.9 is
>> currently very experimental support
>> t/nexml.t ......... ok
>> t/Perl.t .......... 1/31 Can't find 'build_params' in _build at
>> /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
>> # Looks like you planned 31 tests but ran 19.
>> # Looks like your test exited with 2 just after 19.
>> t/Perl.t .......... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 12/31 subtests
>> t/PodSyntax.t ..... skipped: Test::Pod 1.00 required for testing POD
>> t/SearchDist.t .... skipped: The optional module Bio::Ext::Align (or
>> dependencies thereof) was not installed
>> t/SeqEvolution.t .. ok
>> t/Species.t ....... 1/23 Can't find 'build_params' in _build at
>> /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
>> # Looks like you planned 23 tests but ran 16.
>> # Looks like your test exited with 2 just after 16.
>> t/Species.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 7/23 subtests
>> t/Symbol.t ........ ok
>> t/TaxonTree.t ..... skipped: All tests are being skipped, probably because
>> the module(s) being tested here are now deprecated
>>
>> Test Summary Report
>> -------------------
>> t/Perl.t        (Wstat: 512 Tests: 19 Failed: 0)
>>  Non-zero exit status: 2
>>  Parse errors: Bad plan.  You planned 31 tests but ran 19.
>> t/Species.t     (Wstat: 512 Tests: 16 Failed: 0)
>>  Non-zero exit status: 2
>>  Parse errors: Bad plan.  You planned 23 tests but ran 16.
>> Files=9, Tests=308,  2 wallclock secs ( 0.11 usr  0.04 sys +  1.80 cusr
>> 0.21 csys =  2.16 CPU)
>> Result: FAIL
>> Failed 2/9 test programs. 0/308 subtests failed.
>> make: *** [test_dynamic] Error 255
>>  /usr/bin/make test -- NOT OK
>> Running make install
>>  make test had returned bad status, won't install without force
>> """
>>
>>
>> I've already tried to install different versions or whatever but nothing
>> works, what can I do?
>>
>> (I'm using a Ubuntu Server 8.04)
>>
>> --
>> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-and-Bio-Root-Version-tp4846737p4846737.html
>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2dcopy1
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Re: GBrowse and Bio::Root::Version

Lincoln Stein
You may have to "force install" BioPerl if some of the tests on the CPAN version are now failing.

It is ironic, but GBrowse only requires about 2% of the total BioPerl functionality, SeqIO being the main one.

Lincoln

On Wed, Sep 28, 2011 at 1:13 AM, Fields, Christopher J <[hidden email]> wrote:
Will check into the tests on the bioperl end.  If one is pulling from github we can't guarantee tests will pass (though we strive to make sure they do).  Also, make sure to disable remote database tests, they tend to be the most fragile.

chris

On Sep 27, 2011, at 10:24 PM, Scott Cain wrote:

> Hello,
>
> So the immediate problem is that BioPerl tests are not passing, which
> is odd, since I just installed BioPerl on a new system a few days ago
> and all the tests passed.  I can tell you with certainty that the
> Species tests don't matter for GBrowse.  The Perl tests are slightly
> more disconcerting, since the point to a more fundamental problem, but
> since the SeqIO and database tests pass, I'm not concerned about these
> failures either.  So, if it doesn't bother you (and you don't need
> BioPerl for anything else that might be impacted by these failures),
> you can force the installation.
>
> Scott
>
>
> On Tue, Sep 27, 2011 at 3:39 PM, lthiberiol <[hidden email]> wrote:
>> Hi you all!
>>
>>
>> I've already installed GBrowse about five times, never had any great problem
>> doing it, but now it's not working at all!!
>>
>> When I perform the "perl Buil.PL" it shows that the Bio::Root::Version is
>> not installed
>> """
>>
>> Checking prerequisites...
>>  requires:
>>    !  Bio::Root::Version is not installed
>>  recommends:
>>    *  Bio::DB::BigFile is not installed
>>    *  Bio::DB::Sam is not installed
>>    *  DBD::Pg is not installed
>>    *  DBD::SQLite is not installed
>>    *  DB_File::Lock is not installed
>>    *  File::NFSLock is not installed
>>    *  GD::SVG is not installed
>>    *  Net::OpenID::Consumer is not installed
>>    *  Template is not installed
>>  * Do not worry if some "recommended" prerequisites are missing. You can
>> install *
>>  * them later if you need the features they provide. Do not proceed with
>> the     *
>>  * install if any of "REQUIRED" prerequisites are missing.
>> *
>>  *
>> *
>>  * The optional Safe::World module does not currently run on Perl 5.10 or
>> *
>>  * higher, and so cannot be installed.
>> *
>>
>>
>> ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
>> versions
>> of the modules indicated above before proceeding with this installation
>>
>> Run 'Build installdeps' to install missing prerequisites.
>>
>> **** WARNING
>> *****************************************************************************************
>> If you are upgrading from an earlier version of GBrowse and wish to use
>> named user accounts, please
>> set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run
>> bin/gbrowse_metadb_config.pl to
>> create/update your user account database.
>>
>> See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
>> ******************************************************************************************************
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'GBrowse' version '2.39'
>> Now run:
>>  ./Build test
>>  ./Build demo          (optional)
>>  ./Build install       (as superuser/administrator)
>>        -or-
>>  ./Build install_slave (optional, for slave installations)
>>
>> Other useful targets:
>>  ./Build register      (to register your copy of GBrowse)
>>  ./Build reconfig      (to reconfigure install locations)
>>  ./Build demostop      (to stop the demo)
>> """
>>
>> but when I try to "cpan Bio::Root::Version" it appears:
>>
>> """
>> Removing previously used /root/.cpan/build/BioPerl-1.6.901
>> Package seems to come without Makefile.PL.
>>  (The test -f "/root/.cpan/build/BioPerl-1.6.901/Makefile.PL" returned
>> false.)
>>  Writing one on our own (setting NAME to BioRootVersion)
>>
>>  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
>>
>> Checking if your kit is complete...
>> Looks good
>> Writing Makefile for BioRootVersion
>> cp BioPerl.pm blib/lib/BioPerl.pm
>> Manifying blib/man3/BioPerl.3pm
>>  /usr/bin/make  -- OK
>> Running make test
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>> t/Alphabet.t ...... ok
>> t/nexml.t ......... 1/125 # WARNING: NeXML parsing for NeXML v0.9 is
>> currently very experimental support
>> t/nexml.t ......... ok
>> t/Perl.t .......... 1/31 Can't find 'build_params' in _build at
>> /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
>> # Looks like you planned 31 tests but ran 19.
>> # Looks like your test exited with 2 just after 19.
>> t/Perl.t .......... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 12/31 subtests
>> t/PodSyntax.t ..... skipped: Test::Pod 1.00 required for testing POD
>> t/SearchDist.t .... skipped: The optional module Bio::Ext::Align (or
>> dependencies thereof) was not installed
>> t/SeqEvolution.t .. ok
>> t/Species.t ....... 1/23 Can't find 'build_params' in _build at
>> /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1284.
>> # Looks like you planned 23 tests but ran 16.
>> # Looks like your test exited with 2 just after 16.
>> t/Species.t ....... Dubious, test returned 2 (wstat 512, 0x200)
>> Failed 7/23 subtests
>> t/Symbol.t ........ ok
>> t/TaxonTree.t ..... skipped: All tests are being skipped, probably because
>> the module(s) being tested here are now deprecated
>>
>> Test Summary Report
>> -------------------
>> t/Perl.t        (Wstat: 512 Tests: 19 Failed: 0)
>>  Non-zero exit status: 2
>>  Parse errors: Bad plan.  You planned 31 tests but ran 19.
>> t/Species.t     (Wstat: 512 Tests: 16 Failed: 0)
>>  Non-zero exit status: 2
>>  Parse errors: Bad plan.  You planned 23 tests but ran 16.
>> Files=9, Tests=308,  2 wallclock secs ( 0.11 usr  0.04 sys +  1.80 cusr
>> 0.21 csys =  2.16 CPU)
>> Result: FAIL
>> Failed 2/9 test programs. 0/308 subtests failed.
>> make: *** [test_dynamic] Error 255
>>  /usr/bin/make test -- NOT OK
>> Running make install
>>  make test had returned bad status, won't install without force
>> """
>>
>>
>> I've already tried to install different versions or whatever but nothing
>> works, what can I do?
>>
>> (I'm using a Ubuntu Server 8.04)
>>
>> --
>> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-and-Bio-Root-Version-tp4846737p4846737.html
>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2dcopy1
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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[hidden email]
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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]>

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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