Bioperl Bio::DB::SeqFeature::Store::berkeleydb adaptor failing tests

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Bioperl Bio::DB::SeqFeature::Store::berkeleydb adaptor failing tests

Fields, Christopher J
Lincoln, Scott,

I noticed that the Bio::DB::SeqFeature::Store::berkeleydb adaptor module is failing two tests.  I can delve into it if you don't have time, but you might have a better idea where to look?

This is on both the master and v1 branches (not a lot of major changes on 'master' yet).  Seems to be something with sequence storage, maybe Bio::DB::Fasta?  Test results below.

The Pg adaptor might also have problems, I'll see if it's version-related.

chris

[cjfields@pyrimidine-laptop bioperl-live (v1)]$ prove -lrv t/LocalDB/SeqFeature_BDB.t
t/LocalDB/SeqFeature_BDB.t ..
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;

ok 38
ok 39
ok 40

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
ok 41
not ok 42

#   Failed test at t/LocalDB/SeqFeature.t line 133.
#          got: '0'
#     expected: '1000'
ok 43
ok 44 - feature names should be case insensitive
ok 45
ok 46
ok 47
ok 48
ok 49
Use of uninitialized value within @_ in list assignment at /Users/cjfields/perl5/perlbrew/perls/perl-5.16.2/lib/5.16.2/Test/Builder.pm line 942.
not ok 50

#   Failed test at t/LocalDB/SeqFeature.t line 158.
#          got: ''
#     expected: 'ttgcgttcgg'
ok 51
ok 52
...
ok 111 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 112 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 113 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 114 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 115 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 116 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
# Looks like you failed 2 tests of 116.
Failed 2/116 subtests
        (less 6 skipped subtests: 108 okay)

Test Summary Report
-------------------
t/LocalDB/SeqFeature_BDB.t (Wstat: 0 Tests: 116 Failed: 2)
  Failed tests:  42, 50
Files=1, Tests=116,  1 wallclock secs ( 0.03 usr  0.01 sys +  0.35 cusr  0.04 csys =  0.43 CPU)
Result: FAIL



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Re: Bioperl Bio::DB::SeqFeature::Store::berkeleydb adaptor failing tests

Lincoln Stein
It is almost certainly related to a change to Bio::DB::Fasta. Someone else must have broken it -- I haven't worked on either module for a long time.

Lincoln


On Wed, Feb 20, 2013 at 10:42 PM, Fields, Christopher J <[hidden email]> wrote:
Lincoln, Scott,

I noticed that the Bio::DB::SeqFeature::Store::berkeleydb adaptor module is failing two tests.  I can delve into it if you don't have time, but you might have a better idea where to look?

This is on both the master and v1 branches (not a lot of major changes on 'master' yet).  Seems to be something with sequence storage, maybe Bio::DB::Fasta?  Test results below.

The Pg adaptor might also have problems, I'll see if it's version-related.

chris

[cjfields@pyrimidine-laptop bioperl-live (v1)]$ prove -lrv t/LocalDB/SeqFeature_BDB.t
t/LocalDB/SeqFeature_BDB.t ..
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;

ok 38
ok 39
ok 40

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
ok 41
not ok 42

#   Failed test at t/LocalDB/SeqFeature.t line 133.
#          got: '0'
#     expected: '1000'
ok 43
ok 44 - feature names should be case insensitive
ok 45
ok 46
ok 47
ok 48
ok 49
Use of uninitialized value within @_ in list assignment at /Users/cjfields/perl5/perlbrew/perls/perl-5.16.2/lib/5.16.2/Test/Builder.pm line 942.
not ok 50

#   Failed test at t/LocalDB/SeqFeature.t line 158.
#          got: ''
#     expected: 'ttgcgttcgg'
ok 51
ok 52
...
ok 111 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 112 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 113 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 114 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 115 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 116 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
# Looks like you failed 2 tests of 116.
Failed 2/116 subtests
        (less 6 skipped subtests: 108 okay)

Test Summary Report
-------------------
t/LocalDB/SeqFeature_BDB.t (Wstat: 0 Tests: 116 Failed: 2)
  Failed tests:  42, 50
Files=1, Tests=116,  1 wallclock secs ( 0.03 usr  0.01 sys +  0.35 cusr  0.04 csys =  0.43 CPU)
Result: FAIL



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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]>

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Re: Bioperl Bio::DB::SeqFeature::Store::berkeleydb adaptor failing tests

Fields, Christopher J
Florent fixed it, here are the changes:

I want to make sure all the changes are working for the GMOD folks, I'll be pushing a new release off the 'v1' branch pretty soon.

chris

On Feb 21, 2013, at 4:06 AM, Lincoln Stein <[hidden email]> wrote:

It is almost certainly related to a change to Bio::DB::Fasta. Someone else must have broken it -- I haven't worked on either module for a long time.

Lincoln


On Wed, Feb 20, 2013 at 10:42 PM, Fields, Christopher J <[hidden email]> wrote:
Lincoln, Scott,

I noticed that the Bio::DB::SeqFeature::Store::berkeleydb adaptor module is failing two tests.  I can delve into it if you don't have time, but you might have a better idea where to look?

This is on both the master and v1 branches (not a lot of major changes on 'master' yet).  Seems to be something with sequence storage, maybe Bio::DB::Fasta?  Test results below.

The Pg adaptor might also have problems, I'll see if it's version-related.

chris

[cjfields@pyrimidine-laptop bioperl-live (v1)]$ prove -lrv t/LocalDB/SeqFeature_BDB.t
t/LocalDB/SeqFeature_BDB.t ..
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;

ok 38
ok 39
ok 40

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
ok 41
not ok 42

#   Failed test at t/LocalDB/SeqFeature.t line 133.
#          got: '0'
#     expected: '1000'
ok 43
ok 44 - feature names should be case insensitive
ok 45
ok 46
ok 47
ok 48
ok 49
Use of uninitialized value within @_ in list assignment at /Users/cjfields/perl5/perlbrew/perls/perl-5.16.2/lib/5.16.2/Test/Builder.pm line 942.
not ok 50

#   Failed test at t/LocalDB/SeqFeature.t line 158.
#          got: ''
#     expected: 'ttgcgttcgg'
ok 51
ok 52
...
ok 111 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 112 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 113 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 114 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 115 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 116 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
# Looks like you failed 2 tests of 116.
Failed 2/116 subtests
        (less 6 skipped subtests: 108 okay)

Test Summary Report
-------------------
t/LocalDB/SeqFeature_BDB.t (Wstat: 0 Tests: 116 Failed: 2)
  Failed tests:  42, 50
Files=1, Tests=116,  1 wallclock secs ( 0.03 usr  0.01 sys +  0.35 cusr  0.04 csys =  0.43 CPU)
Result: FAIL



------------------------------------------------------------------------------
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Download AppDynamics Lite for free today:
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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]>


------------------------------------------------------------------------------
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Download AppDynamics Lite for free today:
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Re: Bioperl Bio::DB::SeqFeature::Store::berkeleydb adaptor failing tests

Lincoln Stein
Looks good to me.

L


On Thu, Feb 21, 2013 at 8:48 AM, Fields, Christopher J <[hidden email]> wrote:
Florent fixed it, here are the changes:

I want to make sure all the changes are working for the GMOD folks, I'll be pushing a new release off the 'v1' branch pretty soon.

chris

On Feb 21, 2013, at 4:06 AM, Lincoln Stein <[hidden email]> wrote:

It is almost certainly related to a change to Bio::DB::Fasta. Someone else must have broken it -- I haven't worked on either module for a long time.

Lincoln


On Wed, Feb 20, 2013 at 10:42 PM, Fields, Christopher J <[hidden email]> wrote:
Lincoln, Scott,

I noticed that the Bio::DB::SeqFeature::Store::berkeleydb adaptor module is failing two tests.  I can delve into it if you don't have time, but you might have a better idea where to look?

This is on both the master and v1 branches (not a lot of major changes on 'master' yet).  Seems to be something with sequence storage, maybe Bio::DB::Fasta?  Test results below.

The Pg adaptor might also have problems, I'll see if it's version-related.

chris

[cjfields@pyrimidine-laptop bioperl-live (v1)]$ prove -lrv t/LocalDB/SeqFeature_BDB.t
t/LocalDB/SeqFeature_BDB.t ..
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;

ok 38
ok 39
ok 40

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
ok 41
not ok 42

#   Failed test at t/LocalDB/SeqFeature.t line 133.
#          got: '0'
#     expected: '1000'
ok 43
ok 44 - feature names should be case insensitive
ok 45
ok 46
ok 47
ok 48
ok 49
Use of uninitialized value within @_ in list assignment at /Users/cjfields/perl5/perlbrew/perls/perl-5.16.2/lib/5.16.2/Test/Builder.pm line 942.
not ok 50

#   Failed test at t/LocalDB/SeqFeature.t line 158.
#          got: ''
#     expected: 'ttgcgttcgg'
ok 51
ok 52
...
ok 111 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 112 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 113 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 114 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 115 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 116 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
# Looks like you failed 2 tests of 116.
Failed 2/116 subtests
        (less 6 skipped subtests: 108 okay)

Test Summary Report
-------------------
t/LocalDB/SeqFeature_BDB.t (Wstat: 0 Tests: 116 Failed: 2)
  Failed tests:  42, 50
Files=1, Tests=116,  1 wallclock secs ( 0.03 usr  0.01 sys +  0.35 cusr  0.04 csys =  0.43 CPU)
Result: FAIL



------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
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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
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>




--
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]>

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse