Summary: | sci-biology/bioperl-db fails tests: Tries to connect to mysql server | ||
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Product: | Gentoo Linux | Reporter: | Diego Elio Pettenò (RETIRED) <flameeyes> |
Component: | New packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | kentnl, patrick, sci-biology |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
URL: | https://tinderboxlogs.s3.amazonaws.com/tbamd64.excelsior.flameeyes.eu/sci-biology%3Abioperl-db-1.6.9%3A20120618-053108.html | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- |
Description
Diego Elio Pettenò (RETIRED)
2012-06-18 08:57:52 UTC
t/15cluster.t ..... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 155/162 subtests t/16obda.t ........ 1/16 ------------- EXCEPTION ------------- MSG: failed to open connection: Can't connect to MySQL server on '127.0.0.1' (111) STACK Bio::DB::DBI::base::new_connection /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/DBI/base.pm:267 STACK Bio::DB::DBI::base::get_connection /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/DBI/base.pm:227 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1498 STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BaseDriver.pm:528 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:945 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195 STACK Bio::DB::Persistent::PersistentObject::create /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/Persistent/PersistentObject.pm:257 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 STACK Bio::DB::Persistent::PersistentObject::store /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/Persistent/PersistentObject.pm:284 STACK toplevel t/16obda.t:36 ------------------------------------- # Looks like you planned 16 tests but ran 6. # Looks like your test exited with 255 just after 6. t/16obda.t ........ Dubious, test returned 255 (wstat 65280, 0xff00) Failed 10/16 subtests Test Summary Report ------------------- t/01dbadaptor.t (Wstat: 65280 Tests: 8 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 23 tests but ran 8. t/02species.t (Wstat: 65280 Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 67 tests but ran 7. t/03simpleseq.t (Wstat: 65280 Tests: 8 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 70 tests but ran 8. t/04swiss.t (Wstat: 512 Tests: 4 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 55 tests but ran 4. t/05seqfeature.t (Wstat: 65280 Tests: 6 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 52 tests but ran 6. t/06comment.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 14 tests but ran 5. t/07dblink.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 21 tests but ran 5. t/08genbank.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 23 tests but ran 5. t/09fuzzy2.t (Wstat: 65280 Tests: 4 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 23 tests but ran 4. t/10ensembl.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 18 tests but ran 5. t/11locuslink.t (Wstat: 65280 Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 113 tests but ran 7. t/12ontology.t (Wstat: 65280 Tests: 6 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 740 tests but ran 6. t/13remove.t (Wstat: 65280 Tests: 3 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 61 tests but ran 3. t/15cluster.t (Wstat: 65280 Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 162 tests but ran 7. t/16obda.t (Wstat: 65280 Tests: 6 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 16 tests but ran 6. Files=16, Tests=109, 5 wallclock secs ( 0.10 usr 0.04 sys + 3.81 cusr 0.46 csys = 4.41 CPU) Result: FAIL Failed 15/16 test programs. 0/109 subtests failed. * ERROR: sci-biology/bioperl-db-1.6.9::gentoo failed (test phase): * test failed After spending a day trying to get these tests passing, I got as far as convincing them to talk to mysql, and then barfing, so I gave up and instead threw a RESTRICT at it. Closing as "resolved", even though its resolved only from a usability perspective. commit: 5ee7db5997fa620007d8d66a1a6dd0cead89a272 author: 2017-07-18 16:37:22 +1200 Kent Fredric <kentnl@gentoo.org> commit: 2017-07-18 16:38:42 +1200 Kent Fredric <kentnl@gentoo.org> gpg-key: E854324B1366A820 sci-biology/bioperl-db: Restrict tests re bug #421701 I've tried an excessive amount to get tests working here. But they still need a lot of love. The work I've done so far only gets a mysql test instance up, ( and then, only tested with mariadb ) Somebody needs to work out what's missing to provision the databases that the tests use. Somebody needs to add support for initializing the other kinds of database. Any help here encouraged, but disabling non-functioning tests is the best we can do for now. Package-Manager: Portage-2.3.6, Repoman-2.3.2 sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild | 51 ++-- sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild | 1 + sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch | 52 ++--- 3 files changed, 58 insertions(+), 46 deletions(-) |